PhyloNext: a pipeline for phylogenetic diversity analysis of GBIF-mediated data.

Background: Understanding biodiversity patterns is a central topic in biogeography and ecology, and it is essential for conservation planning and policy development. Diversity estimates that consider the evolutionary relationships among species, such as phylogenetic diversity and phylogenetic endemicity indices, provide valuable insights into the functional diversity and evolutionary uniqueness of biological communities. These estimates are crucial for informed decision-making and effective global biodiversity management.

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.

Additions to and outline of taxa with branched hyphidia in ().

The genus is a monophyletic group that belongs to () and accommodates species distinguished by strongly branched hyphidia in combination with 3-septate basidiospores. While the original circumscription mainly treated European taxa, here we shift the focus to tropical and sub-tropical material and uncover wider variation in morphology within Still united by hyphidia shape and basidiospore septation, the genus is expanded with 10 taxa having pustulate, cerebriform, or stipitate basidiocarps of yellow to dark brown colours, cylindrical to ovoid basidiospores, and hyphal septa with or without clamps. Monophyly of the amended is confirmed with a phylogeny based on six markers (SSU, ITS, LSU, , , and ).

Global diversity and distribution of nitrogen-fixing bacteria in the soil.

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the H gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates.

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.

DNA barcoding of fungal specimens using PacBio long-read high-throughput sequencing.

Molecular methods are increasingly used to identify species that lack conspicuous macro- or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long-read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens.

Structure and function of the soil microbiome underlying NO emissions from global wetlands.

Wetland soils are the greatest source of nitrous oxide (NO), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the NO emissions from wetland soils are poorly understood. Using in situ NO measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and NO emissions.

: generic delimitation with a multi-gene dataset.

and are two genera of closely related, ectomycorrhizal fungi in the order ; the former stipitate and the latter corticioid. Both are widespread in the Northern Hemisphere and many species from both genera seem to be restricted to old growth forest. This study aimed to: a) identify genetic regions useful in inferring the phylogenetic relationship between and , b) infer this relationship with the regions identified and c) make any taxonomic changes warranted by the result.

Revision of (, ) with notes on morphologically and historically related taxa.

, ) is a genus traditionally defined by corticioid basidiocarps, in contrast to the rest of the class, which is characterized by gelatinous ones. In the traditional circumscription the genus is polyphyletic, and the monotypic family is paraphyletic. Aiming for a more concise delimitation, we revise with a novel phylogeny based on sequences of nrDNA (SSU, ITS, LSU) and protein-coding genes (RPB1, RPB2, TEF1-α) We establish that monophyletic is best characterized not by the corticioid morphology, but by a combination of traits: hyphal clamps, predominantly aseptate thin-walled basidiospores, and low content of carotenoid pigments.

Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi.

The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups).

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

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.

Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe.

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.

Reassessment of the generic limits for and (Thelephorales, Basidiomycota).

DNA sequences from the nuclear LSU and ITS regions were used for phylogenetic analyses of Thelephorales with a focus on the stipitate hydnoid genera and . Analyses showed that and are distinct genera but that the current division, based on basidioma texture, makes paraphyletic with respect to . In order to make genera monophyletic several species are moved from to and the following new combinations are made: , , , , , , , , , , , and .

Solving the taxonomic identity of s.l. (Thelephorales, Basidiomycota) - a multi-gene phylogeny and taxonomic review, integrating ecological and geographical data.

is an ectomycorrhizal, corticioid fungus whose name is frequently assigned to collections of basidiomata as well as root tip and soil samples from a wide range of habitats and hosts across the northern hemisphere. Despite this, its identity is unclear; eight heterotypic taxa have in major reviews of the species been considered synonymous with or morphologically similar to , but no sequence data from type specimens have been available. With the aim to clarify the taxonomy, systematics, morphology, ecology and geographical distribution of and its morphologically similar species, we studied their type specimens as well as 147 basidiomata collections of mostly North European material.

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.

UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi.

Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).

Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits.

Polyozellus multiplex (Thelephorales) is a species complex containing four new species.

Geographic, morphological, and internal transcribed spacer (ITS)-based molecular review of collections identified as Polyozellus multiplex revealed that it is a complex of five phylogenetic species. Average spore size-either less or more than 7 × 6 µm-splits the complex into a small-spored group of two (P. multiplex and P.

Aphyllophoroid fungi in insular woodlands of eastern Ukraine.

Background: Fungi play crucial roles in ecosystems and are among the species-richest organism groups on Earth. However, knowledge on their occurrence lags behind the data for animals and plants. Recent analyses of fungal occurrence data from Western, Central and Northern Europe provided important insights into response of fungi to global warming.

Specificity of fungal associations of Pyroleae and Monotropa hypopitys during germination and seedling development.

Mycoheterotrophic plants obtain organic carbon from associated mycorrhizal fungi, fully or partially. Angiosperms with this form of nutrition possess exceptionally small 'dust seeds' which after germination develop 'seedlings' that remain subterranean for several years, fully dependent on fungi for supply of carbon. Mycoheterotrophs which as adults have photosynthesis thus develop from full to partial mycoheterotrophy, or autotrophy, during ontogeny.

Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands.

Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing.

Sequence-based classification and identification of Fungi.

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes.