Showing papers by "Urmas Kõljalg published in 2020"

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

Abstract: 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.

Regional-scale in-depth analysis of soil fungal diversity reveals strong pH and plant species effects in Northern Europe

Abstract: Soil microbiome has a pivotal role in ecosystem functioning, yet little is known about its build-up from local to regional scales. In a multi-year regional-scale survey involving 1251 plots and long-read third-generation sequencing, we found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional groups. The pH effects were typically unimodal, usually both direct and indirect through tree species, soil nutrients or mold abundance. Individual tree species, particularly Pinus sylvestris, Picea abies, and Populus x wettsteinii, and overall ectomycorrhizal plant proportion had relatively stronger effects on the diversity of biotrophic fungi than saprotrophic fungi. We found strong temporal sampling and investigator biases for the abundance of molds, but generally all spatial, temporal and microclimatic effects were weak. Richness of fungi and several functional groups was highest in woodlands and around ruins of buildings but lowest in bogs, with marked group-specific trends. In contrast to our expectations, diversity of soil fungi tended to be higher in forest island habitats potentially due to the edge effect, but fungal richness declined with island distance and in response to forest fragmentation. Virgin forests supported somewhat higher fungal diversity than old non-pristine forests, but there were no differences in richness between natural and anthropogenic habitats such as parks and coppiced gardens. Diversity of most fungal groups suffered from management of seminatural woodlands and parks and thinning of forests, but especially for forests the results depended on fungal group and time since partial harvesting. We conclude that the positive effects of tree diversity on overall fungal richness represent a combined niche effect of soil properties and intimate associations.

The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa.

Abstract: Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.

Identifying the ‘unidentified’ fungi: a global-scale long-read third-generation sequencing approach

Abstract: Molecular identification methods, in particular high-throughput sequencing tools, have greatly improved our knowledge about fungal diversity and biogeography, but many of the recovered taxa from natural environments cannot be identified to species or even higher taxonomic levels. This study addresses the phylogenetic placement of previously unrecognized fungal groups by using two complementary approaches: (i) third-generation amplicon sequencing analysis of DNA from global soil samples, screening out ITS reads of < 90% similarity to other available Sanger sequences, and (ii) analysis of common fungal taxa that were previously indicated to be enigmatic in terms of taxonomic placement based on the ITS sequences alone (so-called top50 sequences). For the global soil samples, we chose to amplify the full rRNA gene operon using four partly overlapping amplicons and multiple newly developed primers or primer combinations that cover nearly all fungi and a vast majority of non-fungal eukaryotes. We extracted the rRNA 18S (SSU) and 28S (LSU) genes and performed phylogenetic analyses against carefully selected reference material. Both SSU and LSU analyses placed most soil sequences and top50 sequences to known orders and classes, but tens of monophyletic groups and single sequences remained outside described taxa. Furthermore, the LSU analyses recovered a few small groups of sequences that may potentially represent novel phyla. We conclude that rRNA genes-based phylogenetic analyses are efficient tools for determining phylogenetic relationships of fungal taxa that cannot be placed to any order or class using ITS sequences alone. However, in many instances, longer rRNA gene sequences and availability of both SSU and LSU reads are needed to improve taxonomic resolution. By leveraging third-generation sequencing from global soil samples, we successfully provided phylogenetic placement for many previously unidentified sequences and broadened our view on the fungal tree of life, with 10–20% new order-level taxa. In addition, the PacBio sequence data greatly extends fungal class-level information in reference databases.

Mapping and Publishing Sequence-Derived Data through Biodiversity Data Platforms

Abstract: Most users will foresee the use of genetic sequences in the context of molecular ecology or phylogenetic research, however, a sequence with coordinates and a timestamp is a valuable biodiversity occurrence that is useful in a much broader context than its original purpose. To uncover this potential, sequence-derived data need to become findable, accessible, interoperable, and reusable through generalist biodiversity data platforms. Stimulated by the Biodiversity_Next discussions in 2019, we have worked for about 10 months to put together practical data mapping and data publishing experiences in Norway, Australia, Sweden, and Denmark, as well as in the UNITE and the GBIF (Global ‡ § | ¶ # ¤ « » § ˄,˅ ¦ ¤ ˀ,ˁ © Schigel D et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Biodiversity Information Facility) networks. The resulting guide was put together to provide practical instruction for mapping sequence-derived data. Biodiversity data communities remain dominated by the macroscopic, easily detectable, morphologically identifiable species. This is not only true for citizen science and other forms of biodiversity popularization, but is also visible in the university and museum department structures, financial resource allocations, biodiversity legislation, and policy design. Recent decades of molecular advances have increased the power of genetic methods for detecting, describing, and documenting global biodiversity. We have yet to see the wide shift of data generating efforts from the traditional taxonomic foci of biodiversity assesments to the more balanced and inclusive systems focusing on all functionally important taxa and environments. These include soil, limnic and marine environments, decomposing plants and deadwood, and all life therein. Environmental DNA data enable recording of present and past presence of microand macroscopic organisms with minimal effort and by non-invasive methods. The apparent ease of these methods requires a cautious approach to the resulting data and their interpretation. It remains important to define and agree on the organism recording and reporting routines for genetic data. DNA data represent a major addition to the many ways in which GBIF and other biodiversity data platforms index the living world. Our guide is resting on the shoulders of those who have been developing and improving MIxS (Minimum Information about any (x) Sequence), GGBN (Global Genome Biodiversity Network) and other data standards. The added value of publishing sequence-derived data through non-genetic biodiversity discovery platforms relates to spatio-temporal occurrences and sequencebased names. Reporting sequence-derived occurrences in an open and reproducible way has a wide range of benefits: notably, it increases citability, highlights the taxa concerned in the context of biological conservation, and contributes to taxonomic and ecological knowledge.