1.

FUNGI KINGDOM

A fungus (plural: fungi) is any member of the group of eukaryotic organisms that includes
microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These
organisms are classified as a kingdom, fungi, which is separate from the other eukaryotic life
kingdoms of plants and animals.

A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists
is chitin in their cell walls. Similar to animals, fungi are heterotrophs; they acquire their food by
absorbing dissolved molecules, typically by secreting digestive enzymes into their environment.
Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of
which are flagellated), which may travel through the air or water. Fungi are the principal
decomposers in ecological systems. These and other differences place fungi in a single group of
related organisms, named the Eumycota (true fungi or Eumycetes), which share a common
ancestor . This fungal group is distinct from the structurally similar myxomycetes (slime molds)
and oomycetes (water molds). The discipline of biology devoted to the study of fungi is known
as mycology. In the past, mycology was regarded as a branch of botany, although it is now
known fungi are genetically more closely related to animals than to plants.

Abundant worldwide, most fungi are inconspicuous because of the small size of their structures,
and their cryptic lifestyles in soil or on dead matter. Fungi include symbionts of plants, animals,
or other fungi and also parasites. They may become noticeable when fruiting, either as
mushrooms or as molds. Fungi perform an essential role in the decomposition of organic matter
and have fundamental roles in nutrient cycling and exchange in the environment. They have long
been used as a direct source of human food, in the form of mushrooms and truffles; as a
leavening agent for bread; and in the fermentation of various food products, such as wine, beer,
and soy sauce. Since the 1940s, fungi have been used for the production of antibiotics, and, more
recently, various enzymes produced by fungi are used industrially and in detergents. Fungi are
also used as biological pesticides to control weeds, plant diseases and insect pests. Many species
produce bioactive compounds called mycotoxins, such as alkaloids and polyketides that are toxic
to animals including humans. The fruiting structures of a few species contain psychotropic
compounds and are consumed recreationally or in traditional spiritual ceremonies. Fungi can
break down manufactured materials and buildings, and become significant pathogens of humans
and other animals. Losses of crops due to fungal diseases (e.g., rice blast disease) or food
spoilage can have a large impact on human food supplies and local economies.
Advances in molecular genetics have opened the way for DNA analysis to be incorporated into
taxonomy, which has sometimes challenged the historical groupings based on morphology and
other traits. Phylogenetic studies published in the last decade have helped reshape the
classification within Kingdom Fungi, which is divided into one subkingdom, seven phyla, and
ten subphyla.
Characteristics

Fungal hyphae cells

1. Hyphal wall
2. Septum
3. Mitochondrion
4. Vacuole
5. Ergosterol crystal
6. Ribosome
7. Nucleus
8. Endoplasmic reticulum
9. Lipid body
10. Plasma membrane
11. Golgi apparatus

Before the introduction of molecular methods for phylogenetic analysis, taxonomists considered
fungi to be members of the plant kingdom because of similarities in lifestyle: both fungi and
plants are mainly immobile, and have similarities in general morphology and growth habitat.
Like plants, fungi often grow in soil and, in the case of mushrooms, form conspicuous fruit
bodies, which sometimes resemble plants such as mosses. The fungi are now considered a
separate kingdom, distinct from both plants and animals, from which they appear to have
diverged around one billion years ago. Some morphological, biochemical, and genetic features
are shared with other organisms, while others are unique to the fungi, clearly separating them
from the other kingdoms:

Shared features:
 With other eukaryotes: Fungal cells contain membrane-bound nuclei with chromosomes
that contain DNA with noncoding regions called introns and coding regions called exons.
Fungi have membrane-bound cytoplasmic organelles such as mitochondria, sterol-
 containing membranes, and ribosomes of the 80S type. They have a characteristic range
of soluble carbohydrates and storage compounds, including sugar alcohols e.g., mannitol,
disaccharides, e.g., trehalose, and polysaccharides e.g., glycogen, which is also found in
animals.
 With animals: Fungi lack chloroplasts and are heterotrophic organisms and so require
preformed organic compounds as energy sources.
 With plants: Fungi have a cell wall and vacuoles. They reproduce by both sexual and
asexual means, and like basal plant groups such as ferns and mosses produce spores.
Similar to mosses and algae, fungi typically have haploid nuclei.
 With euglenoids and bacteria: Higher fungi, euglenoids, and some bacteria produce the
amino acid L-lysine in specific biosynthesis steps, called the α-aminoadipate pathway.
 The cells of most fungi grow as tubular, elongated, and thread-like (filamentous)
structures called hyphae, which may contain multiple nuclei and extend by growing at
their tips. There are also single-celled fungi (yeasts) that do not form hyphae, and some
fungi have both hyphal and yeast forms.
 In common with some plant and animal species, more than 70 fungal species display
bioluminescence.

Unique features:
 Some species grow as unicellular yeasts that reproduce by budding or fission. Dimorphic
fungi can switch between a yeast phase and a hyphal phase in response to environmental
conditions.
 The fungal cell wall is composed of glucans and chitin; while glucans are also found in
plants and chitin in the exoskeleton of arthropods, fungi are the only organisms that
combine these two structural molecules in their cell wall. Unlike those of plants and
oomycetes, fungal cell walls do not contain cellulose.

Omphalotus nidiformis, a bioluminescent mushroom

Most fungi lack an efficient system for the long-distance transport of water and nutrients, such as
the xylem and phloem in many plants. To overcome this limitation, some fungi, such as
Armillaria, form rhizomorphs, which resemble and perform functions similar to the roots of
plants. Fungi produce several secondary metabolites that are similar or identical in structure to
those made by plants.
Diversity
Fungi have a worldwide distribution, and grow in a wide range of habitats, including extreme
environments such as deserts or areas with high salt concentrations, or ionizing radiation, as well
as in deep sea sediments. Some can survive the intense UV and cosmic radiation encountered
during space travel. Most grow in terrestrial environments, though several species live partly or
solely in aquatic habitats, such as the chytrid fungus Batrachochytrium dendrobatidis, a parasite
that has been responsible for a worldwide decline in amphibian populations. Other examples of
aquatic fungi include those living in hydrothermal areas of the ocean.

Morphology

Microscopic structures

An environmental isolate of Penicillium sp.

1. hypha
2. conidiophore
3. phialide
4. conidia
5. septa

Most fungi grow as hyphae, which are cylindrical, thread-like structures 2–10 µm in diameter
and up to several centimeters in length. Hyphae grow at their tips (apices); new hyphae are
typically formed by emergence of new tips along existing hyphae by a process called branching,
or occasionally growing hyphal tips fork, giving rise to two parallel-growing hyphae. Hyphae
also sometimes fuse when they come into contact, a process called hyphal fusion (or
anastomosis). These growth processes lead to the development of a mycelium, an interconnected
network of hyphae. Many species have developed specialized hyphal structures for nutrient
uptake from living hosts; examples include haustoria in plant-parasitic species of most fungal
phyla, and arbuscules of several mycorrhizal fungi, which penetrate into the host cells to
consume nutrients.

Macroscopic structures

Armillaria solidipes
Fungal mycelia can become visible to the naked eye, for example, on various surfaces and
substrates, such as damp walls and spoiled food, where they are commonly called molds.
Mycelia grown on solid agar media in laboratory petri dishes are usually referred to as colonies.
The fungi are traditionally considered heterotrophs, organisms that rely solely on carbon fixed by
other organisms for metabolism. Fungi have evolved a high degree of metabolic versatility that
allows them to use a diverse range of organic substrates for growth, including simple compounds
such as nitrate, ammonia, acetate, or ethanol.
Reproduction
Fungal reproduction is complex, reflecting the differences in lifestyles and genetic makeup
within this diverse kingdom of organisms. Environmental conditions trigger genetically
determined developmental states that lead to the creation of specialized structures for sexual or
asexual reproduction. These structures aid reproduction by efficiently dispersing spores or spore-
containing propagules.
Asexual reproduction
Asexual reproduction occurs via vegetative spores (conidia) or through mycelial fragmentation.
Mycelial fragmentation occurs when a fungal mycelium separates into pieces, and each
component grows into a separate mycelium. Mycelial fragmentation and vegetative spores
maintain clonal populations adapted to a specific niche, and allow more rapid dispersal than
sexual reproduction.

Sexual reproduction
Sexual reproduction with meiosis has been directly observed in all fungal phyla except
Glomeromycota (genetic analysis suggests meiosis in Glomeromycota as well). It differs in
many aspects from sexual reproduction in animals or plants. In sexually reproducing fungi,
compatible individuals may combine by fusing their hyphae together into an interconnected
network; this process, anastomosis, is required for the initiation of the sexual cycle. Many
ascomycetes and basidiomycetes go through a dikaryotic stage, in which the nuclei inherited
from the two parents do not combine immediately after cell fusion, but remain separate in the
hyphal cells.

Sexual reproduction in basidiomycetes is similar to that of the ascomycetes. Compatible haploid

hyphae fuse to produce a dikaryotic mycelium. However, the dikaryotic phase is more extensive
in the basidiomycetes, often also present in the vegetatively growing mycelium. A specialized
anatomical structure, called a clamp connection, is formed at each hyphal septum. A basidiocarp
is formed in which club-like structures known as basidia generate haploid basidiospores after
karyogamy and meiosis. The most commonly known basidiocarps are mushrooms.

Main groups of fungi

Currently, seven phyla are proposed: Microsporidia, Chytridiomycota, Blastocladiomycota,
Neocallimastigomycota, Glomeromycota, Ascomycota, and Basidiomycota.

Phylogenetic analysis has demonstrated that the Microsporidia, unicellular parasites of animals
and protists, are fairly recent and highly derived endobiotic fungi (living within the tissue of
another species). One 2006 study concludes that the Microsporidia are a sister group to the true
fungi; that is, they are each other's closest evolutionary relative.

The Chytridiomycota are commonly known as chytrids. These fungi are distributed worldwide.
Chytrids and their close relatives Neocallimastigomycota and Blastocladiomycota (below) are
the only fungi with active motility, producing zoospores that are capable of active movement
through aqueous phases with a single flagellum, leading early taxonomists to classify them as
protists. Molecular phylogenies, inferred from rRNA sequences in ribosomes, suggest that the
Chytrids are a basal group divergent from the other fungal phyla.

Blastocladiomycota were previously considered a taxonomic clade within the Chytridiomycota.

Recent molecular data and ultrastructural characteristics, however, place the Blastocladiomycota
as a sister clade to the Zygomycota, Glomeromycota, and Dikarya (Ascomycota and
Basidiomycota). The blastocladiomycetes are saprotrophs, feeding on decomposing organic
matter, and they are parasites of all eukaryotic groups. Unlike their close relatives, the chytrids,
most of which exhibit zygotic meiosis, the blastocladiomycetes undergo sporic meiosis.

The Neocallimastigomycota: Members of this small phylum are anaerobic organisms, living in
the digestive system of larger herbivorous mammals and in other terrestrial and aquatic
environments enriched in cellulose (e.g., domestic waste landfill sites). They lack mitochondria
but contain hydrogenosomes of mitochondrial origin. As in the related chrytrids,
neocallimastigomycetes form zoospores that are posteriorly uniflagellate or polyflagellate.

Members of the Glomeromycota form arbuscular mycorrhizae, a form of mutualist symbiosis

wherein fungal hyphae invade plant root cells and both species benefit from the resulting
increased supply of nutrients. All known Glomeromycota species reproduce asexually. The
symbiotic association between the Glomeromycota and plants is ancient, with evidence dating to
400 million years ago. Formerly part of the Zygomycota (commonly known as 'sugar' and 'pin'
molds), the Glomeromycota were elevated to phylum status in 2001 and now replace the older
phylum Zygomycota. Fungi that were placed in the Zygomycota are now being reassigned to the
Glomeromycota. Medically relevant genera include Mucor, Rhizomucor, and Rhizopus.

The Ascomycota, commonly known as sac fungi or ascomycetes, constitute the largest
taxonomic group within the Eumycota. These fungi form meiotic spores called ascospores,
which are enclosed in a special sac-like structure called an ascus. This phylum includes morels, a
few mushrooms and truffles, unicellular yeasts (e.g., of the genera Saccharomyces,
Kluyveromyces, Pichia, and Candida), and many filamentous fungi living as saprotrophs,
parasites, and mutualistic symbionts (e.g. lichens). Prominent and important genera of
filamentous ascomycetes include Aspergillus, Penicillium, Fusarium, and Claviceps. Many
ascomycete species have only been observed undergoing asexual reproduction (called
anamorphic species), but analysis of molecular data has often been able to identify their closest
teleomorphs in the Ascomycota.

Members of the Basidiomycota, commonly known as the club fungi or basidiomycetes, produce
meiospores called basidiospores on club-like stalks called basidia. Most common mushrooms
belong to this group, as well as rust and smut fungi, which are major pathogens of grains. Other
important basidiomycetes include the maize pathogen Ustilago maydis, human commensal
species of the genus Malassezia and the opportunistic human pathogen, Cryptococcus
neoformans.

Although often inconspicuous, fungi occur in every environment on Earth and play very
important roles in most ecosystems. Along with bacteria, fungi are the major decomposers in
most terrestrial (and some aquatic) ecosystems, and therefore play a critical role in
biogeochemical cycles and in many food webs. As decomposers, they play an essential role in
nutrient cycling, especially as saprotrophs and symbionts, degrading organic matter to inorganic
molecules, which can then re-enter anabolic metabolic pathways in plants or other organisms.

Symbiotic Features of Fungi

Many fungi have important symbiotic relationships with organisms from most if not all
kingdoms. These interactions can be mutualistic or antagonistic in nature, or in the case of
commensal fungi are of no apparent benefit or detriment to the host.

With plants
Mycorrhizal symbiosis between plants and fungi is one of the most well-known plant–fungus
associations and is of significant importance for plant growth and persistence in many
ecosystems; over 90% of all plant species engage in mycorrhizal relationships with fungi and are
dependent upon this relationship for survival. The mycorrhizal symbiosis is ancient, dating to at
least 400 million years ago.It often increases the plant's uptake of inorganic compounds, such as
nitrate and phosphate from soils having low concentrations of these key plant nutrients. Some
fungal species inhabit the tissues inside roots, stems, and leaves, in which case they are called
endophytes. Similar to mycorrhiza, endophytic colonization by fungi may benefit both
symbionts; for example, endophytes of grasses impart to their host increased resistance to
herbivores and other environmental stresses and receive food and shelter from the plant in return.

With algae and cyanobacteria

Lichens are a symbiotic relationship between fungi and photosynthetic algae or cyanobacteria.
The photosynthetic partner in the relationship is referred to in lichen terminology as a
"photobiont". The fungal part of the relationship is composed mostly of various species of
ascomycetes and a few basidiomycetes. Lichens occur in every ecosystem on all continents, play
a key role in soil formation and the initiation of biological succession, and are prominent in some
extreme environments, including polar, alpine, and semiarid desert regions. They are able to
grow on inhospitable surfaces, including bare soil, rocks, tree bark, wood, shells, barnacles and
leaves. As in mycorrhizas, the photobiont provides sugars and other carbohydrates via
photosynthesis to the fungus, while the fungus provides minerals and water to the photobiont.
The functions of both symbiotic organisms are so closely intertwined that they function almost as
a single organism; in most cases the resulting organism differs greatly from the individual
components. Lichenization is a common mode of nutrition for fungi; around 20% of fungi—
between 17,500 and 20,000 described species—are lichenized.

With insects
Many insects also engage in mutualistic relationships with fungi. Several groups of ants cultivate
fungi in the order Agaricales as their primary food source, while ambrosia beetles cultivate
various species of fungi in the bark of trees that they infest. Likewise, females of several wood
wasp species (genus Sirex) inject their eggs together with spores of the wood-rotting fungus
Amylostereum areolatum into the sapwood of pine trees; the growth of the fungus provides ideal
nutritional conditions for the development of the wasp larvae. At least one species of stingless
bee has a relationship with a fungus in the genus Monascus, where the larvae consume and
depend on fungus transferred from old to new nests. Termites on the African savannah are also
known to cultivate fungi, and yeasts of the genera Candida and Lachancea inhabit the gut of a
wide range of insects, including neuropterans, beetles, and cockroaches.

Fungi as pathogens and parasites

Many fungi are parasites on plants, animals (including humans), and other fungi. Serious
pathogens of many cultivated plants causing extensive damage and losses to agriculture and
forestry include the rice blast fungus Magnaporthe oryzae, tree pathogens such as Ophiostoma
ulmi and Ophiostoma novo-ulmi causing Dutch elm disease and Cryphonectria parasitica
responsible for chestnut blight, and plant pathogens in the genera Fusarium, Ustilago,
Alternaria, and Cochliobolus. Some carnivorous fungi, like Paecilomyces lilacinus, are predators
of nematodes, which they capture using an array of specialized structures such as constricting
rings or adhesive nets. Many fungi that are plant pathogens, such as Magnaporthe oryzae, can
switch from being biotrophic (parasitic on living plants) to being necrotrophic (feeding on the
dead tissues of plants they have killed). This same principle is applied to fungi-feeding parasites,
including Asterotremella albida, which feeds on the fruit bodies of other fungi both while they
are living and after they are dead.

Some fungi can cause serious diseases in humans, several of which may be fatal if untreated.
These include aspergillosis, candidiasis, coccidioidomycosis, cryptococcosis, histoplasmosis,
mycetomas, and paracoccidioidomycosis. Furthermore, persons with immuno-deficiencies are
particularly susceptible to disease by genera such as Aspergillus, Candida, Cryptoccocus. Other
fungi can attack eyes, nails, hair, and especially skin, the so-called dermatophytic and
keratinophilic fungi, and cause local infections such as ringworm and athlete's foot. Fungal
spores are also a cause of allergies, and fungi from different taxonomic groups can evoke allergic
reactions.

Human uses of Fungi

The human use of fungi for food preparation or preservation and other purposes is extensive and
has a long history. Mushroom farming and mushroom gathering are large industries in many
countries. The study of the historical uses and sociological impact of fungi is known as
ethnomycology. Because of the capacity of this group to produce an enormous range of natural
products with antimicrobial or other biological activities, many species have long been used or
are being developed for industrial production of antibiotics, vitamins, and anti-cancer and
cholesterol-lowering drugs. More recently, methods have been developed for genetic engineering
of fungi, enabling metabolic engineering of fungal species. For example, genetic modification of
yeast species—which are easy to grow at fast rates in large fermentation vessels—has opened up
ways of pharmaceutical production that are potentially more efficient than production by the
original source organisms.

Therapeutic uses
Many species produce metabolites that are major sources of pharmacologically active drugs.
Particularly important are the antibiotics, including the penicillins. Other antibiotics produced by
fungi include: ciclosporin, commonly used as an immunosuppressant during transplant surgery;
and fusidic acid, used to help control infection from methicillin-resistant Staphylococcus aureus
bacteria. Widespread use of antibiotics for the treatment of bacterial diseases, such as
tuberculosis, syphilis, leprosy, and others began in the early 20th century and continues to date.
Other drugs produced by fungi include griseofulvin isolated from Penicillium griseofulvum, used
to treat fungal infections, and statins (HMG-CoA reductase inhibitors), used to inhibit cholesterol
synthesis. Examples of statins found in fungi include mevastatin from Penicillium citrinum and
lovastatin from Aspergillus terreus and the oyster mushroom. Fungi produce compounds that
inhibit viruses and cancer cells. Specific metabolites, such as polysaccharide-K, ergotamine, and
β-lactam antibiotics, are routinely used in clinical medicine. The shiitake mushroom is a source
of lentinan, a clinical drug approved for use in cancer treatments in several countries, including
Japan. In Europe and Japan, polysaccharide-K (brand name Krestin), a chemical derived from
Trametes versicolor, is an approved adjuvant for cancer therapy.

Cultured foods
Baker's yeast or Saccharomyces cerevisiae, a unicellular fungus, is used to make bread and other
wheat-based products, such as pizza dough and dumplings. Yeast species of the genus
Saccharomyces are also used to produce alcoholic beverages through fermentation. Shoyu koji
mold (Aspergillus oryzae) is an essential ingredient in brewing Shoyu (soy sauce) and sake, and
the preparation of miso, while Rhizopus species are used for making tempeh. Several of these
fungi are domesticated species that were bred or selected according to their capacity to ferment
food without producing harmful mycotoxins, which are produced by very closely related
Aspergilli. Quorn, a meat substitute, is made fromFusarium venenatumedible mushrooms
Edible mushrooms include commercially raised and wild-harvested fungi. Agaricus bisporus,
sold as button mushrooms when small or Portobello mushrooms when larger, is the most widely
cultivated species in the West, used in salads, soups, and many other dishes. Many Asian fungi
are commercially grown and have increased in popularity in the West. They are often available
fresh in grocery stores and markets, including straw mushrooms (Volvariella volvacea), oyster
mushrooms (Pleurotus ostreatus), shiitakes (Lentinula edodes), and enokitake (Flammulina
spp.).
Bioremediation
Certain fungi, in particular white-rot fungi, can degrade insecticides, herbicides,
pentachlorophenol, creosote, coal tars, and heavy fuels and turn them into carbon dioxide, water,
and basic elements. Fungi have been shown to biomineralize uranium oxides, suggesting they
may have application in the bioremediation of radioactively polluted sites.