Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311(T) = IBT 12289(T)). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species

Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

Conservation and management of marine biodiversity depends on biomonitoring of marine habitats, but current approaches are resource‐intensive and require different approaches for different organisms. Environmental DNA (eDNA) extracted from water samples is an efficient and versatile approach to detecting aquatic animals. In the ocean, eDNA composition reflects local fauna at fine spatial scales, but little is known about the effectiveness of eDNA‐based monitoring of marine communities at larger scales. We investigated the potential of eDNA to characterize and distinguish marine communities at large spatial scales by comparing vertebrate species composition among marine habitats in Qatar, the Arabian Gulf (also known as the Persian Gulf), based on eDNA metabarcoding of seawater samples. We conducted species accumulation analyses to estimate how much of the vertebrate diversity we detected. We obtained eDNA sequences from a diverse assemblage of marine vertebrates, spanning 191 taxa in 73 families. These included rare and endangered species and covered 36% of the bony fish genera previously recorded in the Gulf. Sites of similar habitat type were also similar in eDNA composition. The species accumulation analyses showed that the number of sample replicates was insufficient for some sampling sites but suggested that a few hundred eDNA samples could potentially capture >90% of the marine vertebrate diversity in the study area. Our results confirm that seawater samples contain habitat‐characteristic molecular signatures and that eDNA monitoring can efficiently cover vertebrate diversity at scales relevant to national and regional conservation and management.Maersk Oil; Qatar National Research Fund. Grant Number: NPRP 7 ‐ 1129 ‐ 1 – 201; Naturvidenskab og Teknologi, Aarhus Universite

Danish Fungi 2020 - Not Just Another Image Recognition Dataset

We introduce a novel fine-grained dataset and bench-mark, the Danish Fungi 2020 (DF20). The dataset, constructed from observations submitted to the Atlas of Danish Fungi, is unique in its taxonomy-accurate class labels, small number of errors, highly unbalanced long-tailed class distribution, rich observation metadata, and well-defined class hierarchy. DF20 has zero overlap with ImageNet, al-lowing unbiased comparison of models fine-tuned from publicly available ImageNet checkpoints. The proposed evaluation protocol enables testing the ability to improve classification using metadata - e.g. precise geographic location, habitat, and substrate, facilitates classifier calibration testing, and finally allows to study the impact of the device settings on the classification performance. Experiments using Convolutional Neural Networks (CNN) and the recent Vision Transformers (ViT) show that DF20 presents a challenging task. Interestingly, ViT achieves results su-perior to CNN baselines with 80.45% accuracy and 0.743 macro F1 score, reducing the CNN error by 9% and 12% respectively. A simple procedure for including metadata into the decision process improves the classification accuracy by more than 2.95 percentage points, reducing the error rate by 15%. The source code for all methods and experiments is available at https://sites.google.com/view/danish-fungi-dataset

Diversity of fungus-growing termites (Macrotermes) and their fungal symbionts (Termitomyces) in the semiarid Tsavo Ecosystem, Kenya.

Fungus-growing termites of the subfamily Macrotermitinae together with their highly specialized fungal symbionts (Termitomyces) are primary decomposers of dead plant matter in many African savanna ecosystems. The termites provide crucial ecosystem services also by modifying soil properties, translocating nutrients, and as important drivers of plant succession. Despite their obvious ecological importance, many basic features in the biology of fungus-growing termites and especially their fungal symbionts remain poorly known, and no studies have so far focused on possible habitat-level differences in symbiont diversity across heterogeneous landscapes. We studied the species identities of Macrotermes termites and their Termitomyces symbionts by excavating 143 termite mounds at eight study sites in the semiarid Tsavo Ecosystem of southern Kenya. Reference specimens were identified by sequencing the COI region from termites and the ITS region from symbiotic fungi. The results demonstrate that the regional Macrotermes community in Tsavo includes two sympatric species (M. subhyalinus and M. michaelseni) which cultivate and largely share three species of Termitomyces symbionts. A single species of fungus is always found in each termite mound, but even closely adjacent colonies of the same termite species often house evolutionarily divergent fungi. The species identities of both partners vary markedly between sites, suggesting hitherto unknown differences in their ecological requirements. It is apparent that both habitat heterogeneity and disturbance history can influence the regional distribution patterns of both partners in symbiosis.Peer reviewe

Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads

From Illumina sequencing of DNA from brain and liver tissue from the lion, Panthera leo, and tumor samples from the pike-perch, Sander lucioperca, we obtained two assembled sequence contigs with similarity to known retroviruses. Phylogenetic analyses suggest that the pike-perch retrovirus belongs to the epsilonretroviruses, and the lion retrovirus to the gammaretroviruses. To determine if these novel retroviral sequences originate from an endogenous retrovirus or from a recently integrated exogenous retrovirus, we assessed the genetic diversity of the parental sequences from which the short Illumina reads are derived. First, we showed by simulations that we can robustly infer the level of genetic diversity from short sequence reads. Second, we find that the measures of nucleotide diversity inferred from our retroviral sequences significantly exceed the level observed from Human Immunodeficiency Virus infections, prompting us to conclude that the novel retroviruses are both of endogenous origin. Through further simulations, we rule out the possibility that the observed elevated levels of nucleotide diversity are the result of co-infection with two closely related exogenous retroviruses.Full Tex

Species Delimitation in Taxonomically Difficult Fungi: The Case of Hymenogaster

False truffles are ecologically important as mycorrhizal partners of trees and evolutionarily highly interesting as the result of a shift from epigeous mushroom-like to underground fruiting bodies. Since its first description by Vittadini in 1831, inappropriate species concepts in the highly diverse false truffle genus Hymenogaster has led to continued confusion, caused by a large variety of prevailing taxonomical opinions.In this study, we reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work. The ITS rDNA sequence dataset was subjected to phylogenetic analysis as well as clustering optimization using OPTSIL software.Among distinct species concepts from the literature used to create reference partitions for clustering optimization, the broadest concept resulted in the highest agreement with the ITS data. Our results indicate a highly variable morphology of H. citrinus and H. griseus, most likely linked to environmental influences on the phenology (maturity, habitat, soil type and growing season). In particular, taxa described in the 19(th) century frequently appear as conspecific. Conversely, H. niveus appears as species complex comprising seven cryptic species with almost identical macro- and micromorphology. H. intermedius and H. huthii are described as novel species, each of which with a distinct morphology intermediate between two species complexes. A revised taxonomy for one of the most taxonomically difficult genera of Basidiomycetes is proposed, including an updated identification key. The (semi-)automated selection among species concepts used here is of importance for the revision of taxonomically problematic organism groups in general

Students’ experience of the sketchbook/journal model in art education

The problem of this study was to investigate the extent to which largely self directed, individualized work in student sketchbooks constitutes valid art experience in terms of current guidelines for art education (CSEA, B.C. Ministry of Education, DBAE, various authors). The research questions were: 1) What does the sketchbook content consist of? 2) What is the experience of the participants in regard to a) content, b) context, and c) process? 3) When students are directing their own learning within the structure of this model, what do they say they are learning? 4) To what extent does the work constitute valid content and experience, and provide intellectual development while serving the diverse interests and ability levels of high school art students? The research consisted of the analysis of video taped interviews with a purposive sample of six high school students. The interviews were transcribed and correlated to photocopies of the sketchbook pages for analysis. The data was analyzed using the Macintosh computer program HyperRESEARCH. It is concluded that the sketchbook is a versatile and engaging medium for meaningful, contextual learning and a viable means for evaluating progress and achievement. It is both an adjunct and a driver of studio work. It is frequently the most travelled book in a student’s school bag and the last one to be put away at night. Where clientele is the most diverse, in multi-grade, multi-course split classes, where disabilities and weak language skills demand special attention, the sketchbook is invaluable in tracking progress and in accommodating individual goals, interests and rates of learning. If it is to provide intellectual development and experience, as recommended by current guidelines, the sketchbook needs to be more than a book for sketching in. Clear goals and criteria need to be in place along with classroom support and enabling skills. Teaching strategies may then make provisions for individualized curricula in a process that encourages the development of a depth and breadth of knowledge, awareness of multiple cultural values, participation in the traditions of the history of art, critical thinking and the development of lifelong learning skills.Education, Faculty ofCurriculum and Pedagogy (EDCP), Department ofGraduat

Systems Biology of the Secondary Metabolism in Filamentous Fungi

Filamentous fungi constitute a rich reservoir of pharmaceutically relevant bioactive small molecules. These compounds, commonly referred to as secondary metabolites, are widely used as antibiotics for the treatment of microbial infections, but also as other pharmaceuticals such as immunosuppressors, cholesterol lowering agents and anticancer drugs. Although fungal derived antibiotics have been known for almost a century, genome sequencing has revealed that the biosynthetic potential of fungi is not fully exhausted.The Penicillium genus consists of around 350 accepted species, and many of these are well-known producers of pharmaceuticals and industrially exploited for this. The genus as a whole, however, is grossly understudied at the genomic level. To assess the potential for secondary metabolite biosynthesis in the Penicillium genus, we sequenced the genomes of ten species that produce diverse arrays of secondary metabolites in culture. One of the sequenced isolates was described as a new species, and we mapped secondary metabolites detected in culture to the corresponding biosynthetic gene clusters. The ten sequenced genomes were analyzed together with published Penicillium genomes, altogether 24, and we developed a pipeline to group biosynthetic gene clusters and map them to known pathways. We found a large untapped potential for biosynthesis of secondary metabolites, encoded in the genomes of these species, that potentially could fill the drug discovery pipeline. Based on our predictions, we experimentally identified a novel compound from the antifungal class of antibiotics called yanuthones.Since heterologous expression of secondary metabolite pathways has proved troublesome, the ten genome-sequenced Penicillium species were evaluated as cell factories in controlled bioreactor fermentations. Compared to an industrially relevant strain, the ten Penicillium species showed growth characteristics that encourage further exploration of their industrial potential. Transcriptome analysis of six of the species enabled the identification of a metabolic network that is responsible for precursor formation of secondary metabolites. This network provides important insight into the further industrial development of Penicillium cell factories, and could be used in designing metabolic engineering strategies for optimization of secondary metabolite production.Altogether this thesis provides novel insights into genetic and metabolic aspects of fungal secondary metabolism. Our findings propose that industrial production of secondary metabolites can be effectively established on the basis of native producers. Penicillium species constitute a rich source of drug leads, and possess promising physiological characteristics to be established as industrial production platforms