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4.1.3 The untrue fungi

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Chytridomycota
• Members of the phylum Chytridiomycota, often referred
to as chytrid fungi or chytrids, are morphologically
simple organisms with a global distribution and
approximately 700 described species that can be found
from the tropics to the arctic regions.
• Chytrids occur in aquatic environments such as streams,
ponds, estuaries and marine systems, living as parasites of
algae and planktonic organisms.
• Many chytrids, perhaps the majority, occur in terrestrial
forest, agricultural and desert soils, and in acidic bogs as
saprotrophs on difficult-to-digest substrata like pollen
grains, chitin, keratin and cellulose. Some soil chytrids are
obligate parasites of vascular plants..
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Chytridimycota
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Oomycota & Hyphochytriomycota

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What is Zoospores?
• an independently motile spore especially : a
motile usually naked and flagellated asexual
spore especially of an alga or lower fungus
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Oomycota
• Oomycota, phylum of funguslike organisms in the kingdom Chromista. Oomycetes
may occur as saprotrophs (living on decayed matter) or as parasites living on
higher plants and can be aquatic, amphibious, or terrestrial.
• The species Phytophthora infestans famously destroyed Ireland’s potato crop
with late blight and caused the Great Famine of 1845, which resulted in a mass
migration of Irish people to the United States. Other economically destructive genera
include the water molds (notably Saprolegnia), Aphanomyces (the cause of
root rot of peas), Plasmopara (a cause of downy mildews), and Albugo (white rusts).
• Unlike true fungi, members of the phylum Oomycota lack chitin in their cell walls
and have a life cycle that is dominantly diploid (having two sets of chromosomes).
• The organisms are distinguished by their production of asexual reproductive cells,
called zoospores.
• Zoospores move through the use of one or two whiplike swimming structures known
as flagella, and individuals may germinate from these spores.
• Mature organisms may also reproduce sexually, with the resulting fertilized eggs
being converted into nonmobile spores, or oospores, which then also germinate into
mature individuals.
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Heterothallic
• having male and female reproductive organs on
different thalli.
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Hypochytrimycota
• Hyphochytriomycota, phylum of mostly
aquatic funguslike organisms in the kingdom
Chromista.
• The taxonomy of the group is contentious but is
generally thought to contain about 20 species.
• The phylum is distinguished by the asexual
production of motile cells (zoospores) with a
single, anterior, feathery, whiplike flagellum.
• Sexual reproduction has not been found among
these organisms.
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4.2 Mycellium the hyphal mode

of growth
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4.3 Fungal cell and tissue

differentiation: Mycelial
differentiation, Making spores
• Rhythmic, or cyclical, growth of colonies on solid
medium is an excellent example of this interaction
between the environment and the genetic capability
of the mycelium.
• Regular concentric banding of colonies grown in
vitro is seen quite often in many different fungi.
• It results from regular changes in hyphal extension
rate and branch formation as hyphae react to local
conditions as part of an endogenous or externally-
regulated circadian clock (a roughly 24-hour
cycle).
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• hese circadian rhythms are generated

endogenously; under constant environmental
conditions they are self-sustaining, and their period
is determined genetically.
• However, they can be modulated by changes in
external cues such as light, temperature and
nutrients.
• Temporal rhythms are ubiquitous in eukaryotes and
common regulatory patterns in circadian systems
extend from fungi through to mammals.
• The formal study of biological rhythms (that may be
daily, weekly, seasonal, annual or with an even
longer period) is called chronobiology and covers an
enormous range of animal (including human) and
plant physiology.
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• But cyclical changes are clearly evident in fungi and their

causes are frequently more accessible than they are in other
eukaryotes.
• Circadian rhythms are biological rhythms with periods of
about 24 hours.
• Circadian clocks are molecular circuits that allow organisms
to coordinate many processes, including gene expression, with
a rhythm that is close to the daily 24-hour cycle.
• Rhythmic processes described in fungi include growth rate,
stress responses, developmental capacity, and sporulation, as
well as many metabolic processes
• Generally, fungi use clocks to anticipate daily environmental
changes. Rhythmicity is endogenous and self-sustaining when
environmental conditions are constant; the length of the
rhythmic cycle being genetically determined.
• Rhythmically changing environmental signals, particularly of
light and temperature, set the phase of the endogenous
rhythm and adjust it to exactly 24 hours.
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• Circadian clocks are self-sustaining timekeepers

found in almost all organisms on earth.
• They have arisen at least three times through
evolution, in prokaryotic cyanobacteria, in cells
that evolved into higher plants, and in the
opisthokont clade, the group of organisms that
eventually became the fungi and the animals .
• They do not require complex tissue
organisation, and even single cells can express
rhythmicity.
• A negative feedback loop comprises the core of
the circadian system in fungi and animals,
centred on the transcription of clock genes and
translation of clock proteins.
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• The positive element in the loop is

the transcriptional activation of one or more clock
gene(s) through binding of paired transcriptional
activators on the clock gene promoter; they are paired
by interaction through PAS domains .
• Translation of the transcribed message of the clock gene
(which is subject to additional regulation) generates
a clock protein that is the negative element of the
feedback loop.
• This blocks activation of the clock gene so the amount
of clock gene mRNA declines and eventually the levels of
clock protein also decline.
• These processes generate a daily cycle of clock gene
mRNA and clock proteins and forms an oscillator that
creates what is known as an ‘output’ that is the basis of
the timing signal that controls rhythmical cellular
functions (which might be organism-, organ- or even
cell-specific)
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• A circadian system can be made up of one or

more interconnected feedback loops forming
quite a complex network.
• In addition, the system receives inputs of
ambient light and temperature to adjust its
phase so that the internal day matches the
external day, and then uses the time information
it generates to regulate the life of the cell and of
the whole organism.
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• Many clock gene proteins have a common structural motif

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known as the PAS domain.

• The name PAS is an acronym created from ‘PER-ARNT-Sim’
and PAS domains were first identified in
the Drosophila proteins PER and ARNT and they were later
found in a wide range of organisms.
• PAS domains are involved in many signalling proteins where
they are used as a signal sensor domain.
• In circadian rhythmicity the PAS-domain proteins act as
heterodimeric transcriptional activation complexes to drive
expression of clock genes.
• Interestingly, though, PAS domains mediate protein-protein
interactions in response to stimuli when cofactors bind within
their hydrophobic cores, so they have important roles as
sensory modules for a wide range of environmental conditions
including oxygen tension, redox potential, carbon monoxide
and nitric oxide, as well as light intensity and temperature; all
of which are the main inputs to the Neurospora circadian
oscillators.
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• The circadian clock of Neurospora, still the best studied fungal
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model, involves proteins (which are transcription factors) of mutant
genes called white collar-1 (the protein is called WC-1), white
collar-2 (WC-2), and frequency (gene symbol frq) (Koritala & Lee,
2017).
• FRQ (the protein encoded by the frq gene) is the core clock
component and complexes with other proteins, physically
interacting with the WC transcription factors reducing their activity;
the kinetics being strongly influenced by progressive
phosphorylation of FRQ.
• When FRQ becomes sufficiently phosphorylated that it loses the
ability to influence WC activities, the circadian cycle starts again.
Environmental cycles of light and temperature influence frq and
FRQ expression and thereby reset the internal circadian clocks.
• Light acts in Neurospora to induce transcription of the negative
elements that reset the clock and synchronise the cell to the daily
light/dark cycle.
• Temperature-influenced translational regulation of FRQ synthesis
in Neurospora sets the physiological temperature limits over which
the clock operates.
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• The circadian system of Neurospora is an

important model system used to understand
circadian rhythms in other organisms.
• There is evidence for conservation of rhythmicity
mechanisms in filamentous fungi in general;
when tested for homology
with Neurospora FRQ, WC-1 and WC-2
sequences, scores for similarity were high in
genomes of Basidiomycota, and zygomycetes as
well as other Ascomycota
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• The Neurospora circadian system contains at least three

oscillators:
• the FRQ/WC-dependent circadian oscillator, the core
components of which are FRQ, WC-1, WC-2, and two other
proteins, FRH and FWD-1;
• the WC-dependent circadian oscillator;
• and one or more FRQ/WC-independent oscillators.
• A survey of 64 fungal proteomes for homologues
of Neurospora clock proteins found that the FRH and FWD-1
proteins were probably present in the last common ancestor
of all the fungi surveyed.
• Homologues of WC-1 and WC-2 were absent from chytrids
and Microsporidia but were present in all other major clades.
• In contrast, FRQ homologues were restricted taxonomically
within the Ascomycota to Sordariomycetes, Leotiomycetes
and Dothideomycetes.
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• Our interpretation of these findings is that the

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components of the Neurospora circadian clock are

widely conserved in fungal evolution, but the way
they are assembled into a working oscillator
in Neurospora is only one of several possibilities.
• The regulators that make up the clocks are involved
in other cellular control events; for example, one of
the FRQ homologues in the fungus.
• Botrytis cinerea regulates virulence when the
fungus is infecting its plant host Arabidopsis
thaliana.
• So, the development and evolution of a clock circuit
will depend on the balance between the different
selection pressures exerted on the different
functions of its component parts.
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A clock-mutant of Podospora anserin

• A clock-mutant of Podospora anserin a clock-
mutant of Podospora anserina which forms
concentric bands of aerial growth within the colony
grown on agar media.
• The banding arises from a difference in growth
pattern of aerial and submerged hyphae.
• Enhanced growth and increased branching of
hyphae on the agar surface eventually cause growth
of aerial hyphae to stop, perhaps because of the
accumulation of excretory products (known as
‘staling substances’), so further extension on the
surface is limited by this ‘induction event’.
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• On the other hand, submerged hyphae do not show

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this pattern of increased branching; they escape the

restriction to growth and continue to extend and
reach the surface some distance beyond the stopped
surface mycelial front .
• Emergence of the submerged hyphae prevents
further growth of the old surface mycelium but
produces a new generation of surface hyphal tips
which go through the same process of branching,
staling and growth limitation.
• Repetition of the cycle gives rise to zones of
alternately dense and sparse surface mycelium
which are visible as a regular series of bands on the
surface.
• Reduced extension rates and increased branching in
this mycelium of Podospora anserina are
accompanied by increased oxygen uptake and
exposure to light.
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• This example makes it clear that rhythmic growth is

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a differentiation process which separates hyphae with

different functions and properties in space and time.
• In this case, extending hyphae, exploring for new
substrates, are separated spatially from stationary
surface hyphae, which may differentiate into sporing
and/or resting structures after their extension growth is
stopped.
• Concentric rings and radial zonations of the mycelium
are common expressions of mycelial growth rhythms.
• Evidently, an induction event must be detected and this
suggests that membrane sensors play an important role
in these sorts of reactions.
• The evidence indicates that many different sensory
modules reacting to a wide range of environmental
conditions (gases, redox, light, temperature) can input
signals to a common oscillator that generates the
rhythmic output (see the Rhythms, oscillators and clock
genes .
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• The homogeneous growth and branching pattern of the

vegetative hyphae is disturbed by the inducing event and
differentiation of the mycelium results.
• This may be an intra hyphal differentiation, as in spore
differentiation, or a concerted co-differentiation of
several or many hyphae to produce the equivalent of a
differentiated tissue, as in the concentric rings and zonations
we have just been discussing.
• Even in more complex fungal structures, like fruiting bodies,
similar mechanisms may exist to change the hyphal growth
and branching patterns to form functionally-distinct fungal
tissues.
• Certainly, experiments based on transferring such tissues to
artificial environments in vitro indicate that hyphal cells
differentiate in response to signals they receive from their
immediate environment within the ‘home’ tissue and that
maintenance of their state of differentiation requires
continual reinforcement from those signals .
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• In fungal spore formation the wall building

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mechanisms that are normally strictly apical are

highly adapted.
• Clearly, wall synthesis at the hyphal apex is far
being the complete story.
• Further synthesis of new wall as well as
modification of existing wall is a frequent
occurrence.
• When and where it occurs is under exquisite control.
There are so many instances in which fungal wall
synthesis is positionally and temporally regulated to
produce regular change in morphology that the
activities located at the apex of the vegetative hypha.
• There are several ways of creating spores and
several ways of organising the walls of spores and, as
you might imagine, several terms have been coined
to describe these.
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• The term ‘wall building’ has been coined to describe the

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process and three types:

• apical, in which the ultrastructural secretory vesicles
responsible for producing cell wall material are
concentrated at the hyphal tip and form a cylindrical
hypha by distal growth, in which the youngest wall
material is at the extreme apex (Fig. 3A);
• diffuse wall building, in which the synthetic secretory
vesicles are distributed all over the apical region at a low
concentration, resulting in swelling of the cylindrical
hypha through alteration of the pre-existing wall (Fig.
3B);
• ring wall building, in which wall synthesis is
concentrated in a ring below the tip and produces new
wall by proximal growth, so a cylindrical hypha is
formed in which the youngest wall material is always at
the base (Fig. 3C).
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• And that accounts for both the enormous biodiversity in

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asexual sporulation throughout the fungi, and the central

role in classical taxonomy played by those spores and
spore-bearing structures.
• Conidiophores are usually morphologically distinct
from the vegetative hyphae on which they arise.
• They may be branched or unbranched and often have
inflated apices supporting groups of conidiogenous cells.
• Conidiogenous cells differ in the way they produce
conidia, which may be formed singly, in clusters, or
in succession.
• When conidia are produced in succession, the chains
that are formed may have the oldest conidium located at
the apex of the chain, being pushed upward as younger
ones form at the base, or conversely the chain may be
formed by successive production of the youngest
conidium at the apex.
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• Mature conidia may be smooth or bear

ornate sculpturing, and their surface layers
may be modified to make them hypdrophobic or
hydrophilic.
• Conidia are often round or ellipsoid but may be
curved, coiled, or of more elaborate shape.
• Conidia are usually single cells, but may be made
up of two to several cells.
• Some are colourless, but many form pigmented
walls, accumulations appearing white, blue,
green, yellow, brown, or black.
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• Some fungi produce spores by transforming an

intercalary cell (that’s a cell ‘in amongst others’ or
within the body of a hypha) into a chlamydospore by
rounding up of the cells and deposition of wall
thickening (= diffuse wall building and secondary
wall formation).
• Chlamydospores are released when the parent
hypha disintegrates.
• This is one of two basic sorts of conidiogenesis,
called thallic development (the other is
called blastic).
• In thallic conidiogenesis (Fig 4A) the spore initial
differentiates after it has been delimited by
completion of one or more septa, and the spore is
differentiated from a whole cell..
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• The spore initials are delimited by septa formed after

apical growth of the fertile hypha has ceased.
• Chlamydospores are enlarged and enlargement occurs
only after the septa are formed.
• Spores that undergo this type of development but
without enlargement are often given special names such
as oidia, found on haploid monokaryotic mycelia of
many of the smaller mushrooms, like Coprinopsis, or
arthrospores, which are formed by fragmentation of
hyphal branches of members of the Ascomycota
like Geotrichum, but they are all thallic conidia.
• However, they may be distinguished
as holothallic or enterothallic on the basis that the
former type uses the original wall of the parent
conidiogenous cell, while in enterothallic conidiogenesis
the conidial wall is newly formed and does not use the
original wall of the conidiogenous cell (Fig. 4A).
Enterothallic conidia are relatively uncommon.
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•.
• Blastic development is characterised by
differentiation of a spore initial from part of a cell
rather than the whole cell, and occurs before it is
separated off by a septum (Fig. 4B).
• These spores are called blastic conidia, and, again,
may be distinguished as holoblastic (using the
original wall) or enteroblastic (using only newly-
formed wall).
• Blastic conidia may be produced from a
specialised (conidiogenous) cell that is sometimes
another conidium (that is, they may form in chains).
• One to several conidiogenous cells may be produced
from and supported by a conidiophore, a specialised
hypha or hyphal branch.
• When mature, conidia separate readily from the
conidiogenous cell, so the spore is described as
deciduous
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• Thallic conidial development is remarkably similar to

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division of fission yeast, Schizosaccharomyces pombe, in

which septation involves chitin deposition in a ring
defined by a pre-formed ring of actin microfilaments
(Fig. 5).
• Blastic development has similarities to budding
in Saccharomyces cerevisiae, because the conidial initial
emerges from a specific localised region of the
conidiogenous cell and may enlarge considerably before
being cut off by a septum.
• Ring wall building creates the emergent conidial initial,
and then diffuse wall building within the initial causes it
to balloon from the parent cell.
• As the conidial initial increases in size a nucleus
migrates from the parent cell into the young conidium,
which is finally separated from the parent cell by
centripetal growth of a septum.
• The septum sometimes includes a special abscission
layer that enables conidial release.
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• Enteroblastic conidia are very commonly

encountered.
• Conidiogenous cells differ morphologically and
contribute to the morphological biodiversity of
fungi.
• In some fungi conidiogenous cells are not
specialised for the production of large numbers
of conidia and are very similar to vegetative
hyphae.
• Other common conidiogenous cells are
specialised, non-elongating bottle-shaped cells
with a narrow neck from which the conidia
develop; these are called phialides (Fig. 6).
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• The first conidium on a phialide may form by either

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the holoblastic or enteroblastic method.

• If formed enteroblastically, it ruptures the phialide
wall as it emerges, and the ruptured wall may persist
as a minute collar at the base of the conidial chain.
• Either way, development of subsequent conidia is
enteroblastic, each one originating as the innermost
layer(s) of the phialide wall are extruded through
the ‘mouth’ of the phialide.
• Although they originate on the inner side of the
phialide wall, these layers eventually become the
outermost layers of the conidial wall.
• The septum is formed within the phialide to
separate the exogenous maturing conidium from the
next (endogenous) conidium initial.
• The spores of Aspergillus are the most frequently-
observed conidia that are formed in this way.