Welcome to IMC 2018 International Mycological Congress
Sequence-based diversity of Glomeromycotina – why, how, and where next?
- M. Öpik
Availability of DNA sequencing approaches to identify fungi in samples from nature revolutionized the research on fungi and are now standard. DNA sequencing of fungal specimens and cultures, and natural soil and root samples has considerably changed the understanding of the diversity of Glomeromycotina, fungi forming arbuscular mycorrhiza (AM). It is now possible to identify AM fungal taxa by DNA sequencing irrespective of the presence of microscopically identifiable structures. Further developments of species proxies (Virtual Taxa, VT; Species Hypotheses, SH) and concurrent systematic organization of information about their occurrences in databases provides tools and data for broad research community to target these fungi in studies from taxonomy to physiology and genomics or to ecosystem sciences and beyond. However, several questions remain unsolved. How to handle “unnamed” diversity? How to appropriately delimit DNA sequence based species proxies? How to maintain databases? Do the unnamed AM fungi carry biological properties that differ from those of cultured “lab rats”? To illustrate some of these issues, I will tackle Rhizophagus intraradices-irregularis species group. I’ll present the current knowledge of the phylogenetic diversity within the group in the context of recent genotyping data, the global geographical and habitat-wise distribution in the group, and the share of data in culture collections vs DNA sequences from various samples. I will conclude with future prospects in the direction of unravelling the AM fungal diversity and its patterns in the nature.
Untapping the diversity and function of novel fungal rhizobiomes
- A. Porras-Alfaro
Mycorrhizal and pathogenic fungi dominate curated databases of root-associated fungi limiting our capacity to identify and define specific functions of other fungal symbionts found in plant roots. Next generation sequencing and the use of fungal-plant bioassays can guide studies for the discovery and characterization of novel and specialized fungal species across multiple environments. This talk will discuss the importance of technology integration and collaborations to advance our understanding of plant-fungal interactions, the discovery of dark taxa, and the emergent properties that result from complex microbial interactions. I will focus on the use of targeted culturing efforts based on Illumina sequencing data to discover and characterize abundant but unknown fungal species.
Hawksworthiomyces sequentia ENAS: a case study in DNA-based taxonomy
- Z. De Beer
- T. Duong
- S. Marincowitz
- M. Wingfield
The increasing numbers of studies using environmental nucleic acid sequences (ENAS) to assess fungal diversity have revealed the existence of thousands of previously unknown, and in many cases unculturable, species. It is estimated that more than a third of all fungal DNA sequences in GenBank are of environmental origin. But inconsistent annotation of these undescribed, sequence-based taxa limits functional access to the data. Consequently, these ENAS are rarely considered in other studies, especially not in taxonomic treatments. This problem is confound by the fact that the International Code of Nomenclature for Algae, Fungi, and Plants at present prohibits the description of novel taxa known only from ENAS, which discourages taxonomists to include these sequences in their studies. Various options have been suggested by members of the mycological community to amend the Code to allow the systematic nomenclatural treatment of these ‘orphan’ taxa. One possibility would be to allow DNA sequences as types instead of the typical herbarium specimens, graphic representations or living cultures. As an example, a new species with an ITS sequence as type was recently described in a study based on two matching ITS sequences of fungi inhabiting conifer wood, but that was generated in two earlier, independent studies. One came from an uncultured fungus clone from spruce in Sweden, and the other from a culture from cedar wood in Canada, that later died. The lineage containing these two sequences was phylogenetically different from related species in the Ophiostomatales and was described as “Hawksworthiomyces sequentia sp. nov. ENAS”. It was suggested that in cases like these the ENAS acronym should be used with the species name until a specimen is found and designated as type, after which it can be omitted. Of importance is that this novel ENAS species was described adhering to currently accepted phylogenetic standards in the Ophiostomatales. The inclusion of environmental LSU sequences in the same study, furthermore confirmed the presence of a novel genus in the order that was represented previously only by a single taxon. This genus seems to be biologically and ecologically different from other genera in the order, and thus enhances our understanding of evolutionary processes in this group of fungi. In this rather modest case study we showed that much value can be added by including environmental sequences in taxonomic studies. What is clear is that a decision and guidance is needed from the mycological community that will allow for and enable the systematic naming of sequence-based taxa.
Dealing with taxa known only from DNA sequences
- M. Ryberg
The number of sequences in public sequence databases without specific taxon name are steadily increasing. It is clear that many of these sequences represent taxa that have previously not been recognized by the scientific community, but that are important for our understanding of fungal diversity, ecology, and evolution. For example, Archaeorhizomyces is a group with world wide distribution and many species, but searching biodiversity databases such as GBIF and Species Fungorum there are only two species listed, since they are the only that have been possible to typify and name according to the rules of the International Code of Nomenclature of algae, fungi, and plants (ICN). Even if sequences without specific taxon names are now being included into some taxonomic studies, and species are being described to accommodate them, they are usually ignored due to the lack of valid name under the ICN. What is included in biodiversity datasets does therefore often depend on nomenclature issues rather than taxonomic issues, even if taxa is what are of interest. There are many possible ways to amend this problem, for example: 1) We can separate our biodiversity data from the dependence of names. We then need some other unique identifier, preferably global identifiers that can be used to link different datasets. UNITE provides identifiers in the form of DOIs for species hypotheses, but not species. The identifiers consequently change with the dataset on which the hypotheses are based, and they are not stable taxon identifiers. We could construct another system based for example on the identifiers provided by taxonomic databases. However, DOIs and accession numbers alike may be suitable for database handling, but are less suitable for human communication. 2) We can use names not valid under the code of nomenclature, which are now being provided for some taxa, and include these in biodiversity datasets. The downside with this is that there is no available, agreed upon, rules to govern these names and resolve conflicts between them, i.e. nothing to fill the very function ICN was designed for. 3) We can amend the ICN to include names for taxa without any physical voucher. One possible downside with this is that the number of descriptions of taxa that are in fact not new to sciences may increase significantly, and thereby the number of synonyms, making nomenclature and consequently taxonomy more cumbersome. The extent of the problems with names outside the code and names governed by the code will depends on the actions of the community in promoting good taxonomy and nomenclature through discussions, training and peer-review, but also on the actions of individual researchers. There is likely no system without any risks or drawbacks to deal with the issues of species known only from sequences, but we urgently need a solution to be able to present an as true picture of the fungal diversity as possible.
A methodical approach to revealing dark taxa: Hebeloma as a test case
- U. Eberhardt
- N. Schütz
- L. Davies
- H. Beker
Today, species are increasingly identified by their ITS sequence. Accordingly, any taxon that can be recognized by its ITS alone can hardly be viewed a “dark taxon” and such taxa are likely to be discovered by concurrently widely applied methods such as barcoding or metagenomics. A different situation applies to taxa that do not have a distinct ITS sequence; these are unlikely to be discovered by these methods. Further, taxa that are represented by types that are not readily accessible to molecular methods often remain neglected. Here, we present an approach that links taxonomy, morphology and molecular data through the use of modern database functions, type studies and multi-locus-sequencing. The use of a digital database allows collection data and species morphology to be recorded as a set of parameters. This facilitates easy comparison of collections. Database queries may be built representing putative species profiles which may then be compared with the results of molecular analyses. Conversely, sets of collections forming clades in molecular analyses may be compared and analysed to determine which characters they have in common and the variation within those characters. After several rounds of comparing results from molecular analyses with sets of collections exhibiting common characters and refining the characters and character value ranges to a query, species descriptions may be assembled automatically from the database, corresponding to clades generated within phylogenetic trees. These descriptions have two major advantages over traditional methods: (i) they are based on easily traceable data, and (ii) they can be re-adjusted if more material becomes available. Keys may also be built, tested and refined through the same process. By entering into the database character values for types, existing names may be linked to sets of collections representing putative taxa. If molecular data is available for a type, this provides another line of evidence. More often than not, as the data sets are enriched, ecological and biogeographical patterns emerge to support the validity of the delimited taxa. Furthermore, multi-locus sequencing can also provide additional evidence on the species delimitation. This methodology allows the identification of taxa that could not be recognized by ITS alone. Our subject is Hebeloma, a genus of ectomycorrhizal fungi, which are often similar in appearance and for which molecular species divergence is low. In Europe, we managed to link 55 species to existing names and discover 29 new species through this approach. In North America, based on 944 collections contributed through the mycologist community and type collections loaned from herbaria, we have discovered 38 species not known from Europe. For 18 of these, we have been able to establish that they have been described before under at least one legitimate name.
Creatures from the black lagoon: Generating reference sequences for uncultured marine fungi
- K. Picard
- K. Pryer
High-throughput sequencing (HTS) has ushered in a new age of mycological exploration, revealing uncharacterized fungal diversity across disparate habitats. However, efforts to infer the true phylogenetic affinities of many novel fungal phylotypes are hampered by the maximum read lengths of most sequencing platforms (< 500 bp), which often provide little phylogenetic signal. Moreover, the increasing adoption of next-generation sequencing methods to characterize fungal communities supplants traditional culturing surveys, decreasing the generation and availability of high-quality reference sequences. Taxonomic identification of OTUs observed in environmental surveys hinges on well-curated databases of complete or nearly-complete reference sequences. Consequently, despite the detection of wholly unknown groups among the fungi, we are unable to put these taxa into a robust phylogenetic framework, nor can we add them to existing databases to inform future HTS studies. For this study, I explored using a third-generation sequencing platform (PacBio) to generate long reads suitable for phylogenetic analysis and improved taxonomic identification of uncultured fungi from poorly sampled habitats. I targeted a nearly 2,000-bp region of fungal rDNA spanning three loci commonly employed in environmental surveys of fungi: ITS1, ITS2, and LSU. Using a mock community approach, I calculated the error profile for PacBio’s default parameters, from which I developed an analysis pipeline for environmental samples. Amplicon libraries from water and sediment samples originating from diverse marine habitats were then sequenced on the PacBio platform. I observed over 200 OTUs, with Ascomycota and Chytridiomycota exhibiting the highest diversity. Phylogenetic analyses placed most OTUs in the Dikarya to known marine genera, but marine OTUs allied to the zoosporic lineages represented novel clades. Locus-specific databases were shown to vary widely in their ability to assign the correct phylum-level taxonomy to marine OTUs outside of the Dikarya, demonstrating that biases in the taxonomic composition of extant reference databases can result in the failure to recognize OTUs from the early-diverging phyla in environmental sequence datasets.