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Have you ever picked up something and wondered, "what is that?" Taxonomists help answer that question by dutifully documenting phenotypic (trait) and genotypic (genetic) differences among living things that allow them to be quickly distinguished and identified. Placing organisms into categories is useful so that instead of describing a slew of characteristics, we can simply use broad categories as reference points to inform us not only about the nature of an individual, but also about its relationship to other similar organisms. A new organism classified as a vertebrate, for example, will be commonly understood to have a spine composed of vertebrae. For scientists, taxonomic groups are touchstones of understanding: a foundation upon which to build new knowledge. This metaphor communicates the fundamental importance of taxonomy, but it implies a stability that taxonomic classification lacks.

For much of scientific history, fungi have been a botanist's domain. Until very recently — reasonably within a human lifetime — fungi remained classified as plants as part of a centuries-old division that can be summed up by an axiom attributed to Carl Linnaeus: "Plants grow and live; Animals grow, live and feel." This "father of modern taxonomy" (and ) classified living organisms into 2 categories: either animals or plants. This paradigm can be rephrased as animals and "not animals," as the category "plants" long represented a ragtag group of unrelated organisms. Without the context of evolution, these classifications sought to place organisms by perceived, oberservable similarity, instead of "relatedness" in a modern, genetic sense.

Classifying fungi as plants has led to some curious events. The earliest description of fungi pathogenic to insects (likely Cordyceps militaris) by the French entomologist René Antoine Ferchault de Réaumur was as a plant root. The Mycological Society of America was established while fungi were still considered plants, and the society's journal originated from the New York Botanical Garden. This garden continues to maintain one of the world's largest collections of fungi in their herbarium. This pairing of fungi with plants is a present problem: misclassification matters because how we classify organisms affects how we understand, support (financially and culturally) and engage with them.

Why Were Fungi Ever Considered Plants?

Today, we know that fungi are not plants, but the botanical history of fungi provides an interesting perspective on our scientific biases, on how we classify organisms and how these impact our collective knowledge.

Taxonomic classifications are in constant flux, as we refine our understanding of the incredible diversity that surrounds us. Even in the age of genomics, we have only just scratched the surface of this diversity. Because we don't have a full picture of the diversity of life, our best laid classifications can be (and are) routinely shifted by a newcomer or fresh evidence. Today, we have the luxury of molecular tools for classification, but taxonomic classifications can be traced back before the discovery of DNA, the concept of evolution and the invention of the microscope. Early classifications were limited by the tools (and views) available to them.

We must keep this caveat in mind when examining some of the early attempts at classifying life. Mushrooms were the earliest representatives of fungi to be classified. Based on observations of mushrooms, early taxonomists determined that fungi are immobile (fungi are not immobile) and they have rigid cell walls that support them. These characteristics were sufficient for early scientists to determine that fungi are not animals and to lump them with plants.

Reason 1: Fungi Lack Chloroplasts

We have arrived at our first reason fungi are not plants: fungi lack chloroplasts. This verdant, unifying feature of plants is readily observable to the eye, and these chlorophyll-containing plastids continue to be an important milestone for our modern understanding of plant evolution. Of course, there are plants that lack functional chloroplasts, such as , but we know these flowering plants ("higher plants," once upon a time) lost chlorophyll during their evolutionary history. This evolutionary context was lacking until Darwin came along, but demonstrates how callously uncooperative biology is with our artificial delineations. Broad outlines for our categories for living things were based on what we could see, and microbes, including fungi without a fruiting body to observe, were an afterthought.

Reason 2: Fungi Have a Unique Mode of Acquiring Nutrients

Old paradigms for classifying life were so ingrained that challenging them was a difficult task. Still, the various groups of fungi provided scientists with a nice tool for the task. In 1955, George Willard Martin challenged the notion that fungi should be classified as plants with . In the introduction, he hazarded a guess that most mycologists at the time would answer ‘yes.' Still, his thorough examination of the topic influenced Robert Harding Whittaker in his pursuit to revolutionize taxonomy.

Whittaker published several articles proposing more kingdoms of life. He eventually settled on 5 kingdoms, but he was engaged in a philosophical, decades-long debate on the appropriate way to catalogue life. While a contemporary taxonomist Herbert Copeland argued for detailed description of features for classification informed by historical understanding, . Whittaker's theory was organisms can play: producers (photosynthesizers), consumers (eaters) and reducers (decomposers).

Arguably, Whittaker's reasoning finally extricated fungi from the kingdom of plants, and so it is our next reason fungi are not plants: fungi have a unique mode of acquiring nutrients. Fungi secrete digestive enzymes, then absorb nutrients from their surroundings. This is in sharp contrast to plants, which make their own food (thanks to their chloroplasts). It was clear to Whittaker that this difference distinguished fungi from plants ecologically, but he was also grappling with a more basic question: why are we classifying organisms? than to divide them?

When the classification of living organisms was first undertaken, we believed the catalog could one day be complete. Whittaker knew that new editions of this catalog were produced each day, so instead of basing taxonomy on features alone, he argued for kingdoms that represented major evolutionary trajectories. These categories would be more useful for evolutionary and ecological questions. He published his , which included separate fungal and plant kingdoms.

Reason 3: Molecular Evidence Demonstrates Fungi Are More Closely Related to Animals Than to Plants

The proposed separation of fungi and plants is indisputably supported by molecular evidence. revealed that fungi are more closely related to us than to plants. Fungi and animals form a clade called opisthokonta, which is named after a single, posterior flagellum present in their last common ancestor. Today, this posterior flagellum propels primitive fungal spores and animal sperm alike.

This is our final reason fungi are not plants: the best available demonstrates fungi are more closely related to animals than plants. These computational and molecular approaches are convincing because they provide robust evolutionary histories that indicate organismal relationships and estimate when they diverged from common ancestors. A molecular understanding of life has uncovered 3 possible major domains of life: Bacteria, Archaea and Eukarya (). These are distinguished by cellular components (e.g., membrane-bound organelles) and the composition of the cell membrane.

Although they've been granted their own kingdom, fungi continue to demand taxonomic attention. Molecular approaches reveal that mycologists have described some fungi more than once. Various names for sexual (i.e., producing mushrooms) and asexual forms of the same fungus have inspired an effort to revise fungal taxa, humbly called "" This initiative continues today, but the challenge is immense, with databases like listing synonyms and citations with descriptions of fungi.

What has the (incorrect) classification of mycology as a botanical pursuit done to the advancement of the field? The more we know about fungi, the better prepared we are to protect ourselves (and other organisms) from fungal infections. Fungi have so much to uniquely teach us about (to name just 3 examples) evolution, ecology and cellular biology. Plant science departments continue to train many mycologists across the country, but where would mycology be if this discipline were supported with a similar number of departments? Would more microbiome studies explicitly include the mycobiome? Would we be better prepared for if the U.S. Department of Agriculture instead had a Animal, Plant *and Fungi* Health Protection Service? We have much to learn about fungi, but one thing is for certain: fungi are not plants.