Illustrated Generic Names of Fungi (An Ode to Fungi)

ILLUSTRATED GENERIC NAMES of Fungi, a 451-page book with over 1,000 original watercolors of Fungi life stages (many viewed under the microscope), “created with passion and fervor by Miguel Ulloa,” would be at home in natural history and art museum bookstores/gift shops. “Not only do these illustrations give the book a sense of artistic value, but they also serve to distinguish it from the usual mycology texts,” write Mexico City-based authors Miguel Ulloa and Elvira Aguirre-Acosta, who hope the book “will be well received and useful to students of this fascinating group of organisms.”

Though a good reference volume for science libraries, artists will be inspired by the otherworldly beauty and structural diversity found within the biological kingdoms Fungi, Chromista and Protozoa. The latter two kingdoms having until recently been considered Fungi. The book is published by the St. Paul, Minnesota-based American Phytopathological Society (APS), a scientific society, many of whose members focus on preventing plant diseases (some caused by Fungi) of agricultural importance from negatively impacting world food supplies. The text and watercolors portray 1,592 of the 8,000+ known Fungi genera. Over a million Fungi species are known, and just mentioning them all by name would be an encyclopedic endeavor. But in the age of Internet collaborations, we may yet get there.

“The 1,592 generic names of these 3 kingdoms (Fungi, Chromista, Protozoa) are arranged alphabetically,” and “the genera included are from all over the world, describing fungal diversity from 5 continents,” write the authors. “Brief diagnostic morphological characteristics of each genus are presented. These descriptions also mention the ecology and mode of nutrition of each species of each genus as parasites on organisms ranging from protozoa to vertebrate hosts, including human mycoses caused by fungi, and symbionts with insects and many groups of arthropod hosts, as well as those fungi associated with plants (decomposers, mycorrhizae, and pathogens).”

“An important aspect of the content of this book is etymology, which is the study of the origins and meanings of words,” say the authors. “For the generic names of fungi, the etymology rests on knowledge of the origins, structures and transformations of words. The etymological meaning of any word is an essential part of linguistics —indispensable to speaking and writing with the accuracy, clarity, precision, and elegance that distinguishes academic and scientific language. The technical and scientific vocabulary are derived from ancient words, mainly Greek and Latin, from which innumerable words or neologisms have been derived.”

For example, a Fungi genus found on mossy soils, trees and old wood is named Cora, from the Greek word kόre for “pupil of the eye, young, virgin, beautiful woman, maiden, doll, for the colorful reniform, circular or semicircular thallus…of loosely interwoven hyphae that extend over substrate…to form a delicate pileus.” Additional sources (e.g. botanical dictionaries, Google) will likely be necessary to lookup mycological terms such as pileus (Latin for cap) and thallus (Latinized Greek, referring to twig-like undifferentiated vegetative tissue).

The well-known genus Aspergillus is the combination of Latin words for rough (asper) and the vessel used for sprinkling holy water (gillo), which is what the fungal conidial head resembles under the microscope (vividly shown in Ulloa’s watercolors). Penicillium refers to Latin diminutives for the brush (penicillus) or feather-duster appearance of conidiophores magnified 1,500 times under the microscope.

Etymology also provides “a powerful aid to memory to more easily recall the meaning of a word.” In past eras, write Ulloa and Aguirre-Acosta, “it was a little more common for authors to follow the norm of explaining the origin of scientific names used, including genera and species, a norm that unfortunately very few follow at present. The present work is intended to make up for these types of omissions and contribute to filling a void.”

Plant pathologists focus on Fungi and microbes because of their association with epidemics and famines like the potato blight that ravaged 19th century Ireland. Rusts, smuts, bunts, ergots and other Fungi have infested grain crops since ancient times, and still threaten world food supplies. The Fungi genus Claviceps includes ergots infecting wheat and rye. Clavus is Latin for walking stick or nail; ceps is Neo-Latin “derived from Latin caput, capitis, head, for the club shape of the ascocarps.”

Ergot-contaminated rye flour baked into bread caused epidemic ergotism, mass poisonings known in medieval times as St. Anthony’s fire. The “holy fire” could generate intense body heat and consume whole bodies, leaving behind only charred limbs. Ergot alkaloids cause widely varying symptoms: lethal gangrene (from blood vessel constriction), painful muscle convulsions, seizures, coma, dementia and visions. Sometimes “holy” and sometimes horrific, these visions ranged from shining bright colors and spatial shifts to scream-inducing hallucinations. Symptoms could last for days, weeks, months or years, when not quickly lethal. Ergotism was dubbed Kriebelkrankheit in Germany because it felt like insects crawling under the skin.

Ergot poisonings, sometimes blamed on witchcraft, were the basis of Scandinavian witch trials right up to modern times. Some “witches” admitted intentionally poisoning food with the black rye ergot in acts of vengeance against their enemies. Fungal ergots also became the basis of crude, sometimes deadly medieval medicines used by midwives and physicians for “quickening” childbirth. Modern medicine uses ergot alkaloid derivatives similar to those causing gangrene to constrict blood vessels and relieve migraine headaches.

Plenty of practical reasons for studying Fungi to make life on planet Earth more pleasant, including self-healing concrete; and a caterpillar fungus called Cordyceps used in Chinese medicine, which could be particularly useful for certain brain strokes where modern medicine lacks effective drugs and treatments. Just as botulism toxin was modified into a best-selling pharmaceutical, researchers study Fungi poisons and bioactive compounds as sources of antibiotic, antioxidative, antitumor, immunosuppressive and other products potentially useful in agriculture and medicine. Fungi biochemicals can also be fermented for industrial use.

“Few fungi have had as broad an economic impact as Aspergillus flavus,” because “the fungus will grow and produce aflatoxin in almost any stored crop seed,” wrote USDA-ARS researcher Maren Klich (2007) in the journal Molecular Plant Pathology. Aspergillus species produce aflatoxins, whose poisonous and carcinogenic presence is monitored and limited to a few parts per billion in human, animal and pet foods worldwide. Epidemics from contaminated pet food have killed animals in kennels. Consumers of contaminated corn have been killed in Africa. Honeybees infected with Aspergillus suffer from a disease called stonebrood.

In the USA, the estimated economic cost of mycotoxins is at least a billion dollars annually; and near $100 million for California almonds and walnuts. “In the field, aflatoxin is associated with drought-stressed oilseed crops including maize, peanut, cottonseed and tree nuts. Under the right conditions, the fungus will grow and produce aflatoxin in almost any stored crop seed,” said Klich. “As human pathogens, Aspergillus species have become increasingly important because immunosuppressed people are very susceptible to infection,” and “A. flavus is also an allergen causing allergic bronchopulmonary aspergillosis.”

“Interestingly, the one cooking process that does drastically reduce aflatoxin is the nixtamalization process (soaking and cooking of maize in an alkaline solution) used in making tortillas,” said Klich. “Thousands of papers have been written on Aspergillus flavus and aflatoxins, so a complete review of the literature is not possible.”

Breads, cheeses, wines, beers, yoghurt, sake, tofu, miso, tempe, soy sauces, numerous biological pest controls and medicines are among the many beneficial Fungi products mostly taken for granted without thinking of their microbial origins. Fungi can also be useful for environmental remediation. Every year 500 million to 1 trillion polyethylene plastic bags are used worldwide, and fungi can be part of recycling solutions. In India, two common fungi, Mucor circinilloides and Aspergillus flavus, were found biodegrading polyethylene shopping bags in landfills; micro-algae degraded discarded plastic bags in shallow suburban waters.

Fungi in the genera Penicillium, grown industrially to produce the antibiotic penicillin and ripen blue cheeses, also produce enzymes biodegrading plastics. One idea is industrial-scale bio-factories where multiple organisms decompose plastics into simpler compounds such as carbon dioxide, an overly maligned and demonized minor atmospheric gas essential to photosynthesis, plant growth and animal life on planet Earth.

Fungi survive in some of Earth’s harshest environments, such as South America’s Desierto de Atacama or Atacama Desert. The remarkable survival skills of Fungi even extend into outer space. Scientists periodically revisit speculations that Fungi existed on other planets, such as Mars in its early phases, or were introduced to planet Earth from regions unknown. The Illustrated Generic Names of Fungi devotes 2 pages and 6 watercolors to Aspergillus, which are among the Fungi whose life stages can survive up to 6 years of the low temperatures, vacuums and irradiation typical of outer space.

Aspergillus and Penicillium are also among the Fungi identified living on the surfaces of spacecraft and the International Space Station. “Exteriors of human and robotic space vehicles are inhabited by millions of microbial cells, many of which are carried as spores that are highly resistant to the adverse environmental effect,” wrote Novikova et al. (2015). “One of the crucial challenges of space exploration is planetary quarantine or how it can be ensured.” Though at various times scientists, including Francis Crick who shared the Nobel Prize for identifying the structure of DNA, have suggested the reverse, that microbial life traveled through outer space and colonized planet Earth.

Back on planet Earth, May and Adams (1997) estimated that Aspergillus Fungi had a $45 billion dollar positive impact on the USA economy from large-scale production of citric acid and industrial enzymes such as amylases, proteases and lipases. There are over a million filamentous Fungi species. But “no governmental agency, except the USDA, has acknowledged the relative importance of filamentous fungi to the health of the general population and their importance to our national economy, let alone to the global economy,” wrote May and Adams. “This group of organisms is likely to tell us much about ourselves and how cells have solved many fundamental problems in biology.”

Enjoy the Illustrated Generic Names of Fungi for its unique combination of beautiful watercolors combined with Etymology. It is like an illuminated manuscript, a window hinting at an underlying fungal reality dwarfing imaginations. A good springboard for delving deeper into the Fungi.

Untold Stories, Beyond Methyl Bromide

“THE IDEA TO write this book came to me after I retired in 2005 and was cleaning out, re-reading, and reorganizing 40 years of files…in spite of three books and more than 200 journal publications and book chapters, my files filled with history and unpublished data were headed for the trash bin…the greater my urge to somehow pull the stories together into a single read-through description of my career…unique, it is the approach I took and the philosophy behind my approach to do hypothesis-driven research starting in the field, followed by the laboratory,” writes R. James Cook in the “Preface” to his book, Untold Stories (APS Press, 2017).

In 1974, Cook and Kenneth F. Baker co-authored a landmark book, Biological Control of Plant Pathogens. That book, which in some ways is a precursor to Untold Stories, summarized scientific evidence relevant to creating ecological balances favoring beneficial organisms (e.g. biocontrol agents, antagonists, competitors) as pesticide alternatives to control pathogens capable of weakening and destroying plants, including major food crops such as potato and wheat. Human medicine has at various times in various places employed a similar biological approach, such as using bacteriophages to fight diseases such as cholera, but for an array of reasons biological control has found more fertile ground in agriculture. Ecological balances can be tilted or nudged from pathogens to beneficial organisms in various ways, including via soil pH adjustments, tillage systems, cropping sequences, fallows, composts, amendments, nutrients, etc. The specifics can vary widely among crops, individual fields, regions, soil types, etc. Dr. Cook, as the Untold Stories subtitle, “Forty Years of Field Research on Root Diseases of Wheat,” hints, found wheat a fertile microcosm for exploring the phenomena of naturally disease suppressive soils for producing healthy crops.

Cook’s job when he joined the USDA Agricultural Research Service included soil diseases afflicting wheat, one of humanity’s most ancient crops and a worldwide dietary staple. The USA grew 45.7 million acres of wheat in 2017, most of it winter planted varieties, the lowest acreage since record keeping began in 1919. USA farmers grow twice as much corn and soybean, roughly 90 million acres of each. Wheat exports earn the USA roughly $6 billion a year, out of $140 billion in total agricultural exports. Though wheat helps the USA balance of trade, family farms growing wheat are not sustainable or economically viable if soil pesticides are used. Dr. Cook’s challenge was curing wheat soil diseases without costly pesticides. In the 1970s, the mainstream view was that solving pest problems without pesticides was drug-induced organic hippie crazy talk, a near impossible task with low probability of success.

Fortunately Dr. Cook possessed sound inner instincts complemented by scientific understanding of ecology and microbiology, with an emphasis on biological control of plant diseases absorbed working alongside Kenneth Baker and others at the University of California, Berkeley where biological control was still honored and respected despite falling from its early 20th century heights during the synthetic pesticide era. Cook briefly acknowledges Louis Pasteur, the famous French freelance microbiologist, chemist and entomologist who developed modern medical germ theory and laid the foundations for modern epidemiology while alleviating a mysterious silkworm colony collapse (disease epidemic) depressing the mid-19th century French economy.

On page 236 of Untold Stories, Cook quotes Pasteur: “In the field of observation, chance favors the prepared mind.” I would go back one step more to Pasteur’s mentor, chemist Jean Baptiste Dumas, who according to French-borne microbiologist René Dubos, persuaded a reluctant Pasteur to tackle the silkworm problem despite an insect ignorance for which he was widely ridiculed: “To Pasteur’s remark that he was totally unfamiliar with the subject, Dumas had replied one day: ‘So much the better! For ideas, you will have only those which shall come to you as a result of your observations!’” Microbiologist Alexander Fleming, famous for the fungal antibiotic penicillin, noted another important factor: “Louis Pasteur in his youth and throughout his life believed in hard work. He lived for his work and put his whole heart and soul into it. His was not a 40-hour week. He worked so constantly in his laboratory that it was inevitable that he became a beautiful technician…”

Another message embedded in Cook’s Untold Stories: Successfully tackle hard problems that appear insoluble to everyone else, and the probability of job security and life success increase. Cook developed an expertise in finding cooperative wheat farmers and locating fields where natural biological controls seemed to be working on their own. Then did a laboratory form of reverse ecological process engineering to find out why these fields developed a disease immunity or natural suppression of wheat soil pathogens. When you can replicate or duplicate the phenomena experimentally, then a degree of understanding can be claimed.

 

Untold Stories feels like the real nitty-gritty, with behind-the-scenes stories about how research projects are accomplished. The type of details typically omitted from science journals, by design. If anyone dared put into their journal article the details of how they obtained funding, navigated the bureaucracy to win support, or cleverly acquired a piece of new equipment, it would no doubt get edited out. This is a reason Roald Hoffmann in his book, The Philosophy, Art, and Science of Chemistry (Oxford University Press, 2012), suggested a new kind of science journal allowing first person “voice” and personal experience. Actually, it would only be “new” in the “retro” sense that “everything old is new again.” In the early days of modern science, personal autobiographical expression, musings and miscellany were common. These early science articles could be confusingly messy and hard to decipher, perhaps harking back to the deliberately obscure days of alchemy. However, personal observation and experience was handled well by agricultural researchers in the early 20th century. Which is not meant to denigrate the utility and immense value of standardized journal formats with introduction, methodology, results, discussion, etc. There is room in the world for both.

Untold Stories embeds science in a wider human context, beyond what is possible in the modern journal format, which necessarily excludes the human dimension, but leaves behind an unintended residue, a subjective impression of a science rendered lifeless by the invisibility of its practitioners. Cook family members pitched in to write the forward, edit, design and deliver their father’s book ready for printing by the American Phytopathological Society (APS) Press. Cook’s attitude towards public service is refreshing, and clearly extended into his so-called retirement. Judging from the 2005 start date and the 2017 book publication date, Dr. Cook put over a decade into this “Magnum Opus” book project. Wife and family were promised this would absolutely be his last book. One might lament, but I have to believe Dr. Cook mined his past experiences so thoroughly as to be able to rest on his laurels and not feel that much was left out that could not be remedied in a few journal articles.

A mathematical ratio of untold stories to published stories would be interesting, and Dr. Cook is in a position to be the expert. Let’s say the Untold Stories:Published Stories ratio was 1:1 and had a certain “volume.” Then the “volume” (e.g. measured in pages, articles/books, person-years of work, or whatever) of untold stories could be multiplied by the number of scientists or the amount published in a given time period to yield an estimate of how much scientific research ends up in the proverbial trash bin.

The Untold Stories photo caption on page 52 brought to mind a much maligned molecule, methyl bromide, a research tool and experimental control integral to scientific investigation of naturally disease suppressive wheat soils. Salt marsh microbes naturally produce methyl bromide as an antibiotic type weapon in waging ecological warfare for survival against competitors and antagonists. The caption: “A discussion session in progress at a Pacific Coast Research Conference on Soil Fungi with Professor S.D. Garrett, Cambridge University, as the discussion leader…Steve Wilhelm from UC Berkeley, credited with the introduction of soil fumigation to the California strawberry industry, is in the front row…”

Dr. Wilhelm, who I knew to also be interested in promising methyl bromide alternatives such as steam, marigold cover crops and green manures, crops up again on page 186 of Cook’s book: “it was not until the middle of the twentieth century that soil fumigation was used on a large scale…Steve Wilhelm at UC Berkeley…together with Albert Paulus at UC Riverside, did the pioneering work on the use of mixtures of chloropicrin and methyl bromide to control soil-borne pathogens and weeds before planting strawberries in California starting in the late 1950s. Strawberry yields were roughly 5 tons per acre in fields not fumigated and up to 25 tons per acre in fields that were fumigated.”

Soil fumigation with methyl bromide and chloropicrin worked so well that California had near zero untreated strawberry fields available to investigate for naturally suppressive soils, which is unfortunate, as methyl bromide use is being phased out under the Montreal Protocol as an ozone depleting substance. Something I learned about in more depth working with the late Jamie Liebman, a plant pathologist at BIRC (Bio-Integral Research Center), where as subcontractors we helped develop a Montreal Protocol methyl bromide alternative research agenda for funding by the U.S. EPA and United Nations. I wrote a short chapter on this period in history titled “Rowland’s Recipe for Climate Treaty Success” in an ABC-CLIO book titled Science and Political Controversy, edited by David E. Newton in 2014. In 2015, attending agricultural, soil and entomological science meetings in Minneapolis, not far from APS headquarters, I was pleased to find that research agenda still extant and going deeper. Funny what a mere photo caption can trigger in human memory. No doubt Untold Stories will have similar effects on readers whose interests and paths intersected with those of Dr. Cook.

California’s $2 billion strawberry industry, which produces about 90% of the USA crop, an awesome 1.7 billion pounds on about 40,000 acres (43,000 pounds of strawberries per acre), was for all practical purposes birthed into existence by injecting chloropicrin and methyl bromide into soils under plastic tarps. California’s hyper-productive strawberry growers, like Florida tomato and inland Pacific Northwest potato growers, can earn back methyl bromide soil fumigation costs. Family wheat farms would be bankrupted and abandoned to tumbleweed and erosion by soil fumigation costs. Scientifically, the less prosperous economics of wheat growing were fortuitous, as Dr. Cook was precluded from earning a living testing and recommending soil pesticides. Instead, as Dr. Cook’s book rigorously details, applied science became indistinguishable from pure science (much as it did for Pasteur) as it delved into the microbiology, ecology and non-chemical remedies for soil pathogens causing unhealthy plants and crop failures.

A key scientific discovery was that growing wheat in the same field again and again, year after year without interruption or rotation, can result in soils becoming naturally suppressive or functionally immune to disease pathogens. But this goes against centuries of accumulated wisdom arguing that toxic root secretions (allelopathy) poison the soil, and are best alleviated by crop rotations. Cook’s objection on page 227: “this makes no mention of a role for root diseases and ignores one of the most fundamental principles of plant pathology taught to beginning students in plant pathology, that growing the same crop in the same soil increases the populations of pathogens of the roots of that crop…It takes a long time to replace the first explanation with the correct explanation for almost any phenomenon in nature.” It also takes time, as those who have studied ecology know, for pathogen, prey or pest populations to build up to peaks before predator and natural enemy populations reduce or crash them down to low levels. Dr. Cook’s mission was to shorten that time.

One set of wheat experiments described in the “Take-All Decline” chapter 7, owed inspiration to 1950s’ potato scab disease research in Washington State, where small amounts (10%) of suppressive soil (presumably containing beneficial microbes) were added to disease-susceptible soils. Within 2-3 years, wheat soils were growing healthy plants. “Although I never repeated this experiment (nor did it need to be repeated), it would turn out to be the most influential experiment of my career,” wrote Dr. Cook on page 144. “It led to my award of a Guggenheim Fellowship…to my first competitive grant awarded by the USDA Competitive Grants Research Office (CARGO) in 1978…to the USDA ARS approving the formation of the Root Disease and Biological Control Research Unit in 1984; and to the USDA ARS providing permanent funds for me to hire…”

This only scratches the surface of a truly remarkable book likely to become a classic of science.