Cover of The Fungal Kingdom: Diverse and Essential Roles in Earth's Ecosystem

There's more to fungi than just mushrooms. Fungi are the cause of scores of life-threatening diseases, they are the earth's best degraders of organic matter and they are proving to be more useful to science and manufacturing every year. They come in many forms, ranging from single-celled yeasts on the order of ~10 ÌM to mushrooms the size of dinner plates to thin, powdery coatings of mold. Despite the diversity that science has revealed about fungi and their myriad roles in health, ecology and industry, much about these organisms remains a mystery.

The American Academy of Microbiology convened a colloquium Nov. 2–4, 2007, in Tucson, Ariz., to discuss fungi, the current state of research in fungal biology (mycology) and the gaps in our understanding of this important group of organisms. Experts in mycology, medicine, plant pathogens, genetics/ genomics, ecology and other areas developed specific recommendations for advancing fungal research.

Recent studies have revealed that fungi are more closely related to animals than many other eukaryotic organisms, and these 2 successful kingdoms diverged from their last common ancestor (a unicellular organism that lived in the oceans propelled by a flagellum) on the order of a billion years ago. Thus, fungi have a great deal to teach us about more complex organisms, including ourselves. The fungal kingdom comprises at least 11 separate groups (7 phyla plus 4 subphyla of the polyphyletic Zygomycota) with diverse genetics, morphologies and life histories. Genomics (research that uses all or part of an organism's genetic material to learn more about that organism) has opened many new windows on the fungal world, but future progress in fungal genomics will likely be hindered by challenges in fully exploiting the sequence data. Continued support for fungal genomics is critical considering the real possibility that genome sequencing will eventually lead to improvements in the detection, prevention and treatment of fungal disease. Colloquium participants agreed that the highest priority is to establish a Fungal Genomes Database to assemble and organize genome sequence data, annotation data and links to the relevant literature.

Research that records which genes are expressed (transcriptional profiling) is also revolutionizing fungal research, and comparing gene expression of the same fungus under different conditions, or different fungi under the same conditions, will be essential to preventing and treating fungal disease. Now that transcriptional profiling is moving from array-based technology to sequence technology, these data have become portable in the sense that results from one laboratory can easily be compared to those from another by computation. To facilitate these comparisons, a central database is essential. Finally, environmental sequencing (metagenomics) has begun to impact fungal biology, and these data will need to be accommodated in a database to make it possible to compare fungal communities across different environments.

A global fungal census, which would describe the various locations and species of fungi that exist in nature, is recommended. Fungi are present in every ecosystem where they perform many tasks, including biomass degradation and participation in mutually beneficial symbiotic associations with plants. And, like any other organism, fungi may behave very differently in the wake of ecosystem disturbance or when introduced in a particular ecosystem from other regions of the world, even causing outbreaks of disease in humans and plants. In recent history, humans have been responsible for initiating a number of fungal invasions into new geographic regions, sometimes with devastating consequences. More research is needed on fungi in the environment—their diversity, their numbers in different locations, their functions—before scientists can effectively manage introduced fungal diseases or cope with fungal contamination in homes and businesses. A global fungal census, which would describe the species of fungi that exist in nature in the context of their habitats, is recommended. It also remains unclear whether there are fungi whose presence promotes the health of the host, as has been shown for some members of the bacterial component of an animal's microbiota.

Not only is the fungal global ecology of interest, but also the human fungal ecology. It is a little known fact that many different fungi live on and in the human body. Of the estimated 1.5 million fungal species that exist today, more than 200 species have been associated with humans, either as pathogens or as commensal organisms that apparently do us no harm. A census of the fungi associated with the human body is necessary to promote understanding and lead to ways to prevent human disease and is highly recommended. Although many fungal diseases are associated with patients with depressed immune systems, some fungal infections, including sinusitis and vaginitis and athlete's foot, strike healthy people, and fungi may also be linked to asthma, allergies and sick building syndrome. Given that the incidence of fungal diseases is on the rise, it is also important to continue developing new vaccines and new types of treatments for overcoming these diseases. Diagnostics for fungal diseases are utterly inadequate when, in fact, accurate and early diagnosis of fungal diseases is critical for managing disease and saving lives. New and more rapid techniques are needed for diagnosing fungal infections.

Fungi synthesize a seemingly limitless array of secondary metabolites, including many antibiotics, such as cyclosporin A, a revolutionary drug that inhibits the rejection of transplanted organs, and statins, which are widely used to treat elevated lipid and cholesterol levels and reduce the risk of heart disease. Many fungi and fungal enzymes are used in industry in processes ranging from fermentation to food production to the conversion of biomass to ethanol. Further genomic sequencing of key fungi promises to provide additional insights into the nature and synthesis of novel biologically active natural products and untapped metabolic potential.

Certain fungi can infect both plants and animals, overcoming significant differences between these very different hosts. Known trans-kingdom pathogens include Aspergillus flavus, which infects and damages oilseed crops, insects and humans. Pathogenic fungi are dangerous potential biological weapons because they are inexpensive to acquire, and many are easy to culture in large quantities. The potential for fungi and fungal toxins to be used as weapons is seriously underestimated and understudied. The field needs advocacy to raise the consciousness of fungi as potential bioweapons and ensure that this kingdom benefits from bioterrorism-related funding.


Arturo Casadevall, Joseph Heitman, Merry Buckley. 2008. The fungal kingdom: diverse and essential roles in earth's ecosystem.

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