Unseen, Unidentified, but Abundant: Dark Fungal Taxa and the Debate in the Mycological Community

Fungi are more than meets the eye, according to a recently published study in Mycokeys. When we usually think of fungi, we tend to imagine the common forms that mycologists have studied for decades. This might include mushrooms, mold, kombucha, and bakers yeast — something that holds a physical form or can be grown on a culture dish in a lab. However, the new DNA sequencing study has found overwhelming evidence of fungi that do not hold the physical form of a fruiting body nor can be grown in a scientific setting. Scientists now know they exist, but we currently cannot observe them outside of their DNA code. These fungal groups are often referred to as “dark taxa” and are much more common than we think. This discovery challenges how the mycological community has been classifying and naming fungi and provides a new dimension of fungal diversity research.

The dark matter of the mycology world

Dark matter is a term used in astronomy to describe matter that is not visible by any light-detecting instruments such as a telescope. Though scientists have not yet seen this matter’s physical form, they believe it makes up around 85% of the matter in the universe.

Dark taxa is a very similar concept, as they are not detected through means of direct observation nor defined by morphology but rather through their DNA sequencing (1). In a study of global soil fungi, researchers used ribosomal RNA phylogenetic analysis to determine several unidentified sequences that make up the fungal tree of life and relate to major fungal lineages (2). Through the sequencing of the soil samples, they found around 10-20% new groups of fungi using the genetic information of dark fungal taxa (DFT).

The problem with identifying and classifying DFT

The world of fungi is vast and diverse, with around 2.2 to 3.8 million different species. Molecular data uses the DNA sequence of fungi to explore other fungi and fungal communities. Scientists utilize a specific genetic marker in a DNA sequence called the internal transcribed spacer (ITS) to identify different kinds of fungi (3). Over a million ITS sequences are stored using an identification process called metabarcoding for reference in databases. 

One database called UNITE organizes and shares information about the DNA sequence data of fungi. UNITE has over 450,000 “species hypotheses” that allow various studies to reference their data based on similarities in their DNA sequences, as each one has a unique ID to find more information about it. Many species of DFT are within the UNITE database, but contemporary mycologists believe DFT has little to no real and objective existence in the biological world (4). DNA barcoding allows data to be easily stored online, but this data has limitations with its amount of information and its difficulty in linking different sources of information together. Since DFTs have DNA that has not yet been identified on a species level, they create a challenge for integrating biodiversity data with shared classification names (5). 

The International Code of Nomenclature (ICN) for algae, fungi, and plants defines the scientific naming and description of fungal species. It does not allow species descriptions based solely on typified DNA sequences, so DFT has been ignored from any formal classification. However, DFT has significant scientific value in discovering information about new species, branching orders, overlooked taxa, and ecological patterns (6).

Efforts to include DFT in the mycological community

The authors of the new study argue that scientists should include DFT in the DNA-based typification system because these fungi can later be identified or used to identify and understand new species of fungi. They observe that the traditional approaches used to recover fungal species should be updated because environmental DNA sequencing is most effective at identifying all forms of fungi, including DFT (7). Regardless of DFT’s lack of physical form, the authors found that they hold much significance in the fungal kingdom and should no longer be ignored by mycologists. 

In an interview with Eurek Alert lead author Henrik Nilsson from the University of Gothenburg, Sweeden notes, “species and groups that cannot be named formally, well, they tend to fall between the cracks. They’re typically not considered in nature conservation initiatives. They are often left out from efforts to estimate the evolutionary history of fungi, and their ecological roles and associations are largely overlooked when we try to figure out how mass and energy flow in ecosystems. They’re essentially treated as if they didn’t exist.” 

Despite major debates within the mycological community, a recent effort to revise the ICN’s definition of formal species naming was declined by a majority vote (8). This rejection demonstrates how DFT is still perceived as irrelevant to the fungi world. Despite the lack of support from many mycologists, the authors have requested minimal changes to be made to the nomenclatural rules to include official naming for the most well-known and documented species of DFT. These changes to the ICN would exclude any DFT that is not yet well-defined. By updating the naming system, the significant forms of DFT will not become outdated and irrelevant. The research behind DFT is ongoing and remains to be further debated by the mycological community.

 “The nomenclatural aspects of dark fungi will presumably be discussed at some length at next year’s international mycological congress in Maastricht, the Netherlands. We’re hopeful that the mycological community will reach meaningful agreement on integration of the dark fungi into the rules of nomenclature. After all, mycologists are used to negotiating and solving non-trivial questions on a day-to-day basis, and this one is hardly any different,” says Marisol Sanchez-Garcia of the Swedish Agricultural University.

Even with the debates in the community, mycologists hope to reach a consensus about integrating DFT into the rules of nomenclature. Using DNA sequencing to identify and classify fungal groups as distinct species may be a novel approach; however, this method can potentially recognize and add several thousand more fungi to existing databases for future research. Therefore, scientists can one day better understand the role of certain fungal groups like DFT, which are abundant in both soil and water ecosystems. Still, further research is necessary for scientists to fully understand the characteristics and functions of DFT.

References

1. Lücking, Robert, M. Catherine Aime, Barbara Robbertse, Andrew N. Miller, Takayuki Aoki, Hiran A. Ariyawansa, Gianluigi Cardinali, et al. 2021. “Fungal Taxonomy and Sequence-Based Nomenclature.” Nature Microbiology 6 (5): 540–48. https://doi.org/10.1038/s41564-021-00888-x.
2. Tedersoo, Leho, Sten Anslan, Mohammad Bahram, Urmas Kõljalg, and Kessy Abarenkov. 2020. “Identifying the ‘Unidentified’ Fungi: A Global-Scale Long-Read Third-Generation Sequencing Approach.” Fungal Diversity, August. https://doi.org/10.1007/s13225-020-00456-4.
3. Arita, Makoto, Ilene Karsch-Mizrachi, and Guy Cochrane. 2020. “The International Nucleotide Sequence Database Collaboration.” Nucleic Acids Research 49 (D1): D121–24. https://doi.org/10.1093/nar/gkaa967.
4. Nilsson, Rolf Henrik, Karl-Henrik Larsson, Andy F S Taylor, Johan Bengtsson-Palme, Thomas S Jeppesen, Dmitry Schigel, Peter Kennedy, et al. 2019. “The UNITE Database for Molecular Identification of Fungi: Handling Dark Taxa and Parallel Taxonomic Classifications.” Nucleic Acids Research 47 (Database issue): D259–64. https://doi.org/10.1093/nar/gky1022.
5. Page, Roderic D. M. 2016. “DNA Barcoding and Taxonomy: Dark Taxa and Dark Texts.” Philosophical Transactions of the Royal Society B: Biological Sciences 371 (1702): 20150334. https://doi.org/10.1098/rstb.2015.0334.
6. Khan, Faheema, Kerri L Kluting, Jeanette Tångrot, Hector Urbina, Tea Ammunet, Shadi Eshghi Sahraei, Martin Rydén, Martin Ryberg, and Anna Rosling. 2020. “Naming the Untouchable – Environmental Sequences and Niche Partitioning as Taxonomical Evidence in Fungi.” IMA Fungus 11 (1). https://doi.org/10.1186/s43008-020-00045-9.
7. Nilsson, R. Henrik, MartinRyberg, Christian Wurzbacher, Leho Tedersoo, Sten Anslan, Sergei Põlme, Viacheslav Spirin, et al. 2023. “How, Not If, Is the Question Mycologists Should Be Asking about DNA-Based Typification.” MycoKeys 96 (October): 143–57.https://www.nature.com/articles/s41564-021-00888-x
8. May, Tom W., Scott A. Redhead, Lorenzo Lombard, and Amy Y. Rossman. 2018. “XI International Mycological Congress: Report of Congress Action on Nomenclature Proposals Relating to Fungi.” IMA Fungus 9 (2): xxii–xxvii. https://doi.org/10.1007/bf03449448.