DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee .

Background: More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such “molecular operational taxonomic units” (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well-equipped, well-funded molecular laboratories are not readily available in many biodiverse countries.Results: We here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyperdiverse fly family Phoridae (Diptera). We sequenced 7059 specimens collected in a single Malaise trap in Kibale National Park, Uganda, over the short period of 8 weeks. We discovered > 650 species which exceeds the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3500 barcodes per flowcell. This was achieved by adopting 1D sequencing, resequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; > 99% of specimens) and revealed that 90% of the putative species belong to the neglected, megadiverse genusMegaselia. We demonstrate for oneMegaseliaspecies how the molecular data can guide the description of a new species (Megaselia sepsioidessp. nov.).Conclusions: We document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 200,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

A total of 317 species of Mycetophilidae are recorded from the Gemer region in central Slovakia. The material was obtained mainly in the years 2008-2011 by means of Malaise traps and by individual collecting by the authors. A new species of Mycetophila Meigen, M. gemerensis sp. n., is described and additional 47 species are recorded as new to Slovakia. A new synonym is proposed: Mycetophila quadra Lundström, 1909 = M. chamberlini (Laffoon, 1957) syn. n.

Two new Mycetophilidae species, Neuratelia jabalmoussae sp. n. and Neuratelia salmelai sp. n. are described on the basis of material collected from Lebanon, Estonia and Finland. Detailed figures of male terminalia and photographs of general facies are provided along with discussions of their morphological distinction from sibling species. For the first time molecular characters are used to distinguish new fungus gnat species. Molecular analysis relies on cytochrome oxidase subunit one (COI) but has additionally been corroborated by information from the 28S and ITS2 regions of nuclear ribosomal DNA. Situations where morphological and molecular data provide conflicting evidence for species delimitation are discussed. A new country record from Georgia is provided for Neuratelia caucasica.

The following 24 new species of Manota are described: M. abakiga (Uganda), M. aculifera (Ghana, Uganda), M. afra (Uganda), M. bracteata (Uganda), M. clurina (Uganda), M. comata (Ghana, Uganda), M. dissidens (Ghana), M. foliolata (Uganda), M. freerki (Uganda), M. ghanaensis (Ghana), M. katusabei (Ghana, Uganda), M. kibaleensis (Uganda), M. pedicellata (Uganda), M. petiolata (Uganda), M. pilosa (Uganda), M. pinnata (Uganda), M. pinnulata (Uganda), M. redunca (Uganda), M. relicina (Uganda), M. senticosa (Uganda), M. simina (Uganda), M. toomasi (Uganda), M. toroensis (Uganda), and M. usubi (Uganda). New records for the following species are given: M. lachaisei Matile (Uganda), M. mabokeensis Matile (Uganda), M. mazumbaiensis Søli (Ghana, Uganda), M. teocchii Matile (Uganda) and M. whiteleyi Jaschhof & Mostovski (Uganda). Redescriptions of M. lachaisei and M. teocchii as well as drawings of the hypopygium of M. mazumbaiensis are given. Altogether 51 species of Manota are presently known from the Afrotropical region.