The curse of the uncultured fungus

The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se

Global patterns in endemicity and vulnerability of soil fungi

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

Structure and function of the global topsoil microbiome

Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1–4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial–fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially

Ammattiosaamisen näytöt yrityksen ja ammattiopiston yhteistyössä

Opinnäytetyön aiheena oli selvittää, miten ammattiosaamisen näytöt toimivat paikallisen osuuskaupan ja ammattiopiston yhteistyössä koskien ravintolan salipuolen tarjoilijoita. Ammattiosaamisen näytöt ovat olleet käytössä työssäoppijoiden arvioinnissa viisi vuotta. Tavoitteena oli saada tietoa näyttöjen hyödyistä työantajanäkökulmasta katsottuna sekä löytää mahdollisia kehittämiskohteita. Opinnäytetyön teoreettisessa osassa selvennettiin työssäoppimisen ja ammattiosaamisen näytön käsitteitä, mikä on niiden merkitys ammattikoulutuksessa ja toisaalta niiden merkitys työelämälle. Lisäksi selvitettiin yritysten rekrytointikäytäntöjä ja sitä, mitä on työelämän ja oppilaitosten yhteistyö. Tutkimuksen empiirisessä osassa käytettiin puolistrukturoitua teemahaastattelua. Haastateltavat olivat paikallisen osuuskaupan ravintoloiden esimiehiä, ja haastattelut tehtiin kuudelle henkilölle. Haastattelut nauhoitettiin ja litteroitiin sanasta sanaan tietokoneelle jatkoanalyysia varten. Tutkimuksen tuloksena vahvistui se, että ammattiosaamisen näytöt ovat kaikille selkeä asia ja niistä on hyötyä sekä työnantajalle että opiskelijalle. Yhteistyö osuuskaupan ja ammattiopiton kanssa toimii hyvin, eivätkä näyttötilanteet ole aiheuttaneet suurempia ongelmia. Ainoastaan työssäoppijan osaamisen arviointi koetaan hankalana nykyisellä asteikolla. Alan ammattiopistotasoista koulutusta tarvitaan edelleen Joensuun alueella, ja tutkimuksen mukaan sitä pitäisi jopa lisätä. Koulutetun työvoiman puute ei vielä ole maakunnassa suuri ongelma verrattuna pääkaupunkiseutuun, mutta uhkakuvia on jo nyt havaittavissa. Tähän tulisi yhteistyökumppaneiden kiinnittää huomiota, jotta jatkossa Joensuun alueella koulutetaan riittävästi työvoimaa alalle.The purpose of the thesis was to find out how the collaboration between a company and vocational college works concerning vocational skills demonstrations of restaurant waiters. In addition, the task was to examine if there is any benefit of skills demonstrations for the company, and how to develop co-operation. Partners for the study are a local hotel and restaurant company and a local vocational college. The information was gathered from literature, journals, the Internet and by interviewing. In the theoretical part of the study the main issue was to explain what on-the-job learning is and what vocational skills demonstrations are, and what their consequence is for vocational education and for work life. Also how companies carry out their recruitment was clarified. Data for this study were collected by interviewing six supervisors in partner restaurants. The results of the study show that vocational skills demonstrations are perceived well without any complexities. Rather the results indicate more utilities for students, for the company and for the vocational school. The final result of this thesis was that it is important to keep on vocational education in Joensuu and even to enhance it. Now the lack of trained waiters is a fact in southern Finland. A vision is that it will be a threat also in eastern Finland in the future. To ensure professional labour for hotel and restaurant business, companies support for vocational education is essential

Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks

Background: Below-ground linkage between plant and fungal communities is one of the major drivers of terrestrial ecosystem dynamics. However, we still have limited knowledge of how such plant-fungus associations vary in their community-scale properties depending on fungal functional groups and geographic locations. Methods: By compiling a high-throughput sequencing dataset of root-associated fungi in eight forests along the Japanese Archipelago, we performed a comparative analysis of arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic associations across a latitudinal gradient from cool-temperate to subtropical regions. Results: In most of the plant-fungus networks analyzed, host-symbiont associations were significantly specialized but lacked "nested" architecture, which has been commonly reported in plant-pollinator and plant-seed disperser networks. In particular, the entire networks involving all functional groups of plants and fungi and partial networks consisting of ectomycorrhizal plant and fungal species/taxa displayed "anti-nested" architecture (i.e., negative nestedness scores) in many of the forests examined. Our data also suggested that geographic factors affected the organization of plant-fungus network structure. For example, the southernmost subtropical site analyzed in this study displayed lower network-level specificity of host-symbiont associations and higher (but still low) nestedness than northern localities. Conclusions: Our comparative analyses suggest that arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic plant-fungus associations often lack nested network architecture, while those associations can vary, to some extent, in their community-scale properties along a latitudinal gradient. Overall, this study provides a basis for future studies that will examine how different types of plant-fungus associations collectively structure terrestrial ecosystems

Greenhouse seedlings of Alnus showed low host intrageneric specificity and a strong preference for some Tomentella ectomycorrhizal associates

Ectomycorrhizal (ECM) fungal associates of Alnus are relatively few in comparison with those associated with other tree hosts. The composition of ECM assemblages associated with Alnus seems to change very little across the Northern Hemisphere. However, Alnus-associated ECM assemblages from the Western United States, Mexico, and Argentina tend to differ from those in eastern North America and Europe, presumably due to their different biogeographic histories. Alnus glutinosa is a northern European species subjected to diverse environmental conditions. To address intrageneric host preference within two distantly related Alnus species (Alnus acuminata and A. glutinosa), we tested the ECM colonization on seedlings of both species inoculated with natural soil from A. acuminata forests. Two tomentelloid ECM fungi from A. acuminata natural soils were determined from the anatomotyping and molecular analysis. Both species colonized A. glutinosa seedlings and presented similar relative abundances. Additional soil sequence data from A. acuminata sites suggest that a variety of tomentelloid taxa occur, including several unidentified Tomentella lineages. Maximum-likelihood and Bayesian inference analyses based on internal transcribed spacer (ITS) sequences from various locations do not reflect associations of taxa based on their biogeographic origin, and clades are in general constituted by sequences from diverse regions, including South America, Mexico, USA, and Europe. Results illustrate the probable role of specific tomentelloid fungi in the early colonization of seedlings in A. acuminata forests as well as their importance in the structure of the ECM propagule community at the sites.Fil: Nouhra, Eduardo Ramon. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Pastor, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Becerra, Alejandra Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Sarrionandia Areitio, Estibaliz. Universidad del País Vasco; EspañaFil: Geml, Jozsef. Leiden University; Países Bajo