Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative proteincoding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter-and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.DNA barcoding | fungal biodiversity T he absence of a universally accepted DNA barcode for Fungi, the second most speciose eukaryotic kingdom (1, 2), is a serious limitation for multitaxon ecological and biodiversity studies. DNA barcoding uses standardized 500-to 800-bp sequences to identify species of all eukaryotic kingdoms using primers that are applicable for the broadest possible taxonomic group. Reference barcodes must be derived from expertly identified vouchers deposited in biological collections with online metadata and validated by available online sequence chromatograms. Interspecific variation should exceed intraspecific variation (the barcode gap), and barcoding is optimal when a sequence is constant and unique to one species (3, 4). Ideally, the barcode locus would be the same for all kingdoms. A region of the mitochondrial gene encoding the cytochrome c oxidase subunit 1 (CO1) is the barcode for animals (3, 4) and the default marker adopted by the Consortium for the Barcode of Life for all groups of organisms, including fungi (5). In Oomycota, part of the kingdom Stramenopila historically studied by mycologists, the de facto barcode internal transcribed spacer (ITS) region is suitable for identification, but the default CO1 marker is more reliable in a few clades of closely related species (6)...

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.

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|

UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode—the nuclear ribosomal internal transcribed spacer (ITS) region—and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.

The mechanisms of carbon starvation: how, when, or does it even occur at all?Recent observations of increasing vegetation mortality events appear to be a result of changing climate, in particular, an increase in the frequency, length and intensity of droughts (e.g. Allen et al., 2010). The threat of widespread increases in future mortality has rekindled interest in the mechanisms of plant mortality and survival because we do not yet understand them well enough to confidently model future vegetation dynamics (Sitch et al., 2008). In this issue of New Phytologist, provide a viewpoint on the 'carbon (C) starvation hypothesis ' (McDowell et al., 2008). Their viewpoint is invaluable for stimulating our field to explicitly refine our definitions and identify the key experiments needed to understand mechanisms of vegetation survival and mortality. Two important conclusions of their paper were that mortality can occur at nonzero carbohydrate levels and that careful experiments focused on the explicit mechanisms of C starvation, as well as on partitioning the roles of hydraulic failure and C starvation, are needed to understand the physiological underpinnings of how plants die. We applaud these conclusions, and agree that hasty acceptance of any hypothesis before adequate testing is foolish. In this commentary, we highlight some of the valuable ideas from Sala et al. and provide additional comments that we hope will prompt careful future tests on the mechanisms of plant mortality.When the C-starvation hypothesis was proposed (McDowell et al., 2008), it represented an attempt to summarize and interpret the existing literature on vegetation mortality, of which there was a wealth of indirect studies, but a paucity of true, mechanistic tests. The original formulation of the hypothesis suggested that stomatal closure minimizes hydraulic failure during drought, causing photosynthetic C uptake to decline to low levels, thereby promoting carbon starvation as carbohydrate demand continues for maintenance of metabolism and defense. The plant either starves outright, or succumbs to attack by insects or pathogens, whichever occurs first. By contrast, failure to maintain xylem water tension lower than its cavitation threshold results in embolisms, which, if unrepaired, can eventually lead to widespread hydraulic failure, desiccation and mortality. We hoped that the C-starvation and hydraulic failure hypotheses would generate discussion and new ideas; and 'The paucity of studies that quantified mortality forces scientists to use data from nonmortality studies to develop hypotheses … we do this at the risk of confusing stress responses with mortality mechanisms.' , as summarized by Sala et al., active discussion is taking place. A primary conclusion from the discussion is that we need clarification of the various mechanisms by which C starvation can occur, if it occurs at all.Plants maintain metabolism through respiratory processes that consume carbohydrates, and in doing so their C budgets must obey the law of conservation of energ...