The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered.

UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.

"My naturesound" - nature observations with sound recordings.

BACKGROUND: Online systems for observation reporting by citizen scientists have been operating for many years. iNaturalist (California Academy of Sciences 2016), eBird (Cornell Lab of Ornithology 2016) and Observado (Observation International 2016) are well-known international systems, Artportalen (Swedish Species Information Centre 2016) and Artsobservasjoner (Norwegian Biodiversity Information Centre 2016) are Scandinavian. In addition, databases and online solutions exist that are more directly research-oriented but still offer participation by citizen scientists, such as the PlutoF (University of Tartu Natural History Museum 2016) platform. The University of Tartu Natural History Museum maintains the PlutoF platform (Abarenkov et al. 2010) for storing and managing biodiversity data, including taxon observations. In 2014, development was started to integrate an observation app "Minu loodusheli"/"My naturesound" (University of Tartu Natural History Museum 2017b) (My naturesound, Fig. 1) within PlutoF system. In 2017, an English language version of the app (University of Tartu Natural History Museum 2017c) was launched that includes nearly all major sound-producing taxon groups in its taxonomy. The application also acts as a practical tool for collecting and publishing occurrence data for the Global Biodiversity Information Facility (Global Biodiversity Information Facility 2017) in standardized Darwin Core format together with download links to the multimedia files. Although the sound recording ability of mobile phones opens new opportunities to validate taxon occurrences, current technological solutions limit the use of recordings in biodiversity research.The "My naturesound" allows the user to record taxon occurrences and to provide audio recordings as evidence. After installing the application, the user is promted to login with PlutoF system credentials or to register with PlutoF. The application is targeted primarely to citizen scientists, but researchers themselves can also use it as a tool for easy annotation of taxon occurrences. NEW INFORMATION: The dataset consists observation data of birds, amphibians and insects by citizen scientists with on site audio recordings. The dataset gives the possibility to analyze the suitablility of mobile devices for recording animal vocalizations and their use in reporting.

Fungal biogeography. Global diversity and geography of soil fungi.

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.

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.