Introduction to

the world of Fungi

Let us learn about fungi correctly
What do you think of when you hear the word “fungi”? Many people have misconceptions. So, let us startby understanding correctly what kind of organisms fungi are.

What do you think of when you
hear the word “fungi”?
Organisms other than fungi are also included in the

Escherichia coli
Lactobacillus
Paramecium

Koji moldﬁgure to your left. Which are fungi?
Myxomycetes (E) and Dictyostelium discoideum (G) areconsidered to be fungi in a broad sense. Although
Escherichia coli (Daicho-kin) and Lactobacillus (Nyusankin)have “-kin” in their name, they actually are not fungi(kin-rui). First, let’s understand how to define thecharacteristics of fungi.

Dictyostelium
discoideum
Chlamydomonas
Myxomycetes

Fungi are neither animals nor
plants; they are also not bacteria.
Kingdom Fungith
Ve roprteobra da
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degradation of both animal and plant remains (sapro-

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ecosystem balance and nutrient and carbon cycling and

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phytes). Hence, they contribute to the maintenance ofare now recognized to form a kingdom distinct from bothanimals and plants. As bacterial cells do not contain anucleus surrounded by a nuclear membrane, they are

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plants, and fungi. Today, fungi are considered to be

is

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absorption

considerably diﬀerent from eukaryotes such as animals,
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Monerathese plants and other animals. On the other hand, fungi
derive nutrients in other ways, such as througherAschelminthes

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synthesis and animals derive nutrients through eating

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Chytridiomycetes

Oomycetes

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Eukaryotes

When all the organisms were classiﬁed as either animals
or plants, fungi were categorized as plants. However, they

BasidiomycetescTra
Ascomycota

Kingdom Animalia

Zygomycota

Kingdom Plantae*atmeukaryotic and often produce mycelia, a basic ﬁlamentous
structure; further, they have no photosynthetic functions
and contain a cell wall mainly composed of chitin andchitosan. Moreover, they mainly reproduce via sporulation.

When the ﬁve kingdom system was proposed by Whittaker (1969), fungi was distinguished fromplants and animals on the basis of nutrition mode. Fungi absorb nutrition by degradingmaterials while plants produce their nutrition by photosynthesis and animals digests theirnutrients internally by eating from their mouths (ingestion). The three members of the
kingdoms represented producers (plants), consumers (animals), and decomposers (fungi),
respectively in nature. The concept was largely based on the ecological nature of the organisms.
The system was cited in the biology textbooks for decades, but it does not explain thephylogeny. Now, fungi are known to be closer to animals than plants (see the ﬁgure in page 7).

Bacterial cells are smaller than

Both molds and mushrooms consist

fungal cells and have no nuclei.

of mycelia (ﬁlamentous cells linked
together).

Fungi are neither animals nor plants, and neither are they bacteria.
1This is why fungi are important
All animals and plants cannot live without fungi. This may seem like exaggeration, but recent research
has shown that even plants that acquire nutrients from photosynthesis require fungi. In addition,
especially for the Japanese people, they are essential life partners. Letʼs think about the relationships
between our lives and fungi.

Fungi are our life partners
Edible mushrooms, bread, soy sauce, and sake: These cannot
be separated from the lives of the Japanese. Soy sauce and miso
are prepared through fermentation by the koji mold (Aspergillus

Foodoryzae). Seasonings, such as sake and mirin and dried bonito arealso prepared using fungi. Bread, wine, and beer are all preparedthrough fermentation by yeast. Fungi are involved in the
production of various fermented foods, thereby adding value toour lives.

Medicinal supplies and ornaments: The very ﬁrst antibiotic

Living(drugs to suppress bacterial growth) was penicillin, which
was produced by a type of mold. A variety of physiologically
active substances are also known to be produced by fungi;
they are indeed an important biological resource for
medicinal products. Moreover, pigments from fungi can be

Kamakura-bori is processed using thespores of black mold.

used as dyes (e.g., mushroom dye), and they are often usedin arts, thereby enriching our lives.

Substances made by fungi can be used in the

Cloth

manufacture of drugs.

Using fungi to treat material: You may wonder
whether clothes and fungi are related. As the enzymes
produced by fungi degrade a variety of substances,
they are used to remove stains and process ﬁbers. For
instance, when denim is processed by an enzyme
called cellulase, it creates a stone-washed texture
where the surface is partially broken. An enzyme
Clothes before

Fuzz is pressed down

enzymatic treatment

after enzymatic treatment

lipase, which degrades oil, is also used in detergent.

(e.g., with cellulase).

Fungi are our important life partners
2Representative blue mold that produces penicillin.
Penicillium chrysogenum.

Nematode-eating fungi. These are types of moldsthat trap and eat nematodes. The image shows
Arthrobotrys.

A laboulbeniomycete（Rickia sp.) parasitize thesurface of a tickʼs stomach. They are special fungi
evolved as insect parasites.

Striking Diversity
Fungi live not above ground, but also grow below ground in thesoil, as well as in inland water environments,and even oceans. They
all show a striking diversity in morphology and ecology. Letʼs have alook at their diversity.

Estimated
Estimated number
numberofof species
species

1,500,000
species
species3

An example of a beautiful mushroom, Amanita
caesareoides. This mushroom produces mycorrhizaewith Fagaceae plants. This is an edible mushroom.
Please do not confuse it with a poisonous mushroom
with similar appearance, Amanita muscaria.

Cordyceps nutans is a relatively well-studied
Ophiocordyceps sinensis, a type of mushroom
produced on insects.

Leratiomyces erythrocephalus , found in New
Zealand, has a stem but no gills. It is partially similar
in appearance to fungi that fruit belowground(hypogeoous), and is considered to be an intermediate form between hypogeous fungi andepigeous (aboveground) mushrooms.

Exobasidium gracile causes swollen leaves in
Sasanqua camellia called Sasanqua mochi-byo. This
plant pathogen causes the deformation andwithering of plants.

Molds on mushroom. Some of the molds parasitize
mushrooms. The image shows a type of Spinellus,
parasitizing a mushroom.

A representative of ocean fungus, Corollospora.
Spores have thorns and ﬂuttering attachments,
which make it easier to capture nutrients.

Batrachochytrium dendrobatidis is an amphibianpathogen, which has caused the extinction ofseveral animal species. Zoospores (running spores)
are formed within a pot-like structure.

Glomus species can form arbuscular mycorrhiza (atype of beneﬁcial fungal and plant interaction). The
fungus provides the plant with phosphorous andnitrogen from the soil i in return for photosynthesis
products.

Luminescent mushroom Mycena chlorophos. Some
mushrooms are known to illuminate. However, theclear reasons remain uncertain.

Auricularia auricula-judae, which is written as “a earof tree”, also belongs to fungi. There are various
mushrooms that have jelly-like fungal fruiting body.

Cyttaria is a rare fungus only parasitize on
Nothofagaceae in the southern hemisphere, suchas Australia and New Zealand

A type of Hysterangium, Hysterangium sp. Among
mushrooms, some of them have adapted to theunderground life, like this species.

Calvatia craniiformis has the dumpling-like funny
structure; this species evolved from a mushroom
with a cap.

Polyporaceae is a general term to describe bracket
mushrooms. Most of them are wood-decay (saprophytic) fungi.

Known Species
Approximately

97,000species

So far, known fungi are consisted ofaround 97,000 species. However,estimated number of fungi is said tobe around 1,500,000 species, whichmeans that fungi are the second
largest guild following insects onearth. This is signiﬁcantly larger than
270,000 and 44,000 of tracheophytes
and vertebrates, respectively.

Bloom-like branched mushroom, Ramaria sp. A
variety of types are known to belong to this species.

Fungi are diverse organisms; most of them have not yet been discovered.
4

Familiar fungi that appear in textbooks
Koji mold Aspergillus oryzae
How to obtain: The easiest way is to purchase commercially available koji. It
may be dry and store. How to observe: Observe using a loupe and stereoscopic
microscope. Pick a small amount using a dissecting needle or tweezers.
Important morphological: A swollen structure called vesicle contains cells that
produce spores, and from here, spores are continuously produced as if they arepushed out. Characteristics observed: Koji are important as they are used to
produce miso, soy sauce, and sake. They produce a variety of enzymes that canbe applied in many ﬁelds. Moreover, this is the ﬁrst fungus whose genome wasanalyzed.

The surface of koji is closely packed with koji mold. Take a small
amount, loosen as shown below on this page, and observe.

Microscopic image of koji moldLentinula edodes
How to obtain: The easiest way is to purchase commercially available
shiitake-mushroom at a supermarket. How to observe: Vertically slice the gill of
mushroom into thin strips, prepare a specimen for microscopic observation,and microscopically observe spores and basidia. You may press down a part of
the gill for observation. Commercially available mushrooms may remain
premature and are therefore not ideal for observation by beginners (beginners
are recommended to use Russulaceae). Important morphological: It produces
four colorless spores on a long a narrow basidium. Characteristics observed:
Japan was the ﬁrst to industrially produce this mushroom. It has value as foodand has a historical importance. If you tear a part of the mushroom and preparea specimen for observation, you may observe that mushrooms are indeed
composed of hyphae.
Fibers that you see when you tear up are the bundle of hyphae.

If you slice the gill and observe, you willsee basidia and spores at the edge.

This is how to observe
Depending on the samples, you may omit some of the procedures.
For example, a drop of yeast solution can easily be observed bydirectly placing it on a glass slide. In the case of mushrooms, samples
may need to be pressed down. Therefore, an appropriate observation
method depends on the characteristics of each sample.

5

Place a droplet of water on a slide glass. Take a small amount of sample (material toobserve) using a dissecting needle or tweezers.

Fungi are described in textbooks for junior high school and senior high school. However, few
seem to accurately describe the shape of fungi. Let us introduce some of the familiar fungithat appear in textbooks.

Neurospora crassa
How to obtain: Request and purchase from a strain collection organization.
Unfortunately, if you are not an expert, they will be diﬃcult to isolate fromnature. How to observe: Cultivate on an appropriate medium for the fungal
fruiting body (called perithecium) to form. Take the perithecium, prepare thespecimen for microscopic observation, and observe. Important morphological:
Eight spores are formed within the ascus formed in perithecia. Characteristics
observed: As Neurospora crassa is fast growing and stably forms a perithecium,
it has been used in genetic studies for many years. Beadle and Tatum used thisfungus to proposed the one gene-one enzyme hypothesis.

Perithecium of Neurospora crassa. A sac called ascus is found in theblack grain structure.

Ascus of Neurospora crassa. Eight spores

They are transparent at ﬁrst but darken as

are present within.

they ripen.

Saccharomyces cerevisiae
How to obtain: Easiest is to purchase as dry yeast at a supermarket (frozen anddried bread yeast). How to observe: Dissolve in approximately 5% sugar water
and warm for 1‒2 h at room temperature (you may warm it up to 37°C). Later,
prepare a specimen for microscopic observation and observe with an optical
microscope. Important morphological: They form unicellular bodies ofspherical-oval shapes. They form daughter cells (budding) from a part of the cell
as if it germinates and proliferates. Characteristics observed: They are used in
the fermentation of Japanese sake, beer, wine, and bread. In addition to alcohol
production during fermentation, they also produce carbon dioxide, acharacteristic that is utilized in the production of bread and beer. Better strains
are being continuously isolated in nature.
Carbon dioxide foam produced through the activity of bread yeast.

Budding yeast cells.

Fungi are important in various ﬁelds such as biology and applied science.

Loosen a sample using a dissecting needle
and tweezers (or two dissecting needles).

Place a cover glass carefully toprevent trapping air bubbles.

Press down the cover glass using a toolsuch as the shaft of a dissecting needle.

Place on a microscope and observe.

6

The latest fungi news and trivia
The science of fungi progresses every day. Here we provide the recent important news.

Biological position of fungi revealed

Eukaryotic Domain（Eukarya）
Chromalveolata

Fungi neither actively move like animals

Oomycetes

nor are they autotrophic like plants.
Then, do they share a common
ancestor with some organisms?
Until the middle of the 20th century, fungi were considered as

Amoebozoa Hyphochytridiomycetes

Opisthokonta
Animals
Fungi(Eumycetes)

Deformation fungi
Dictyostelium
AmoebaOthersBrown algae diatoms
Malaria parasite
Labyrinthula
Dinoﬂagellates , etc.

Plants
MossesFern
Red algae
Green algae
Otherslower plants without chlorophyll.
Later, it gradually became apparent

Rhizaria

Foraminifera
Nekobukabi
etc.

Excavatathat fungi are distinct from plants;

Euglena
Trichomonasetc.

however, their ancestors remained
uncertain for many years. At the end of the

Eukaryotes

20th century, a variety of techniques weredeveloped to elucidate the relationship between variousorganisms based on DNA nucleotide sequences or proteinamino acid sequences (molecular phylo- genetic analysis).

Prokaryotes

Consequently, fungi were revealed to be very closely related
to animals! Currently, the relationship between fungi andanimals has been widely acknowledged, and they havebeen grouped together as Opisthokonta, including several
other unicellular organisms.

Archaea Domain（Archea）

Eubacteria Domain(Eubacteria）

Are the scientiﬁc names of fungi going to change greatly?
A note on nomenclature revision rules

7

Most of the fungi reproduce by two reproductive methods:

This is an exceptional case in the nomenclature of organisms.

asexual or sexual. In most cases, the former are recognized asToday, organisms can be linked based on molecular information;molds, whereas the latter are considered as mushrooms. However,hence, it was decided to give only one name to these fungi

some mushrooms reproduce like molds. As they are(“International Code of Nomenclature for algae, fungi, andmorphologically distinct from each other, when they are in theplants”, 2011). The rule concerning the scientiﬁc names of fungi

period of mold, they have been considered as “imperfect fungi”

was implemented on January 1, 2013; however, the sorting andand given diﬀerent scientiﬁc names from the mushroom phase.

arranging of actual names has taken longer than expected.

Fungi are the only organisms to be given two distinct scientiﬁcCurrently, discussion is ongoing to decide which name to selectnames.

in each group of fungi.

Radiation and mushrooms
Fungi are the representatives of the most diverse organisms in
the forest ecosystem. Numerous spores are present in soils, andmushrooms and their growth environment. Therefore, it is highly
erroneous to believe that all the mushrooms are dangerous.

various types of mycelia have been established. Mycelia degrade

In contrast, continuous monitoring of cesium concentration in

not only fallen leaves and trees but also form relationships withmushrooms can reveal the natural circulation of cesium. Several

living plants through roots by constructing symbiotic systems

research groups of the Mycological Society of Japan aresuch as mycorrhiza, which exchange nutrients. In such manner,planning to monitor cesium concentration in mushrooms overmycelia are tangled together in complex ways in soil to form

the next several decades as a part of fungal research.

networks.
Because most fungi exist in soil, their role in cycling of carbon
and nutrients in the soil is enormous. In particular, many types ofmushrooms absorb a variety of substances through mycelia
which are accumulated in fungal fruiting body. Radiation is not
an exception. Many mushrooms accumulate higher
concentration of radioactive cesium than plants and animals.
After the incident at the nuclear power plant associated with
the Great East Japan earthquake, wild and log-grown outdoor
mushrooms at various locations around eastern Japan werereported to contain relatively high concentrations of radioactive

Germanium
semiconductor detector

cesium. However, after some investigation, it was revealed that not
all the mushrooms accumulate radioactive cesium. Cesium
concentration signiﬁcantly varies depending on the types of
Schizophyllum commune

Morchella esculenta

The roles of fungi, more than degradation
Where do plants obtain necessary water, nitrogen, andminerals to live? The eﬃciency at which plants obtain these

Treasures of forests such as matsutake, Lyophyllum shimeji, andtruﬄes are also mycorrhizal fungi.

from the soil is doubled when facilitated by symbiotic
mycorrhiza. The relationship of plants with fungi begins from
germination and continues through blooming until thecompletion of their lives; however, during the process ofnutrient absorption from soil, their symbiotic relationship with“mycorrhizal fungi” is essential. In the rich natural environmentof Japan, the role of universal mycorrhizal fungi tends to beignored. However, if mycorrhizal fungi disappear, forests andmeadows will also disappear. Forest trees, such as pine trees andoaks are in symbiotic relationships with mycorrhizal fungi (e.g.,
many Basidiomycota and Ascomycota) and various other plants
symbiotically live with arbuscular mycorrhizal fungi

A type of Russula, a representative mycorrhizal fungus(Glomeromycota). Some of the plants, such as certain orchids
and Monotropa hypopitys, became chlorophyll-free plants andtherefore completely dependent on mycorrhizal fungi. To begin
with, terrestrial plants are considered to have originated fromthe symbiosis with mycorrhizal fungi near shores approximately
400 million years ago. The mycelium of mycorrhizal fungi is the
major microbial biomass in soil; therefore, they are also
considered to play a key role in the global carbon cycle. Several
thousand types of mycorrhizal fungi are thought to be
distributed in Japan; however, their details remain uncertain.

Ectotrophic mycorrhiza
formed on the root of pinetree

Surface structure of mycorrhiza. Mycelia are
deformed and cover root cells.

Secrets of fungi have been revealed one by one! Letʼs update our knowledge too!
8

The future of fungi and humans
Crush woods

From petroleum to biomass:
Fungi which support sustainable society
Various “materials” that support our lives have been created frompetroleum products. However, to mitigate the shortage of petroleum
resources and reduce the environmental burden, we need to produce
various materials using plantderived sustainable resources. Biomass
such as wood is a representative sustainable resource. A variety of fungi
are involved in the processes, including sacchariﬁcation andfermentation, which are necessary for the production of such materials.

Trichoderma reesei, a representative
cellulose-degrading enzyme-producing
fungusTalaromyces cellulolyticus, domestic
cellulose-degrading enzyme-producing
fungusFor the artiﬁcial cultivation of matsutake
Matsutake are diﬃcult to cultivate and are therefore sought after
and traded at a high price. Domestic production of matsutake has
declined drastically, and many imported mushroom have been
widely traded. Thus, a variety of studies have been in progress for
its cultivation. A potential diﬃculty in cultivation is that matsutake
is a mycorrhizal mushroom living symbiotically with the roots ofplants such as Japanese red pine in forest areas. Therefore, there
are various ongoing projects to facilitate the growth of matsutake
by developing the forest environment suitable for the growth themushroom. In addition, to artiﬁcially introduce matsutake fungi
into a forest area, matsutake-fungi have been inoculated to theroots of Japanese red pine that have been antisepticallyMatsutake mycorrhiza formed on theseedling of Japanese red pine. The arrowgerminated within a sealed container. The pine seedlings wereindicates the mycelia of matsutake covering

then planted outdoors for the establishment and propagation of

the root surface.

fungi in the ﬁeld. In contrast, some studies are also ongoing basedon the pure culture of matsutake, rather than using the symbiotic
system with plant roots. The cultivation of Lyophyllum shimeji,

9also a type of mycorrhizal mushroom, has already achieved

The seedling of Japanese red pine grows

success.

symbiotically with matsutake.

Fungi are important biological resources which support our future. Here are some applications using these fungi.

Conversion of sugars into various
chemicals by yeast

Conversion of cellulose into sugar
by fungal enzymes

Ultra-yeast+
Saccharomyces cerevisiae enables
absorption and degradation of large
amount of sugar.

+
Heat-resistant
Kluyveromyces marxianus

Aid and salt resistance ofIssatchenkia orientalis

Institutions that archive fungal stock that meet the need for fungi
to be a biological and genetic resource
Fungi are already essential within our lives; however, they also
form biological and genetic resources with the future potential to be
used as new materials in the ﬁelds of medicine and biotechnology.
Organizations that mainly collect microbes such as fungi asbiological and genetic resources and store the live strains using on
freezing and drying methods are called “strain conservation
organizations” (culture collection or bio-resource centers). Academia
and corporates can use the various stored cultivated strains foreducation and research. In contrast, not all fungal strains can beeasily cultivated, and some strains, such as mycorrhizal fungi andother symbiotic fungi, are diﬃcult to isolate or cultivate. Strain
conservation organizations are also actively involved in various
research areas, such as the isolation or development of fungi,
thereby contributing to the use of fungal resources.

Isolation of wild mushroom (Sarcomyxa serotina).

Fungal strains cultivated and stored in test tubes.

Liquid nitrogen tanks and cryopreserved fungal strains.

Fungi are our important partners that support our lives, and they are also importantresources. The wise and sustainable use of fungi is therefore imperative.
10

About the Mycological Society of JapanThe Mycological Society of Japan was established in February 1956,
aiming to promote and familiarize academic research involved in fungi. The
society is a representative academic organization that widely exchanges
research information concerning fungi. We mainly target materials that havetraditionally been the focus of fungal researchers (while also focusing on
myxomycetes and oomycetes, already known not to be fungi). The society
has approximately 1,000 members, consisting of researchers (including
students), as well as corporates and fans of fungi.
From the basics to application, we conduct a wide range of scientificstudies in the following fields: biology, plant pathology, microbiology,
agricultural chemistry, fermentation technology, applied mushroom science,
forestry, medical science, pharmacology, and environmental science.
The main activities of the Mycological Society of Japan: An annual general
meeting (normally held in spring), fungi observation meetings (normally heldin fall), lectures, and symposiums aim for academic exchange between
Japanese and international experts along with presentation of research
results and information exchange. We also host non-periodic international
symposiums and actively cooperate with the International Mycological
Association and the Asian Mycological Association. Many researchers fromwith academic or technology researchers from related companies attend▼

several universities and national research and development institutes along

Home page of the Mycological Society of Japan http://www.mycology-jp.org/˜msj7/

such international meetings, contributing to the promotion of mycology andthe sharing of knowledge.
▼

As a fungi observatory meeting

About SNS: Other than the website, the Mycological Society of Japan
provides information on SNS. We have accounts on Twitter (@Mycology▼ At an academic meeting

Japan) and Facebook (the Mycological Society of Japan), and provide aplatform for not only the members but also the many people interested inmycology to communicate and interact. These resources can be used toeasily obtain the latest information on fungi as well as our activities.
Moreover, our SNS account functions as an information hub that introduces
the content of fungal research, the activity of mushroom-meetings, andinformation about books focusing on mushrooms and fungi.

u
Do yo ?
wokn

100 selections of Japanese fungi

In 2009, we established “100 selections of Japanese fungi” by selecting 100 species of fungithat are closely linked to the lives of Japanese people based on various aspects, including basics
and application, nature, and culture. Shiitake (a mushroom whose industrial production was firstsuccessful in Japan) and koji mold (essential for the production of sake, soy sauce, and miso) are
all important fungi that support the lives of Japanese people or are closely linked to the natureand culture of Japan. How many of them do you know? To know, please access the following
link: http://www.mycologyjp. org/˜msj7/WL̲information̲J/100.html

Invitation Guide
Anyone who is interested in fungi and pseudomycetes such as
mushroom, fungi, yeast,or myxomycets are welcome to join. If you wish
to become a member, please read the society regulations, download
the application form, fill in the necessary information, and submit theform to the executive office. (E-mail attachments, fax, or mail)Membership: 11,000 yen
Student Membership: 5,500 yen (50% of Member)
Lifelong Membership: 110,000 yen(10 times of the annual cost of member)
Supporting Membership: 50,000 yen per share (more than one share)

If you become a member: You will receive academic journals (six English
journals, two Japanese journals, and four newsletters per year) as well as otherfree or non-free publications. You may attend meetings, fungi observatory
meetings, and other events such as gatherings. You may present at meetings.

Publication: Mycological Society of Japan
Text and Pictures provided by・Jyunichi Peter Abe・Shigeki Inaba・Takamichi Orihara・Hisayasu
Kobayashi・Ami Shigemori・Kozue Saotome・Yuichi Taneyama・Eiji Tanaka・Yousuke
Degawa・Kentaro Hosaka・Takeshi Hosoya・Tamotsu Hoshino・Akiyoshi Yamada
As long as it is properly referred that the content of the text is edited by the Mycological Society of Japan, it
is allowed to copy this information material and to redistribute. However, the content of this text must not
be modiﬁed or used for commercial purposes.

Please contact the Mycological Society of Japan
c/o National Institute of Advanced Industrial Scienceand Technology, Chugoku,
3-11-32, Kagamiyama, Higashi-Hiroshima 739-0046 Japansecretary-general@mycology-jp.org