DNA Barcoding North America's Fungi — Inside the FunDiS Survey

The Continent Has More Unknown Species Than Known Ones

Mycology has always been a discipline of best estimates. Of an estimated 2.2 to 3.8 million fungal species worldwide, formal taxonomy describes roughly 150,000. In North America alone, conservative projections put the undescribed fraction north of 70 percent. Most of the fungi pulled out of the leaf litter on a fall foray have no Latin binomial. They have, in many cases, never been sequenced.

The Fungal Diversity Survey, known to participants as FunDiS, is the largest coordinated North American effort to change that. Operating since 2018 as the successor to the North American Mycoflora Project, FunDiS coordinates citizen mycologists, herbaria, and academic labs to collect, document, and DNA-sequence vouchered specimens across the continent. The project is non-profit, distributed, and explicitly built around the premise that the amateur forager is the only practical fieldwork engine large enough to characterize the continent's fungal diversity in this generation.

How a Mushroom Gets Sequenced

The submission pathway is deliberately friendly to non-academic volunteers but rigorous on the back end. A participant photographs a fruiting body in situ, records GPS coordinates, habitat, and substrate, then collects, dries, and labels the specimen for shipment to a partner herbarium. The observation itself almost always goes into one of two citizen-science platforms first, iNaturalist or Mushroom Observer.

iNaturalist is the broader of the two, a general-biology observation network used across all taxa, with computer-vision-driven instant identification suggestions and a community-confirmation workflow. For fungi, iNaturalist's CV model can resolve common genera in the field but consistently struggles with cryptic species and closely related lineages where morphology converges. A research-grade iNaturalist observation, the platform's quality threshold, requires multiple community identifiers to agree at species level. That agreement is sometimes wrong in ways only DNA can clarify.

Mushroom Observer is the fungus-specific older sibling, narrower in taxonomic scope but deeper in the chain-of-custody features mycologists need. Observation records include detailed microscopy fields, spore-print colour and dimensions, chemical reaction notes, and habitat parameters that iNaturalist's general schema does not accommodate. The two platforms are interoperable enough that a single observation often exists in both, cross-referenced by observation ID.

Both platforms are wired into the FunDiS pipeline. A volunteer can submit an observation to either, indicate that they have collected and preserved a physical voucher, and then route the dried specimen to a partner herbarium with an observation ID that links the digital record to the physical material. At the partner lab, a tissue subsample is excised and run through an ITS sequencing protocol, the internal transcribed spacer region of fungal ribosomal DNA, the de facto barcode for fungi. The resulting sequence is deposited in GenBank with the herbarium accession number, the photographs, and the observation ID. The same record propagates back to iNaturalist or Mushroom Observer with the GenBank accession appended. A specimen collected by a hobbyist on a Sunday morning can be observed, sequenced, accessioned, and globally citable within weeks.

The Labels Bridge — From Observation to Specimen

The unsexy practical problem at the heart of citizen-science vouchering is that every dried mushroom in a herbarium needs a label, and the label has to carry enough information to link the physical specimen back to its digital observation record. Pencilling collector name, date, location, and observation ID onto a paper slip works for a half-dozen specimens. It does not scale to the thousands of vouchers a Mycoblitz weekend can generate.

The iNaturalist Label Generator, hosted at images.mushroomobserver.org/labels and used by both iNaturalist and Mushroom Observer participants, is the standard tool that fills this gap. A volunteer feeds in a list of observation identifiers, iNaturalist numbers, Mushroom Observer IDs in the MO12345 format, or full URLs, and the tool retrieves the metadata for each observation and lays out printable specimen labels in PDF or RTF format. Labels can include the species determination, common name, date, collector, location, additional notes, and a QR code that resolves directly back to the originating observation record. Variable label sizing accommodates everything from small fungal packets to larger specimen sheets, and the tool also supports BugGuide identifiers for entomological vouchering and conversions between Mushroom Observer and iNaturalist record formats.

The QR-code feature is the part that matters most for downstream sequencing work. When a sequencing lab receives a batch of specimens for ITS barcoding, the QR code on each label gives the technician an immediate, machine-readable handle for cross-referencing the observation's photographs, habitat data, and field notes during the molecular analysis. The same handle is what GenBank uses when the sequence is eventually deposited, the observation ID becomes part of the public record. The labels tool does not perform DNA sequencing or store genetic data itself, but it sits at the precise hand-off point where a digital observation becomes a physical specimen that can be sequenced and accessioned.

The tool's existence is also a quiet structural choice. Mushroom Observer maintains it as an open utility for both its own platform and iNaturalist, reflecting a working interoperability between the two communities that the project structure of either platform alone would not suggest. A volunteer fluent in one platform can voucher a specimen documented on the other without rebuilding the metadata.

What the Sequences Are Showing

The yield from FunDiS-style barcoding is consistently surprising even to working taxonomists. Common-looking Lactarius, Russula, and Cortinarius specimens routinely return ITS sequences that fall outside any described species. Two morphologically indistinguishable Amanita fruitings from sites a hundred miles apart turn out to be reproductively isolated lineages. Specimens long lumped under a familiar European binomial, Hygrocybe coccinea, Boletus edulis, Cantharellus cibarius, repeatedly resolve into multiple North American cryptic species, none of which actually carry the European name in the genetic record.

The 2022 description of the genus Atractomyces from material submitted by a FunDiS volunteer in the Pacific Northwest is a representative case. The specimens looked, to an experienced field eye, like a slightly off Lactarius. The sequence placed them outside the genus entirely, eventually outside the family. A formal description followed in a peer-reviewed journal with the original volunteer credited as a co-author, the original iNaturalist observation linked in the paper's supplementary material.

The Continental Mycoblitz Cadence

FunDiS organizes coordinated collection drives called Mycoblitzes, week-long pushes timed to regional fruiting seasons. The Western Mycoblitz typically runs in late fall along the Pacific coast. The Continental Mycoblitz runs across a single weekend each October, drawing in regional clubs from Quebec to Florida to British Columbia. Submission targets are explicit, with quotas allocated by ecoregion. The 2023 Continental Mycoblitz collected over four thousand vouchered specimens in seventy-two hours, processed across eight academic partner labs.

These events double as recruitment funnels. A first-time participant who shows up to a local club's Mycoblitz weekend leaves with a working understanding of vouchering protocol, an introduction to iNaturalist or Mushroom Observer if they are not already a user, a chain-of-custody label printed from the labels tool, and a credible path to having their name appear in GenBank within the year.

The Bottlenecks That Still Limit the Project

Three constraints recur in the project's public communications. Sequencing cost. ITS sequencing at scale runs roughly fifteen to twenty-five dollars per specimen depending on lab and batch size, and FunDiS subsidizes most volunteer submissions through grant funding that does not scale linearly with submission volume.

The morphologist bottleneck on the back end. A sequence without a formal species description is a data point, not a name. The pool of working alpha-taxonomists able to formally describe new species runs in the low hundreds for North American macrofungi, and most of them have day jobs.

Herbarium storage. Vouchered material requires permanent curation, and the network of academic herbaria willing to accession volunteer material is finite. New partnerships, particularly with regional universities, are an ongoing operational priority.

Why It Matters Beyond Taxonomy

The applied implications are wider than the formal-naming work suggests. Conservation status assessments for fungi remain almost entirely absent from federal endangered species frameworks in part because the species have not been formally described. A species without a Latin binomial cannot be listed. Mycoremediation, ethnomycology, and pharmacological screening all benefit from an accurate species-level picture of regional fungal communities. A targeted bioprospecting program looking for novel antibiotics or anticancer compounds needs to know which lineages actually exist in the substrate before it can sample them rationally. FunDiS-generated barcodes feed directly into these downstream applications.

The project also functionally rewires the relationship between hobbyist mushroom hunting and professional mycology. A century ago, most macrofungal species descriptions came from gentleman naturalists whose collections eventually landed in herbaria. FunDiS reconstitutes that pipeline at continental scale and modern resolution, with the herbarium step and the sequencing step both built in by default. Observation platforms, iNaturalist and Mushroom Observer chief among them, have effectively become the largest single feeder into formal academic fungal taxonomy worldwide, with millions of observations annually filtered through community-confirmation pipelines and a steady fraction promoted to physical-voucher and DNA-barcoded status.

What to Watch Next

Three threads of development are worth tracking. The first is the expansion of the same model to neighbouring regions. The Latin American Mycoflora effort and the Caribbean Mycoflora Initiative have both adopted FunDiS-derived protocols. The second is the gradual integration of long-read metabarcoding from soil and plant-tissue samples, which captures the much larger fraction of fungi that never fruit visibly.

The third is the steady improvement of iNaturalist's computer-vision model for fungi, paired with API-driven interoperability between iNaturalist, Mushroom Observer, the labels generator, and FunDiS submission portals. As the CV model becomes more reliable at species level for common taxa, the human-curation effort can concentrate on the cryptic and the genuinely novel, and the barcoding pipeline can prioritize the specimens most likely to reveal undescribed lineages. The project's increasing alignment with formal academic publication pipelines is shortening the gap between volunteer submission and peer-reviewed species description from years to months.

The collected data is, in aggregate, beginning to redraw the working map of North American fungal biogeography. The next decade of fungal taxonomy will, more than any decade before it, have been built by people who started as weekend foragers.