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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 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

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 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
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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Making Spores
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• In fungal spore formation the wall building 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
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 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 the

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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.