Life on top: cryptoendolithic ascomycetes and microalgae isolated from over 6000 m altitude

Rocks are among the oldest terrestrial niches hosting a multiplicity of life forms, of which diversity has been only partially uncovered. Endolithic metacommunities comprise all major groups of microorganisms, such as chemo-organotrophic, chemo-lithotrophic and phototrophic, represented by bacteria, microalgae and microfungi. Their diversity is often difficult to describe and may remain underestimated. Furthermore, knowledge about the diversity of microorganisms colonizing rocks in peculiar niches is even poorer due to the difficulty to retrieve environmental specimens. Here, we report the phylogenetic and phenotypic characterization of a few endolithic fungi and algae isolated from rock fragments collected at high elevation, i.e., on the top of two mountains over 6000 m altitude, Muztagh Ata (China) and Cerro Mercendario (Argentina). The identity of the strains was confirmed by sequencing the nuclear ITS and LSU, the plastidial rbcL loci and by morphological analysis. Three fungal strains belonging to the class Dothideomycetes and one algal strain belonging to the genus Trebouxia were isolated from Muztagh Ata, while six fungal strains belonging to the order Chaetothyriales and four algal strains belonging to the genus Myrmecia were isolated from Cerro Mercedario. The detected species diversity is discussed in an evolutionary and ecological context

PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding

DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called 'better clustering for QIIME' (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100\u2009224 sequences), PLANiTS2 (96\u2009771 sequences) and PLANiTS (97\u2009550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering. Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS

Environmental DNA assessment of airborne plant and fungal seasonal diversity

Environmental DNA (eDNA) metabarcoding and metagenomics analyses can improve taxonomic resolution in biodiversity studies. Only recently, these techniques have been applied in aerobiology, to target bacteria, fungi and plants in airborne samples. Here, we present a nine-month aerobiological study applying eDNA metabarcoding in which we analyzed simultaneously airborne diversity and variation of fungi and plants across five locations in North and Central Italy. We correlated species composition with the ecological characteristics of the sites and the seasons. The most abundant taxa among all sites and seasons were the fungal genera Cladosporium, Alternaria, and Epicoccum and the plant genera Brassica, Corylus, Cupressus and Linum, the latter being much more variable among sites. PERMANOVA and indicator species analyses showed that the plant diversity from air samples is significantly correlated with seasons, while that of fungi varied according to the interaction between seasons and sites. The results consolidate the performance of a new eDNA metabarcoding pipeline for the simultaneous amplification and analysis of airborne plant and fungal particles. They also highlight the promising complementarity of this approach with more traditional biomonitoring frameworks and routine reports of air quality provided by environmental agencies

Two benthic diatoms, nanofrustulum shiloi and striatella unipunctata, encapsulated in alginate beads, influence the reproductive efficiency of paracentrotus lividus by modulating the gene expression

Physiological effects of algal metabolites is a key step for the isolation of interesting bioactive compounds. Invertebrate grazers may be fed on live diatoms or dried, pelletized, and added to compound feeds. Any method may reveal some shortcomings, due to the leaking of wound-activated compounds in the water prior to ingestion. For this reason, encapsulation may represent an important step of bioassay-guided fractionation, because it may assure timely preservation of the active compounds. Here we test the effects of the inclusion in alginate (biocompatible and non-toxic delivery system) matrices to produce beads containing two benthic diatoms for sea urchin Paracentrotus lividus feeding. In particular, we compared the effects of a diatom whose influence on P. lividus was known (Nanofrustulum shiloi) and those of a diatom suspected to be harmful to marine invertebrates, because it is often present in blooms (Striatella unipunctata). Dried N. shiloi and S. unipunctata were offered for one month after encapsulation in alginate hydrogel beads and the larvae produced by sea urchins were checked for viability and malformations. The results indicated that N. shiloi, already known for its toxigenic effects on sea urchin larvae, fully conserved its activity after inclusion in alginate beads. On the whole, benthic diatoms affected the embryogenesis of P. lividus, altering the expression of several genes involved in stress response, development, skeletogenesis and detoxification processes. Interactomic analysis suggested that both diatoms activated a similar stress response pathway, through the up-regulation of hsp60, hsp70, NF-κB, 14-3-3 ε and MDR1 genes. This research also demonstrates that the inclusion in alginate beads may represent a feasible technique to isolate diatom-derived bioactive compounds

Topical corticosteroid phobia in parents of pediatric patients with atopic dermatitis: a multicentre survey

BACKGROUND: Families of children affected with atopic dermatitis (AD) often report fear and anxiety regarding treatment with topical corticosteroids (TCS), which may lead to reduced compliance. The objective of our study was to measure, through a standardized questionnaire, fear of TCS in families of pediatric patients with AD and to identify items associated with fear. METHODS: Families of pediatric patients with AD were enrolled in 9 Italian centers of pediatric dermatology. Enrolled parents were invited to fill in a questionnaire including questions on sociodemographic and clinical characteristics and 3 sets of questions on corticosteroid phobia (general fear, specific fears, behaviours regarding TCS). Determinants of the level of general fear were investigated through multivariable analysis. RESULTS: A total of 300 outpatients with AD were enrolled. Most parents (80%) had a high instruction level. Eighty-one percent reported to have a certain amount of fear of TCS. At the multivariable analysis, fear of TCS was associated with the following items: believing that TCS treatment advantages do not overweight disadvantages (P = 0.011); believing that TCS may be dangerous independently from the specific side effect (P < 0.001). Moreover, TCS fear was associated with fear of applying too much cream (P = 0.001). CONCLUSION: TCS phobia is widespread among Italian families of children with AD. Fear of TCS is associated with fear of applying too much cream, thus increasing the risk of poor compliance and treatment failure. Therapeutic education of families on the use of TCS should be implemented. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13052-017-0330-7) contains supplementary material, which is available to authorized users

An overview of genomics, phylogenomics and proteomics approaches in ascomycota

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi

Immunodetection of IgM, IgT and pIgR in mucosal tissues of Antarctic teleost

We have previously investigated the immune response at hepato-biliary level in the Antarctic teleost Trematomus bermacchii, a species belonging to the Perciform suborder Notothenoidei, the most abundant component of the fish fauna living in the Antarctic ocean. By that time only the IgM isotype was known and well characterized at molecular and biochemical levels in Antarctic fish. Over the past few years we have cloned and sequenced genes encoding other two key molecules of the mucosal immune system, IgT and polymeric Ig receptor (pIgR) of T. bernacchii. The present study aimed at investigating the localization in mucosal tissues of IgM, IgT and pIgR in an attempt to clarify the protein occurrence and transepithelial transport. Biochemical and immunohistochemical data provided convergent data about specific mechanisms operating apical release of IgT in exocrine way, as well as depicting peculiar (maybe ancestral) features compared with well- known mechanisms described for polymeric Igs transport in mammalian tissues