Lebanese University

Faculty of Sciences
Department of Life and Earth Sciences

B1101
Organization of the living organisms

Prepared by
Dr. DOUAIHY Bouchra
Dr. TEMSAH Mirvat

Revised by
Dr. KOBAISSI Ahmad
Dr. SAHYOUN Wafaa

2021-2022
Contents

Old classifications..................................................................................................................... 6
Modern classifications .............................................................................................................. 7

Morphology ............................................................................................................................ 13
Cytoplasm ............................................................................................................................... 14
Cell membrane........................................................................................................................ 15
Capsule ................................................................................................................................... 15
Flagella ................................................................................................................................... 16
Pili and fimbriae ..................................................................................................................... 16
Chemotaxis and Phototaxis .................................................................................................... 17
Metabolic diversity ................................................................................................................. 17
2.8.1 Saprophytes ............................................................................................................................ 18

2.8.2 Symbiotic ................................................................................................................................ 18

2.8.3 Parasitic .................................................................................................................................. 18

Effects of the external factors ................................................................................................. 18

Cell wall.................................................................................................................................. 19
Endospores.............................................................................................................................. 20
Cyanobacteria ......................................................................................................................... 21
Mycoplasma............................................................................................................................ 23

Methanogens........................................................................................................................... 25
Extreme halophiles (Halobacteria) ......................................................................................... 26
Extreme thermophiles or thermoacidophiles ......................................................................... 26
Thermoplasma ........................................................................................................................ 27

Euglenoids: Phylum Euglenophyta ........................................................................................ 31

Diatoms: Phylum of Bacillariophyta ...................................................................................... 31
Golden algae: Phylum of Chrysophyta ................................................................................... 32
Dinoflagellates: Phylum of Dinophyta (Pyrophyta) ............................................................... 32
Green algae: Phylum of Chlorophyta ..................................................................................... 33
Brown algae : Phylum of Pheophyta ...................................................................................... 34
Red Algae: Phylum of Rhodophyta ....................................................................................... 35

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 Useful algae ............................................................................................................................ 36
3.1.1 Edible algae ............................................................................................................................ 36

3.1.2 Animal feeding and agriculture .............................................................................................. 36

3.1.3 Industrial use........................................................................................................................... 36

Harmful algae ......................................................................................................................... 37

The Myxomycetes .................................................................................................................. 37

The Acrasiomycetes ............................................................................................................... 37
The Oomycetes ....................................................................................................................... 39

Chytridiomycetes .................................................................................................................... 43
Zygomycetes........................................................................................................................... 43
Ascomycetes ........................................................................................................................... 44
Basidiomycetes ....................................................................................................................... 47
Deuteromycetes ...................................................................................................................... 48

Lichens.................................................................................................................................... 49
Mycorrhizae ............................................................................................................................ 50

Ecological ............................................................................................................................... 51
Economical ............................................................................................................................. 51
5.2.1 Food and Beverage ................................................................................................................. 51

5.2.2 Pharmaceutical........................................................................................................................ 51

5.2.3 Biocontrol ............................................................................................................................... 51

Pathogens mycetes.................................................................................................................. 51

Adaptations to land colonization ............................................................................................ 53

Plant Kingdom classification .................................................................................................. 54

Class Bryopsida (Mosses) ...................................................................................................... 57

Class of Hepaticopsida (Liverworts) ...................................................................................... 58
2.2.1 Thalloid liverworts (Marchantia polymorpha) ....................................................................... 59

2.2.2 Leafy liverwort ....................................................................................................................... 59

Class Anthoceropsida (Hornworts) ........................................................................................ 60

Organization of the vegetative organs in vascular plants ....................................................... 61

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3.1.1 Roots ....................................................................................................................................... 61

3.1.2 Stems ...................................................................................................................................... 61

3.1.3 Leaves ..................................................................................................................................... 62

Phylum Pteridophyta .............................................................................................................. 62

3.2.1 Class of Psilotopsida (Whisk ferns)........................................................................................ 64

3.2.2 Class of Lycopodiopsida ........................................................................................................ 64

3.2.3 Class Sphenopsida (Equisetum or Horsetail) ......................................................................... 66

3.2.4 Class Filicopsida (Ferns) ........................................................................................................ 68

Phylum of Spermatophytes..................................................................................................... 69
3.3.1 Sub-phylum of Gymnosperms ................................................................................................ 69

3.3.2 Subphylum of Angiosperms ................................................................................................... 73

Photosystems .......................................................................................................................... 79
Clear phase photochemical reactions ..................................................................................... 80
7.2.1 Cyclic phosphorylation ........................................................................................................... 80

7.2.2 Acyclic Phosphorylation......................................................................................................... 81

Dark phase: Calvin cycle ........................................................................................................ 83

The mechanism of C3 plants .................................................................................................. 85

The mechanism of C4 plants .................................................................................................. 85
The mechanism of CAM plants (Crassulacean Acid Metabolism) ........................................ 86

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 Chapter 1 The organization of the living world

1 Taxonomy and systematics

The study of the plant world requires the knowledge of the plants’ classification. Taxonomy or
systematics consists of identifying, nominating and classifying living beings in groups as homogeneous
as possible. The species is the basic systematic unit. It is defined as the set of individuals who are
morphologically similar,can interbreed and give fertile descendants.

The biological classification has begun with the Swedish botanist Carl Von LINNAEUS (1753), who
created the system of binomial nomenclature. Each plant possesses a Latin scientific name, recognized
by an international code that identifies it worldwide with precision. According to the rules of this code,
the name of a species is designated by a double name (Latin binomial): a genus name (or generic name
common for several close species) followed by a species name (or specific name) and accompanied by
the initials or the abbreviation of the botanist name who first described this species. The genus and species
names are written in italics or underlined; the first one is written with uppercase, the second one in
lowercase. The common name of a species in English is the vernacular or vulgar name.
Examples: Pinus silvestris L. is described by LINNAEUS and its vernacular name is scot pine, Pinus
maritimum Lam. described by LAMARCK and its vernacular name is maritime pine.

A species can be subdivided into two or more subspecies, races, varieties or forms which have the same
essential characters and can be distinguished from each other only by minor differences (color,
hairiness...). Following the same principle of classification, several common characters unite species in
genus, genus in family, families in order, orders in class, and classes in phylum (or division). The set of
phylum constitutes the Plants’ Kingdom. We call taxa (sing. taxon) each of these units of classification.
The family names end with -aceae, the order names with-ales, those of class with -opsida, and those of
phylum with -phyta.

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 Example: Maize
Category Taxon
Kingdom Plantae (plants)
Phylum Spermatophyta
Class Liliopsida (monocotyledon)
Order Commelinales
Family Poaceae (grasses)
Genus Zea
Species Z. mays

2 Various classifications

Old classifications

LINNAEUS has classified all living beings in two kingdoms: Animals and Plants. Fungi, Algae, and
Bacteria (Prokaryotes) are organisms unable to move or eat and are grouped in the kingdom Plantae.
Protozoa, single-celled organisms that eat and are able to move are grouped among Animalia. This
traditional division between animals and plants is still used nowadays. In this taxonomic system of two
kingdoms, some microorganisms such as Euglena (Eukaryotes), which are able to move but also capable
of photosynthesis, were classified at the same time in the Plants and the Animals kingdoms.

After LINNAEUS, JUSSIEU (1789) and De CANDOLLE (1778-1841) developed the "natural
classification" of plants based on plant morphology. The plants were divided into three divisions: The
Acotyledons (without embryo), the Monocotyledons (one cotyledon), and the Dicotyledons (two
cotyledons). Then based on some important characters (like the embryo, the stamens, the pistil, or floral
envelope), they have determined new families in which all the
known species have been classified.

According to DARWIN (1859) and LAMARCK, species are

grouped depending on their phylogeny (evolutionary history) and
represented by phylogenetic trees. In a phylogenetic system, each
taxon has to be monophyletic i.e. including organisms from a
common ancestor.
Figure 1 A monophyletic group includes
the common ancestor 1 and all of its
descendants (species A, B, and C)

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After the two kingdoms classification, Ernst Haeckel (1866) divided the living world into three kingdoms
(Protista, Animals and Plants). Later on in 1938, Herbert Copeland added a forth kingdom after dividing
the living world into 2 domains (1) Prokaryotes that included the Monera kingdom and (2) Eukaryotes
that included three kingdoms (Protista, Animals and Plants).

Modern classifications

The recent classifications were based first on biochemistry, particularly the secondary metabolites and
more recently on molecular biology with the sequencing of amino acids and nucleotides. Margulis (1981)
has divided the living world into five kingdoms distinguished by two types of cell organization.
Prokaryotes and Eukaryotes (Greek Karyon: nucleus, Proto: first and Eu: well). Prokaryotes are usually
microscopic organisms, with cells without nuclei and without organelles delimited by membranes
(mitochondria and plastids). They include the only kingdom of Monera (Bacteria and Cyanobacteria). In
contrast, Eukaryotes include organisms mostly multicellular, with organized cells, generally larger and
having nuclei and organelles delimited by membranes. Protista, Mycetes (fungi), Plants and Animals are
the four kingdoms of Eukaryotes.

 Prokaryotes
- Kingdom Monera
 Eukaryotes
- Kingdom of Protista mostly single-celled
- Kingdom of Plantae autotrophs
- Kingdom of Mycota multicellular
- Kingdom of Animals heterotrophs
Protista are mostly single-celled organisms. Plants, mycota and animals include the multicellular
Eukaryotes. These three kingdoms (discussed in details in the following chapters) are distinguished by
structural characteristics, by their development cycles and by their nutritive mode.

Plants are autotrophs i.e. able to synthesize their nutrients through photosynthesis. Fungi and Animals
are heterotrophs: the Fungi feed on the decaying organic matter, while the nutrition of Animals is by
ingestion.

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In the classification based on five
kingdoms, Prokaryotes constitute the
kingdom of Monera, while Eukaryotes are
divided between Protista, Plants, Fungi
and Animals. Over the past twenty years,
taxonomists have admitted that grouping
all Prokaryotes in a single kingdom did not
consider the evolution. By comparing
ribosomal RNA and completely
sequenced genomes of several
contemporary species, the researchers
found that two major strains of
prokaryotes had emerged during the
Figure 2 Classification of th eliving things into 5 kingdoms
evolution: Bacteria and Archaebacteria (or
Archaea). The Archaebacteria are distinguished from Bacteria by many structural, biochemical and
physiological characteristics .

Carl WOESE with a group of researchers have discovered the difference between Bacteria and
Archaebacteria, therefore they proposed a system of six kingdoms: two kingdoms of Prokaryotes
organisms and four of Eukaryotes. However, Bacteria and Archaebacteria have diverged so early in the
evolution and present fundamental differences that WOESE (1977) and many other taxonomists currently
lean on a classification based on three “Domains”, the domain ranging over the kingdom. In this
classification, prokaryotes include two of the three domains: Bacteria and Archaebacteria and the third
domain groups the eukaryotes.

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Figure 3 The tree of the three domains of the living. On the right the phylogenetic tree based on Ribosomal RNA
sequence comparaison.

Figure 4 Classification of the living things into 6 kingdoms

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Table 1 Comparative table between Prokaryotes and Eukaryotes

Prokaryotes Eukaryotes
Organisms Bacteria Protista, Fungi, Plants,
Animals
Cell size (length) Generally Generally
1 to 10 micrometers 5 to 100 micrometers
Cellular organization One cell In majority multicellular
with cellular differentiation
Metabolism Aerobic and anaerobic Aerobic
Nucleus membrane absent present
DNA Circular, in the nucleoid Linear, in the nucleus
Organelles delimited by a Absent Present
membrane

Reproduction Scissiparity Mitosis and meiosis

Table 2 Classification system chronology.

Aristotle (384-322 BC)

2 Kingdoms Plants Animals

Plants Animals
Fungi

Carolus Linnaeus (1735)

2 Kingdoms Plantae Animalia

Organisms Plants Animals
Fungi
Ernst Haeckel (1866)

3 Kingdoms Protista Plantae Animalia

Organism All single-celled Plants Animals
organisms, such as
amoebas and diatoms,
and sometimes simple
multicellular organisms
such as seaweeds.
Herbert Copeland (1938)

PROKARYOTE EUKARYOTE

4 Kingdoms Monera Protista Plantae Animalia

Organism Bacteria Amoebas, Plants Animals
diatoms, and other Fungi
single-celled
eukaryotes, and
sometimes simple
multicellular
organisms, such as
seaweeds.

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 Robert H. Whittaker (1957)

PROKARYOTES EUKARYOTES

5 Kingdoms Monera Protista Fungi Plantae Animalia

Organism Bacteria Amoebas, Multicellular, Multicellular Multicellular
diatoms, and filamentous organisms that organisms
other single- organisms obtain food that ingest
celled that absorb through food
eukaryotes, food photosynthesis
and
sometimes
simple
multicellular
organisms,
such as
seaweeds.

Carl Woese (1990)

PROKARYOTES EUKARYOTES
3 Domains Archaea Bacteria Eucarya
6 Kingdoms Crenarchaeota Euryachaeota Protista Fungi Plantae Animalia
Organisms Ancient Ancient
bacteria that bacteria that
produce grow in high
methane temperatures

3 Traditional classification of the plant kingdom

The plant kingdom can be divided according to the organization of their vegetative apparatus and their
reproductive structures as follows:
- Thallophyta (thallos: thallus and phyton: plant), vegetative apparatus is a thallus: Algae, Fungi
and Lichen.
- Cormophyta (cormos: trunk and phyton: plant), vegetative apparatus is a cormus: Bryophytes,
Pteridophytes and Spermatophytes. This group include the Archegoniates (Bryophytes,
Pteridophytes and Gymnosperms) for which the female reproductive organ is the archegonium
as well as the Angiosperms.
- Cryptogams (kryptos: hidden and gamos: marriage), absence of flowers and seeds: Algae,
Fungi, Lichen, Bryophytes and Pteridophytes.
- Phanerogams (phaneros: obvious and gamos: marriage), presence of flowers and seeds. They
are also called Spermatophytes.

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The Thallophyta and the Bryophyta are non-vascular and therefore devoid of conductive apparatus
(xylem and phloem). The Pteridophyta and the Spermatohyta are vascular plants possessing a conductive
apparatus and roots.
Remark: Currently, almost all authors exclude Fungi from the plant kingdom to form a separate kingdom.

Figure 5 The traditional classification of the plant kingdom

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 Chapter 2 Prokaryotes : Kingdoms of Eubacteria and
Archaebacteria
1 General characteristics

The Bacteria are prokaryotic and mainly unicellular microorganisms. They are structurally the simplest
and most abundant on the earth's surface. Their expansion is due to their high metabolic diversity and their
rapid division.
The vast majority of Bacteria are essential to life on earth. They are a source of significant economic
products such as vitamins and antibiotics and play a role in the decomposition and recycling of the soil
organic matter. However, other prokaryotes cause human plant and animal diseases.

2 Structure and characteristics of Eubacteria and Archaebacteria

Morphology

Prokaryotes come in a great sizes and shapes. Most bacteria range from 0.2-2.0µm in diameter and from
2-8µm in length. Most bacterial species exist as single-celled forms, but some are found as colonies or as
filaments of joined cells. Although thousands of kinds of bacteria are known, they have three main shapes:
spherical coccus, rod-shaped bacillus, and spiral.

Cocci are usually round but can be oval, elongated, or flattened on one side. When cocci divide to
reproduce, the cells can remain attached to one another. Cocci that remain in pairs after dividing are called
diplococci; those that divide and remain attached in chainlike patterns are called streptococci.
Most bacilli appear as single rods. Diplobacilli appear in pairs after division, and Streptobacilli occur in
chains.
Spiral bacteria have one or more twists; they are never straight. Bacteria that look like curved rods are
called vibrios. Others called spirilla, have a helical shape, like a corkscrew. Yet another group of spirals
are helical and flexible; they are called spirochetes.

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The shape of a bacterium is determined by heredity. Genetically, most bacteria are monomorphic; that is,
they maintain a single shape. However, some bacteria, such as Rhizobium, are genetically pleomorphic,
which means they can have many shapes, not just one.

Figure 18 The various forms of prokaryotic organisms.

Cytoplasm

Prokaryotic cells have no nuclei, no mitochondria, no chloroplasts, no endoplasmic reticulum, no

Golgi complex and no lysosomes. A plasma membrane encloses a dense cytoplasm (cytosol) that
contains the ribosomes and the enzymes needed for metabolic activities. Certain bacteria have gas
vacuoles that allow them to float at different depth in an aquatic environment. Prokaryotes do not possess
a true nucleus bounded by a nuclear membrane. The DNA is a single circular chromosome, is a double
strand associated with different proteins, the histones. It is located in a central region of the cell called
nucleoid. One or more plasmids, small extrachromosomal DNA molecules, are capable of replicating
independently of the cellular chromosome (self-replication). Plasmids often bear genes that confer
resistance to antibiotics.

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 Cell membrane

The cell membrane acts as a selectively permeable membrane, i.e. it allows the selective passage of
molecules (nutrients, wastes, ions, etc.). In photosynthetic bacteria membrane invaginations form
thylakoids in which the photosynthesis takes place. The cell membrane is surrounded by a cell wall which
ensures protection, stiffness and resistance to osmotic pressures of some substrates. The cell wall
characteristics differ between the kingdoms of Bacteria and Archaebacteria and will be explained in the
following sections.

Figure 19 The ultrastructure of a bacteria.

Capsule

Many prokaryotes secrete viscous or sticky substances called capsule, forming a protecting layer around
the cell wall. The role of this capsule is to provide the cell with added protection against phagocytosis by
other microorganisms or, in disease-causing bacteria, by the host’s white blood cells. The capsule allows
certain pathogenic bacteria to bind to specific host tissues and protect others from desiccation. The capsule
is also used to cement the cells to each other colonial bacteria. In certain species, capsules are important
in contributing to bacterial virulence (the degree to which a pathogen causes disease).

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 Flagella

Most bacteria have flagella that allow motility. There are different types of flagellar formations:

 Monotrichous arrangement: a single polar flagellum (A).

 Lophotrichous arrangement: several polar flagella (B) (Tracing
movement + oscillating movement).
 Amphitrichous arrangement : a flagellum at each pole (C)
(Oscillatory movement)
 Peritrichous arrangement: flagella surrounding the cell (D)
(helical tracing movement ).
Figure 20 The different types of
bacterial flagella arrangements.

The flagella rotation produces the cell movement in the medium. Others slide by secreting sticky
substances. Besides their role in motility, flagella may be involved in virulence.

Pili and fimbriae

Fimbriae and pili are filamentous structures. Fimbriae (singular fimbria) serve to attach the organism to
a food source or other surfaces. Some pili are involved in the process of conjugation between prokaryotes
(only in the kingdom of bacteria), serving first to connect the two cells and then, by retracting, to draw
them together for the actual transfer of DNA. Some pili are also involved in the pathogenicity of bacteria
for plants and animals. These pili also serve as receptors for specific bacteriophages.

Figure 21 Conjugating Escherichia coli cells The elongated donor cell

at the right in this electron micrograph is connected to the more rotund
recipient cell by a long pilus, which is the first step in conjugation.
Numerous short fimbriae are visible on the donor cell.

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 Chemotaxis and Phototaxis

Many bacteria are capable of oriented movements (taxis) in response to chemical stimuli (chemotaxis) or
light stimuli (phototaxis).

Metabolic diversity

Bacteria have a very high metabolic diversity. Two elements are necessary for the organic compounds
synthesis: energy and carbon.

According to their energy source, Prokaryotes can be :

- Phototrophs: use light as energy source. The process by which organisms convert light energy
into chemical energy is called photosynthesis
- Chemotrophs use either inorganic or organis chemicals as an energy source.
According to their carbon source, Prokaryotes can be :
- Autotrophs (from the Greek autos: itself; trophos: food, feed themselves) using CO2, an
inorganic compound as the sole carbon source.
- Heterotrophs (from Greek heteros: different), which is the case of the majority of prokaryotes,
they need organic compounds (or nutrient), for example glucose, as a carbon source.

The terms used to indicate the energy and the carbon source of Prokaryotes can be used in combination
showing the metabolic diversity of those organisms as shown in the table 2.

Table 3 Metabolic diversity of Prokaryotes.

Carbon source

Heterotrophs
Autotrophs
(use organic compounds other than
(use CO2 as a carbo source)
Energy source CO2 as a carbon source)
Phototrophs
Photoautotrophs Photoheterotrophs
(use light as an energy source)
Chemotrophs
(use organic or inorganic Chemoautotrophs Chemoheterotrophs
chemicals as an energy source)

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The vast majority of heterotrophs are saprophytes (Greek sapros: rotten). Other heterotrophs can be
parasitic or symbiotic :

2.8.1 Saprophytes

They get their carbon from partially degraded or dead organic matter in the presence (aerobic) or absence
of oxygen (anaerobic). They are decomposers and recyclers of organic matter in the soil and ensure the
return to the inorganic state (C, N, S, P).

2.8.2 Symbiotic

Symbiotic association (mutual benefit between two living beings) as Rhizobium lives inside the roots of
legumes and fix a considerable amount of atmospheric nitrogen (N2) which is not directly used by the
plant.

2.8.3 Parasitic

They use organic matter in living animals or plants. If they are at the origin of diseases they become
pathogenic.

Effects of the external factors

Oxygen has an effect on growth. Some species are strict aerobics they require oxygen for respiration.
Others are strict anaerobics they cannot live in the presence of oxygen that poisons them. The facultative
anaerobics are able to live in the presence or absence of oxygen.

Likewise, prokaryotes can be distinguished according to their ability to grow in relation to the temperature.
Psychrophilic can grow at low temperatures. Mesophilic usually develop at moderate temperatures. The
moderate thermophiles grow optimally at high temperatures while the microorganisms having optimum
growth at very high temperatures are termed hyperthermophilic.

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3 Kingdom of Eubacteria or Bacteria

Eubacteria, or true bacteria, are a diverse group that nevertheless conform to certain general
characteristics. They are often classified on the basis of their staining properties, type of metabolism,
shape, cell wall structure, locomotion (motility) type…

Cell wall

The bacterial cell wall contains peptidoglycan (carbohydrate polymers transversely connected by short
polypeptides). According to the wall structure bacteria can be divided into two categories and can be
identified using the Gram stain:
- Gram-positive bacteria: it comprises a single thick layer of peptidoglycan (10-80 nanometers).
- Gram-negative bacteria: it is formed of two layers; a thin inner layer of peptidoglycan (2-3
nanometers) and an outer layer of similar structure to that of plasma membrane composed of
lipopolysaccharide (LPS), and proteins. The toxicity of lipopolysaccharide makes some Gram (-)
bacteria the most dangerous bacteria among pathogenic bacteria.

The peptidoglycan layers of many gram-positive bacteria are densely functionalized with anionic
glycopolymers known as wall teichoic acids (WTAs).

Figure 22 The cell wall structure of Gram (+) and Gram (-) bacteria.

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 Figure 23 The position of the Teichoic acids in the Gram (+) cell wall

Endospores

Endospores are spores formed within the cell wall of a parent cell in Gram+ bacteria:
 First, the chromosome replicates; one of the two copies and a small portion of cytoplasm are
isolated by an ingrowth of the plasma membrane called spore septum.
 The latter becomes a doubled-layered membrane that surrounds the chromosome and cytoplasm.
Thick layer of peptidoglycan are laid down between the two membrane layers.
 Then a thick spore coat of protein forms around the outside membrane. This coat is responsible
for the resistance of the endospores to many harsh conditions.
 Ultimately, the spore is liberated from the parent cell. Generally, the spore will remain dormant
for a period of time before it can be induced to germinate by hydrating to revive the vegetative
state in hospitable environments.

Bacteria increases its ability to survive by producing endospores. They can remain viable (which means
it can multiply) over centuries. Endospores may remain alive (dormant) for many years under conditions
quite unfavourable to growth. They resist desiccation, are not killed by long exposures to temperatures
as high as 80˚C, and may be suspended in boiling water for up to 20 minutes without being killed.

Figure 24 Bacillus anthracis endospores.

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Figure 25 Endospore life cycle

Cyanobacteria

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Cyanobacteria (cyano: blue) or cyanophyceae (formerly called "blue algae") are bluish green, sometimes
purplish photosynthetic bacteria. They have chlorophyll "a" (also present in all photosynthetic
eukaryotes), carotenoids (red or yellow) and other accessory pigments, phycobilins. The color of
cyanobacteria is due to phycobilins involved in capturing light energy and mask chlorophyll. There are
two types of phycobilins: phycocyanin, blue pigment, and phycoerythrin, red pigment. The plasma
membrane form many intracellular invaginations, often concentric and parallel to each other, the
thylakoids. The phycobilins (grouped into pigment complexes, phycobilisomes) are located on the outer
side of the thylakoids. The main sugar reserve is glycogen. Cyanobacteria lack flagella; mobile species
move by sliding. Cyanobacteria are all Gram (-) bacteria. Cyanobacteria can be unicellular, lives in
colonies or form multicellular filaments called trichomes.

Figure 26 The cyanobacterium Anabaena cylindrica showing the thylakoids within the cell.
Cyanobacteria can be unicellular, lives in colonies or form multicellular filaments. Many filamentous
cyanobacteria are capable of fixing atmospheric nitrogen (N2) through specialized cells, heterocysts.
In addition to heterocysts, some cyanobacteria form resistant cells, the akinetes, which are cells with thick
walls and resistant to drought).

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 Figure 27 Filament of Anabaena (a) The first cell at the right
end of the chain is a heterocyst (b) The third cell from the left
is a heterocyst. The large oval body toward the right is an
akinete.

They are found on the bottom of the deep waters and moist soils. Some may develop on the water surface:
they are planktonic species (free-swimming forms or driven by currents).

Mycoplasma

Mycoplasmas are a particular group of bacteria lacking cell walls. These prokaryotes can have many
forms, from small stick to branched filament. They are all parasites causing lung diseases for animals and
phytopathologic diseases in plants.

Figure 28 Mycoplasma

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4 The Archaea

The Archaea (Greek archaios= former) are a group of primitive bacteria that are present since around 3.5
billion years. Biochemically, Archaebacteria (arkhaios = ancient) are very different from other
prokaryotes. One of their most distinguishing features is the absence of peptidoglycan in their cell walls.
They also have unusual lipids in their plasma membranes, and distinctive RNA molecules; their RNA
polymerase is more like that of eukaryotes than that of Eubacteria.

Archaebacteria inhabit extreme environments, completely unsuitable to other organisms: hot springs
whose temperatures may exceed 100C and deep-sea vents that spew sulfide gases. Based on metabolic
characteristics, the Archaebacteria are divided into four groups: Methanogens, Halobacteria, Extreme
thermophile and Thermoplasma.

Some archaea live in the soil, others in the marine environment whose number exceeds that of oceanic
picoplankton (organisms of less than 1-micron size). The Archaea are not pathogens of humans.

Table 3 Comparative table between the three domains: Bacteria, Archaebacteria and Eukaryotes.

Characteristics Bacteria Archaea Eukarya

Cell type Prokaryotic Prokaryotic Eukaryotic
Nuclear envelope Absent Absent Present
Number of 1 1 Many
chromosome
Chromosome shape Circular Circular Linear

Peptidoglycan in the Present Absent Absent

cell wall
Membrane lipids Ester Ether Ester

Organelles Absent Absent Present

(mitochondria and (generally)
plastids)
Cytoskeleton Absent Absent Present
Photosynthesis in the Absent Absent Present
chloroplast
Capacity to grow > No Yes, for some No
100˚C species

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 Methanogens

These prokaryotes produce methane (CH4) from hydrogen (H2) and

carbon dioxide (CO2). They are strict anaerobics chemotrophs. Their
carbon source is either CO2 (autotrophy) or small organic molecules
(heterotrophy). All methanogens use ammonium (NH4+) as a nitrogen
source, but some can fix nitrogen. Methanogens are common in tidal
marshes and the ocean depths. The largest reserves of natural gas used
as fuel nowadays were produced from a historical methanogenic
Figure 29 Micrograph on electronic
prokaryotes activity. microscope of an archaeobacterium
scanning.
They are used as decomposers for biological treatment of wastewater.
Methanogens are also found in the cattle and other ruminant’s intestine, where they play an important role
in the cellulose digestion.

Figure 30 Use of bacteria in the wastewater treatment.

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 Figure 31 Bioremediation after oil spill. A worker sprays
fertilizer on a range of oil, in Alaska. The fertilizer stimulates
the growth of indigenous bacteria that can initiate degradation.
This technique is the fastest and most economical way to clean
the beaches after an oil spill.

Extreme halophiles (Halobacteria)

Halobacteria (Greek halos salt, and pilein : love ) live in areas where the salt concentration is very high,
such as the Great Salt Lake in the United States , the Dead Sea or in the sea water pools for the production
of kitchen salt (sodium chloride , NaCl). Most extreme halophiles require a salt concentration of 12-23 %
for an optimal growth. Their cell walls, ribosomes and enzymes are stabilized by sodium ion (Na+).
Although the necessary amount of oxygen for their breathing is limited by the high salt concentration,
most species need oxygen .Extreme halophiles can be chemoheterotrophs, they find their energy from
the oxidation of organic compounds. For some, the light intervenes in the synthesis of ATP without the
intervention of chlorophyll pigment. ATP production is due to a protein, bacteriorhodopsin present in
the plasma membrane. Bacteriorhodopsin also gives pink color to halophilic colonies forming masses in
seawater.

Extreme thermophiles or thermoacidophiles

Extreme thermophiles live in areas both hot and acidic. Their growth is optimal at a temperature not lower
than 80 ºC and a pH between 2 and 4. Some grow at more than 110 º C. They are strict anaerobes. These
archaea are found in hot places rich in sulfur, such as hot springs and geysers in Iceland, Italy, New
Zealand and Yellowstone National Park in the United States. They also thrive in hydrothermal fissures on
the ocean floor.

26
 Thermoplasma

This group is represented by only one species belonging to the genus Thermoplasma. They lack cell wall
(as mycoplasma), have a small size and can be spherical or filamentary. They live in places where
temperatures range from 32 to 80 ºC. They are capable of both aerobic and anaerobic metabolism.

27
 Chapter 3 Kingdom of Protista

1 Generalities

The kingdom of protista grouped structurally similar organisms (mostly unicellular eukaryotes), but also
served as a catch-all for the multitude of eukaryotic organisms that do not fit the definition of plants,
animals or fungi. The kingdom of protista included a majority of unicellular and microscopic organisms.
But it also contained relatively simple multicellular forms, and even rather complex giants such as
Seaweed.

Protista are the most diverse eukaryotic organisms. Some protista are closer to the plants, animals and
fungi then they are to other Protista. They also have a variety of shapes , with isolated cells provided or
not with cell walls , with or without flagella , amoeboid cells , simple or branched filaments , “leaves”
formed of one or two layers , or multinucleated masses without cell walls.

Most protists are aquatic: in oceans, freshwater lakes, ponds and rivers. Some live in the deep ocean,
coastal, or attached to rocks. Some Protista are found in terrestrial habitats (moist soil, decaying leaves).

Many protista form cells resistant to extreme conditions named the cysts. Protista reproduce asexually.
But many reproduce sexually and have complex development cycles.

Protista include autotrophic, heterotrophic and mixotrophic eukaryotes. Mixotrophy is the ability to
acquire carbon from both auto- and heterotrophy,. Protista are divided into three sub-kingdoms:
- Plant-like photosynthetic protists represented by algae: autotrophic organisms that use light
energy to make their own food.
- Fungus-like heterotrophic protists: feed by absorption.
- Animal-like heterotrophic protists: protozoa that ingest their food.

This chapter will concern only two sub-kingdoms of plant-like and fungus-like protists.

28
2 Sub-kingdom of Algae (phycophytes)

Algae are eukaryotic thallophytes (no stem, leaves or roots). Algae have cellulosic cell walls like in
higher plants. They are (with numerous exceptions) aquatic organisms that (with frequent exceptions)
are photosynthetic, aerobic autotrophs. Some species are benthic (attached to the bottom or on the
coast), others are planktonic. Algae are the primary producers of the marine ecosystem.

The majority of algal groups contain heterotrophic species that obtain organic carbon from the external
environment either by ingesting particles by phagocytosis (phagotrophy), or through uptake of dissolved
organic compound, an ability termed osmotrophy. Some algae referred to as auxotrophs, are incapable
of synthesizing certain essential elements and hence must import them (like vitamins).

Algae range in size from single-celled, microscopic forms to large, multicellular organisms. Their
dimension varies from a few microns to several meters (Laminaria, 60m). The algae thallus present a
morphological diversity which the main forms are:

 Unicells: Some unicellular algae are nonmotile, while others can possess one (or more) flagella.
Such flagellates can be either unicellular or colonial.

 Colonial: they are groups of cells often united with each other by mucilage. Depending on the
organism, cells in a colony may be either flagellated or nonmotile. If the colony is an assemblage
of a predictable number and arrangement of cells that remain constant throughout the life of
individual it is referred to as a coenobium .

 Filaments: Filaments may be unbranched or branched crawling and/or erected

 Parenchymatous: Although the cells of algae do not truly differentiate to form various structures,
these parenchymatous algae often have parts that resemble leaves, stems and roots.

 Coenocytic forms: Less common are algae with a coenocytic or siphonous growth habit. Such
organisms consist of one large multinucleacted cell, without cross walls.

29
 Figure 32 Illustration of different types of algae : (a) unicellular, mobile; (b)
unicellular, non-mobile; (c) in colony; (d) in colony, coenocytes; (e)
parenchymatous (f) filamentous.

All algae have chlorophyll “a” (like in Cyanobacteria and Plants) and supernumerary pigments that
capture certain wavelengths of light poorly absorbed by the chlorophyll a.

Classification of Algae into phyla, or divisions, is largely by pigment composition and energy storage
products. Other characteristics are also used like the cell wall composition, the presence and number
of flagella. In this chapter, we will study the following phylum:
- Chlorophyta (Green algae)
- Pheophyta (Brown algae)
- Rhodophyta (Red algae)
- Euglenophyta (euglenoids)
- Bacilliarophyta (diatoms)
- Pyrrhophyta or dinophyta (dinoflagellates)
- Chrysophyta (golden algae)

30
 Euglenoids: Phylum Euglenophyta

Euglenoids are unicellular algae with no cell wall. Most of

the Euglenoids are photosynthetic, like the well-known
genus, Euglena. Euglena contains chlorophyll a and b and
carotenoids in their chloroplasts. The plasma membrane is
covered from the inside by a flexible or rigid film of protein
strips (bands) located in the cytoplasm called pellicle.
Euglena has two flagella, one is long used for swimming and
the second is reduced. A red eyespot (or stigma), which
along with the short flagellum is associated with light
detection and aids these photosynthetic organisms to move
toward the light, is located in the cytoplasm near the base of
the flagellum. Figure 33 Euglena structure
A specialized organelle known as a contractile vacuole,
collects water from various parts of the cell body and pumps it out of the cell to protect the cell from the
rupture of plasma membrane due to the excess of water moving inside the cell by osmosis. Unlike green
algae, euglenoids plastids do not store starch but granules of a polysaccharide paramylon that are formed
in the cytoplasm. Plastids contain a region rich in protein, pyrenoid.
Some genus are heterotrophic (osmotrophic or phagotrophic) and others are mixotrophic.

Diatoms: Phylum of Bacillariophyta

Diatoms are mostly unicellular, few are colonial organisms that are an important phytoplankton.
Brownish plastids contain chlorophylls a and c and fucoxanthin
a brown golden carotenoid. They have siliceous walls called
frustules formed of two halves or valves (epivalve and
hypovalve) fitted together. The different striations and markings
on the frustules help in the species identification. The reserve
substances of diatoms include lipids and water soluble
polysaccharide, chrysolaminarine stored in vacuoles.
Figure 34 Achantes frustule.

31
 Golden algae: Phylum of Chrysophyta

Chrysophyta are mostly unicellular flagellates with either one or

two flagella. Some golden algae are colorless, while others have
chlorophylls a and c, but the color is largely masked by the
abundance of fucoxanthin. The pigmented cell contains one or
two large chloroplasts. As in diatoms, the reserve carbohydrate is
the chrysolaminarine. Some are mixotrophic.

Figure 35 Scanning electron micrograph of

silica scales and flagella of Synura cells in a
colony.

Dinoflagellates: Phylum of Dinophyta

(Pyrophyta)

Dinoflagellates are mostly unicellular and biflagellate;

most of them are marine phytoplankton, while others live
in fresh water. Many dinoflagellates are covered with a
shell of cellulose plates. Some cells are naked.

Most pigmented dinoflagellates contain chlorophylls a and

c, usually masked by carotenoids such as peridinin; the
characteristic accessory pigment of dinophyta. Other
dinoflagellates have green or blue-green plastids.
Carbohydrate reserve materials are starch.

Figure 36 Dinoflagellate theca

32
 Green algae: Phylum of Chlorophyta

Chlorophyta have green plastids containing chlorophylls "a" and "b" associated with carotenoids (same
pigment as in higher plants). They develop starch by photosynthesis. It is formed in plastids as isolated
grains or grouped around inclusions of protein nature, pyrenoids.
Green algae has a high morphological diversity, with flagellated unicellular forms (Chlamydomonas) or
non flagellated, colonial thallus (Volvox), filamentous (Spirogyra) and branched or parenchymatous thalli
(Ulva or sea lettuce). The thallus is attached to the substrate by a clamp (holdfast). Each cell of the thallus
contains a nuclei and a chloroplast. Not all algae do have a cellular structure. Some consist of coenocytic
fronds or siphon
containing an
undivided
multinucleate
cytoplasm.
Most are
aquatic
(planktonic or
benthic). Many
species are
terrestrial but
restricted to moist
places: wet soils,
snow or tree bark.

Figure 37 Illustration of green algae structure.

33
Figure 38 Algae plastids. (a) Green algae (Bryopsis); Pyrenoid py and thylakoid th (x9000); (b) Red algae (Porohyridium);
the punctuated aspect of the thylakoids is due to the presence of phycobilisomes. Starch a, is located outside the plastid
(x45000); (c) Brown algae (Fucus vesiculeux); thylakoids attached in groups forming like a “giant granum” (x10000). Ep
plastidial envelope.

Brown algae : Phylum of Pheophyta

Brown algae owe their brown or olive-green to the fact that chlorophyll is masked by the presence of large
amounts of a brown carotenoid, the fucoxanthin. Chloroplasts also contain chlorophylls "a" and "c".
They never produce starch. Their reserves are formed by lipids, and a soluble carbohydrate (laminarin).
Their cell wall is rich in algin.

Brown algae, almost all are found in marine environments and live in the sea and on rocky shores. They
are all multicellular, and may range in size from microscopic forms to the largest of all marine algae (up
to 100 m length). Their thallus, vegetative apparatus, consisting of a single filament can in some species
have a complex organization.

 The kelp (Laminaria) is a large alga that can reach several meters in length. Their thallus includes a
pedicel, the stipe, attached to rocks by a clamp (holdfast) and a very long leafy blade (or limbo),

34
 variable in shape depending on the species. Stipe has a tissue (elongated cells separated by screened
plates) specialized in the conduction of nutrients from limbo to the stipe and clamp.

 Fucus, brown alga of rocks. Thallus,

attached to rocks by a holdfast, is a
banded erect blade branched
dichotomously. This blade is provided
with ovoid vesicles filled with air,
acting as a float.

Figure 39 Brown Algae

Red Algae: Phylum of Rhodophyta

The chloroplasts of Red Algae contain chlorophyll "a" and carotenoids. The accessory pigments;
phycobilins (mainly phycoerythrin and few phycocyanin) mask the color of and give algae their
characteristic red or bright pink coloring.

Rhodophyta may modify their pigmentation depending on their depth, in order to optimize
photosynthesis. Thus, they can be black when deep, bright red at medium depths, and greenish in shallow
water (phycobilin in this case becomes less important).

35
Most Red Algae are marine organisms; some live in fresh water or attached
to the rocks. Their thallus are rarely unicellular, usually filamentous or
parenchymatous. Their main reserve materials are floridean starch
granules. Their pecto - cellulosic walls consist of an outer mucilaginous
layer as agar or carrageenan. The emission of mucilage by the Red Algae
prevents colonization by other organisms that can reduce their light exposure
surface.
Some incorporate calcium carbonate in their cell walls and participate in
building “coral” reefs. Few Rodophyta devoid of assimilating pigments are Figure 40 Porphyra unbilicalis
parasitic.

3 Economical importance of Algae

Useful algae

3.1.1 Edible algae

 Edible seaweed: some seaweeds are edible particularly by the populations in the Far East (China,
Japan) because they are rich in vitamins, iodine and other essential minerals. Some are used as
food additives (E400)
 Algin, constituent of the brown algae cell wall, is an important stabilizer and emulsifier used in
the composition of foods (ice cream).
 Agar and carrageenan extracted from red algae, are also used as a gelling agent in the preparation
of many foods (yogurt, jam, custard, ...)

3.1.2 Animal feeding and agriculture

 Animal feeding and agriculture: some algae are used in the manufacture of flours incorporated in
poultry feed
 Other seaweeds have been harvested for a long time and used as fertilizer

3.1.3 Industrial use

36
  The agar is used as a culture medium for bacteria or other microorganisms and for cosmetics, and
in medicine for the manufacture of capsules containing vitamins and medicines.
 carrageenan are used for their high viscosity as stabilizers of emulsions, such as paints, cosmetics
and dairy products.
 Manufacture of biofuel from algae rich in lipid.

Harmful algae

Algae can become dangerous when the water in which they live is polluted.
 some green algae give off toxic gases
 Dinoflagellates can make seafood toxic (oysters, mussels, ...)

4 Sub-kingdom of Fungus-like protists

They are unicellular or multicellular heterotrophic eukaryotic Protista. Their reserve form is the
glycogen. They feed by absorption or ingestion. The sub- kingdom fungiform Protista includes 3 phylum:
the Myxomycetes (Myxomycota) , the Acrasiomycetes (Acrasiomycota) and Oomycetes (Oomycota).

The Myxomycetes

The Myxomycetes are the simplest eukaryotes; their thallus consists of a mobile multinucleate mass,
called plasmodium or plasmodial slime mold that crawls like amoebae. The plasmodium is a coenocytic
mass with no cell wall, a multinucleated continuum of cytoplasm undivided by membranes or wall. In
most species, the nuclei of the plasmodium are diploid.
Myxomycota are saprophytes. During their movement, the plasmodia feed by phagocytosis and live on
damp substrates (leaf litter, decaying wood). Some species are plants parasites.

The Acrasiomycetes

The feeding stage of the Acrasiomycetes is haploid unicellular ameboid structure. When food is scarce,
cells are grouped in multicellular amoeboid clusters; pseudoplasmodium. Although this thallus looks like

37
the plasmodium of myxomycota (slime mold), it differs in that the cells retain their identity and remain
separated by their cell wall.

Figure 41 Myxomycete development cycle of the genus Physarum

Figure 42 Development cycle of the Acrasiomycota (Dictyostelium sp.).

38
 The Oomycetes

Oomycete resemble fungi in appearance. Their fronds are composed of siphoned filaments (ceonocytic)
highly branched that resemble to fungal hyphae. Their
walls are formed largely of cellulose (chitin in fungus).
Some are aquatic, others terrestrial. Aquatic Oomycota
abound in freshwater, they are saprophytes and live on
dead algae and animals, and others are parasites and
cause disease to fish and their eggs. Parasitic Oomycota
of terrestrial plants are plant pathogens causing several
diseases.
Figure 43 Oomycota

39
 Chapter 4 Kingdom of Fungi
1 General characteristics

Fungi or Mycota are heterotrophs (they lack chlorophyll). They use organic matter as a carbon
source and feed by absorption by secreting digestive enzymes. These enzymes break down large food
molecules into soluble molecules that diffuse through their cell walls. This nutrition mode requires fungi
to live as saprophytes, parasites or in symbiosis. Saprophytic fungi are decomposers, they feed on dead
plant and animal organic matter and waste. By doing so, they release water, carbon (as CO2) and mineral
components from organic compounds. Recycling of these elements constitutes an important contribution
to the ecological balance of our world.. The disappearance of saprophytes would end biogeochemical
cycles, and therefore the existence of plants and animals. Parasitic fungi absorb nutrients of living
organism’s cells. Such fungi could be pathogens; they are responsible of diseases, called mycosis, in
plants, animals and humans. Finally, symbiotic fungi establish mutual benefit associations with other
living organisms: mycorrhizae, associations between the roots of vascular plants and fungi, lichens
associations between fungi and algae cells or cyanobacteria.

2 Fungi structure

Figure 44 Fungi structure.

40
Fungi are eukaryotic tallophytes. Fungi are mainly terrestrial organisms occupying a variety of habitats.
Some are unicellular but most are filamentous. Fungal filaments branched structures are called hyphae
(Greek hyphae: tissue; sing. hypha). Hyphae form a tangle mass known as the mycelium that constitutes
the vegetative apparatus of the fungi. Well developed fruiting bodies called carpophore or sporophore
are only found in higher fungi.

In most fungi the hyphae are divided by transverse walls or septa (sing; septum) and consist of long lines
of cells, each containing one or two nuclei. The septum between two cells is perforated by a central pore
allowing the protoplasm of a cell to pass from one cell to another. Others are coenocytic, undivided by
septa, and are something like an elongated, multinucleated giant cell.

Glycogen (glucan) is the main

polysaccharide reserve in fungi. It is
stored in the form of particles
dispersed in the cytoplasm. Lipid
inclusions are common in some
species. The main component of the
fungal cell wall is chitin, an aminated
polysacharride composed of N-
acetylglycosamine, exists only in the
animal kingdom: scales or resistant
exoskeleton of arthropods (insects,
arachnids and crustaceans). Chitin is
more resistant to degradation by
microbes than cellulose.
Some fungi attach to the substrate
through specialized hyphae the
rhizoids. Parasitic fungi have similar
modified hyphae, called haustoria Figure 45 Organization of hyphae.
that directly absorb food by
penetrating their host’s tissues.

41
3 Classification of Fungi

The classification of fungi is based on characteristics of their sexual reproduction cycle. Mycologists
distinguish four groups of fungi: the Zygomycota (Zygomycetes), Ascomycota (Ascomycetes),
Basidiomycota (Basidiomycetes) and Chytridiomycota (Chytridiomycetes). A fifth phylum, considered
artificial, the Deuteromycota (Deutromycetes) groups together all species with unknown sexual
reproduction.

Yeasts are unicellular fungi that do not form a true taxonomic group. Some species reproduce asexually
by budding, they are part of Deutromycetes. Some species reproduce sexually and belong to the
Ascomycetes ,Basidiomycetes or Zygomycetes. Yeasts are used by bakers (to produce CO2) and
winemakers for ethanol production. Some fungi are dimorphic, that is, they exhibit both unicellular
(yeast) and filamentous (mycelium) growth forms, shifting from one form to the other under changing
environmental conditions (temperature, nutrients). It is the case of numerous fungi and particularly those
that are human pathogens. Saccharomyces cerevisiae (Ascomycete) is a filamentous dimorphic fungi, it
changes from yeast to filamentous form when the nitrogen is scarce.

42
 Figure 46 Phylogeny of mycetes.

Chytridiomycetes

Chytrids are the only fungi to have a flagellated phase in their cycle. Almost all of the Chytridiomycete
thalli are coenocytic siphons. Some are unicellular and do not form mycelium. Others have rhizoids
enabling them to be fixed to the substrate. Some species of Chytridiomycetes are saprophytic feeding on
animals and plants debris, others are parasitic.

Figure 47 Chytridiomycetes.

Zygomycetes

43
 Figure 48 Rhizopus stolonifer or black mold growing on bread.

Zygomycetes are fungi whose thallus is siphoned mycelium formed of siphons. Some forms are unicellular
like yeasts. Most are saprophytes and live on plant and animal decaying matter in the soil. Some are
parasites of plants, insects, animals and humans. Other species form symbiotic associations, with plant
roots (mycorrhizes).
Among the most known saprophytes, Rhizopus stolonifer or black mold that grows as cottony masses on
food rich in carbohydrate and/or exposed to the air, such as bread, fruit and vegetables. The mycelium
consists of coenocytic hyphae that rapidly develop through the food and absorb nutrients. Other curved
hyphae or stolons, are fixed to the substrate by rhizoids, and produce sporangiophores that hold at their
ends the sporangia containing spores.

Ascomycetes

Ascomycetes are sometimes referred to as “sac fungi” because their spores, called ascospores, are
produced in little sacs called asci (sing. ascus). The asci are always the terminal cells of special hyphae.
They are usually located in a reproductive structure called the ascocarp (macroscopic fruiting body or
carpophore).

44
The end cells (asci) of the
ascus-bearing hyphae, in many
forms, line the inner surface of
the ascocarp. This surface
layer is the hymenium or
fertile layer. Sterile cells,
called paraphyses, also arise
in the hymenium and are more
numerous than asci. Figure 49 Diagram of a magnified section in an ascomycete fungus.

The hymenial layer is more or less surrounded on the outside and protected by the vegetative haploid
hyphae that form a layer called the peridium.

The mycelium is composed of segmented and perforated hyphae, which allows the cytoplasm and nuclei
to switch from a cell to another cell. Ascomycetes are found both in terrestrial and aquatic habitats. Marine
species are saprophytes.

Many sexually reproducing types of yeast are classified as Ascomycetes, as well as the edible morels and
truffles. Red brown and blue-greens molds are Ascomycetes species which degrade food. Some other
species cause serious plant diseases that ruin fruits and ornamental plants. Other Ascomycetes species are
of great economic importance.

45
Figure 50 Magnified view of a section in an ascocarp Figure 51 The Pins rye (Claviceps purpurea).
hymenium showing ascospores inside mature ascus.

Figure 53 Ascomycetes: ascocarps are the sexual spore making apparatus of ascomycetes.

46
 Basidiomycetes

Sometimes called club fungi, basidiomycetes derive their name from their microscopic club-shaped
basidia (sing., basidium). Basidiomycetes are distinguished from other groups by the formation of basidia
producing basidiospores (reproductive cells).

The basidia are formed on top of mycelial hyphae and gathered in fruiting bodies called basidiocarps or
carpophores. At maturity, the fruiting body (basidiocarp) is formed of a cap (pileus) at the top of a stipe
and sometimes a volva at the stipe base. The lower surface of the cap usually consists of many thin,
perpendicular plates called gills, holding the basidia that radiate from the stalk to the edge of the cap and
form the hymenium. Most of basidiomycetes are saprophytic and play an important role in the
decomposition of wood (lignin) and cellulose debris. The primitive fungi are deprived of carpophores like
rusts and smut that are pathogens of vascular plants, especially cereals.

The mycelium of basidiomycetes is septated by perforated septa.

Figure 54 Plant parasitic basidiomycetes. Puccinia

graminis (Wheat stem rust) on the left and Ustilago zeae Figure 55 Structure of a basidiocarp.
(Maize smut) on the right

47
 The development of the basidiocarp

In some basidiomycetes, early in its development (the button stage) the basidiocarp is completely
surrounded by a thin layer known as the universal veil. The hymenium itself is covered by the “partial
veil” linking the pileus borders to the stipe. As the basidiocarp expands, the veils are torn. In some genera,
remnants of these tissue are visible (patches on the upper surface of the cap and the volva at the base of
the stipe derive from the universal veil while the annulus on the top of the stipe derives from the partial
veil) and are important in recognizing genus and species. The hymenium becomes external on the back
side of the cap.

Figure 56 Successive stages of the development of a basidiocarp

Deuteromycetes

Deuteromycetes are often called imperfect fungi or "Fungi imperfecti ".

Sexual reproduction (perfect stage), that serve as the basis for fungal
taxonomy, is unknown or has not been observed in this artificial group of
fungi. For this reason, they are considered unclassifiable and a second
(deuteron -) class or as "imperfect” form comparing with the sexually
reproducing fungi species.
The majority are saprophytic. Some are human pathogens, that are
responsible of diseases Figure 57 Aspergillus niger

48
The activity of many deuteromycetes is of great economic importance. Penicillium synthesizes the
antibiotic, penicillin, to treat bacterial infections. Penicillium is also used in the manufacture of many
cheeses.
4 Symbiotic associations between fungi and other organisms

Fungi can form symbiotic associations with algae or cyanobacteria forming lichens or with plant roots
forming mychorrizae. These symbiotic associations are of great ecological importance.

Lichens

Lichen is a symbiotic association between a fungus and a green photosynthetic unicellular or filamentous
alga, or Cyanobacteria. The fungus partner (mycobiont) is most often an Ascomycete, although it is
sometimes Basidiomycetes; while green algae are the photosynthetic partner (photobiont) (bios: life,
photo: light, mykes: mushroom).

The fungus gives the lichen its structure and shape. Similarly, the tissues made by hyphae represent the
largest part of the lichen mass. The fungus provides the Algae an ideal environment for physical growth
and absorb the essential minerals from the air or from the rain.
The alga constitutes generally the internal layer; it provides the food to the Eumycete. Cyanobacteria
that are part of the lichen fix the atmospheric nitrogen and convert it into organic nitrogen. These lichens
play an important role in providing nitrogen to many ecosystems.

A cortex, composed of compacted hyphae always forms on the upper or outer surface; and in many
species on the lower as well. A layer of algal cells is situated just below the upper cortex. Below the
algal layer there occurs a variously modified network of mycelium known as the medulla.

Traditionally, three broad categories of lichen have been recognized: crustose (crusty), foliose (leafy)
and fruticose (shrubby).

The lichen hyphae enhance the availability of minerals and can solubilize minerals like phosphorus that
are insoluble in the soil.

49
Lichens are very sensitive indicators of the toxic components—particularly sulfur dioxide—of polluted
air, and they are increasingly being used to monitor atmospheric pollutants, especially around cities.

Figure 58 Lichen structure in a cross section.

Mycorrhizae

A mycorrhiza is a symbiotic association between a mycete and roots of certain plants. Almost all vascular
plants have mycorrhizae. Both associated partners benefit from their alliance. Thus, the fungus provides
minerals (phosphorus, zinc, manganese, copper) it takes from the soil and the plant provides organic
elements it synthesizes.

Figure 60 Experiment proving the benefits of

Figure 59 Mycorrhizae mycorrhizae.

50
5 Importance of fungi

Fungi are important both for their beneficial (ecological, economic) and harmful effects.
Ecological

Nearly 80% of all vascular plants form associations with fungi in their roots (mycorrhizae). Fungi also
form symbiotic relationships with algae and blue-green algae to form lichens. Along with bacteria, fungi
are important in the world's ecosystem as decomposers, releasing carbon dioxide to the atmosphere and
nitrogen and other compounds to the soil where they are available for other organisms. They maintain
the reserves of inorganic nutrients essential for plant growth. Without saprophytes, carbon, nitrogen and
other elements accumulate in organic waste and are no longer available for the nutrition of plants and
animals.
Economical
Fungi are of both positive and negative economic importance, concerning particularly food, medicine
(chemicals and drugs), biocontrol, crop and animal diseases.

5.2.1 Food and Beverage

 The consumption of mushrooms.

 In the manufacture of bread (pasta), wine, beer....
 In cheesemaking: Penicillium intervene in the manufacture of blue cheeses
5.2.2 Pharmaceutical
Some fungi produce antibiotics used to treat bacterial diseases. Penicillin: first antibiotic discovered, was
manufactured by a common mold Penicillium notatum.
5.2.3 Biocontrol
Some Fungi can be extremely useful for controlling insect pests of crops.
Pathogens mycetes

 Fungi are the main cause of plant diseases (powdery mildew, rust, ergot ...)
 Fungi are involved in human pathology in two ways:
o food poisoning related to certain toxic fungi (Amanita, but also Aspergillus which are
capable of producing carcinogenic aflatoxins)
o infections called mycosis.

51
 Chapter 5 Plant Kingdom
1 Generalities

Plants are believed to have evolved from common ancestors: ancient green alga. Plants are multicellular
photoautotrophic eukaryotes. The plant cells are grouped to form functional tissues and different tissues
are grouped to form organs of the plant body. Plants are considered as Cormophytes, i.e. possess an
erect stalk. They are all multicellular plants; their cells contain vacuoles and are surrounded by
cellulosic walls. They are autotrophic and feed by photosynthesis (the main photosynthetic pigments are
chlorophyll a and b, as well as carotenoid accessory pigments) and their carbohydrate is stored in the form
of starch in chloroplasts and other plastids. Plants are for the majority terrestrial except for some groups,
the aquatic plants, that have evolved back with adaptations to the aquatic environments.

Figure 61 The phylogeny of the Plant Kingdom

52
 Adaptations to land colonization

Land colonization was marked by the differentiation of specialized structures for photosynthesis,
reproduction, support and anchor into the ground.

The increased photosynthetic areas, leaves, are provided with pores allowing gas exchange (oxygen and
carbon dioxide). The stems and leaves are covered with a cuticule, preventing water loss. The lignin
thickening of the cellulosic walls confers rigidity allowing the support of aerial organs and the upright
shape. The differentiation of conducting tissues (xylem and phloem) is essential to transport vital
elements (water, minerals and products of photosynthesis) through the plants organs. The roots improve
ground mounting, absorption of water and mineral nutrition.
Simultaneously, increasingly adapted devices to terrestrial conditions will appear, allowing greater
protection of reproductive cells, embryos and spores.
The development cycle of plants shows an alternation of two heteromorphic generations: the haploid
gametophyte and the diploid sporophyte.

Figure 62 Flowering plant organs.

53
Figure 63 Anatomy of a leaf.

Plant Kingdom classification

Plants can be classified by:

 tissue structure: non-vascular
(bryophytes) and vascular plants (all
others),
 reproductive characteristics: non-
flowering or flowering plants,
 reproducing through spores or seeds,
 seed structure: naked or covered seeds
inside a fruit.

Different classification systems are in

common use. In this course, we will use the
following classification system of the plant
kingdom for simplicity purposes :
Figure 64 Representation of the Cormophytes phylogeny

54
 Sub-kingdom of nonvascular
o Phylum Bryophyta
 Class Bryopsida (Mosses)
 Class Hepaticopsida (Liverworts)
 Class Anthoceropsida (Hornworts)
 Sub-kingdom of Vascular
o Phylum Pteridophyta (Plants without seeds)
 Class Psilotopsida (Whisk ferns)
 Class Lycopodiopsida (Club mosses)
 Class Sphenopsida (Horsetails)
 Class Filicopsida (Ferns)
o Phylum Spermatophyta (Seed plants)
Subphylum Gymnosperms
 Class Coniferopsida (Conifers)
 Class Cycadopsida (Cycas)
 Class Gingkopsida (Ginkgo)
 Class Gnetopsida (Clamydosperms)
Subphylum Angiosperms (flowering plants)
 Class Magnoliopsida of Dicotyledons (Dicotyledonous, Dicots)
 Class Liliopsida of Monocotyledons (Monocotyledonous, Monocots).

55
2 Sub- kingdom of nonvascular plants

In many respects, bryophytes are transitional between the green algae (chlorophyte) and the vascular
plants. Bryophytes are the first Embryophytes or Archegoniates, gradually adapted to the terrestrial
environment.
Bryophytes (Greek bruon: mosses) are chlorophyll cormophytes, that means plants with erected stalk or
cormus, provided with lateral appendages. The epidermis is deprived of stomata (with some exceptions).
Perforations, simple pores, allow the gaz exchange between the atmosphere and the internal tissues of the
plant. They have no roots, but rhizoids which mainly provide attachment to the substrate and partially
water uptake. They are small plants, without flowers and seeds (cryptogams), and no real conducting
tissues or vessels.

The development cycle of bryophytes is characterized by an alternation of generations where the

gametophyte dominates the sporophyte:
 Haploid generation: is the gamete producer corresponding to the gametophyte (vegetative
apparatus). Gametes are formed inside the gametangium (plur; gametangia) protected by a wall
consisting of one or several cell layers. Male gametangia called antheridia produce mobile
flagellated sperm (aquatic fertilization). Female gametangia called archegonia, hence the name
given to these plants Archegoniates; produce an egg.
 Diploid generation: the sporophyte that corresponds to the spore producer. The sporophyte
grows as parasite on the female gametophyte from which it takes the necessary water and nutritive
substances.

Most Bryophytes form a more or less dense carpet in the under-storey rich in humus. They form the low
vegetative cover or moss layer in wet and swampy stations, on trunks, walls and rocks. They are able to
withstand long periods of drought by dehydrating and rehydrating with the return of favorable conditions
(reviviscence).
The phylum Bryophyta includes three classes:
 Class Bryopsida (Mosses)
 Class Hepaticopsida (Liverworts)
 Class Anthoceropsida (Hornworts)

56
 Class Bryopsida (Mosses)

Mosses are the most common Bryophytes with nearly 14 000 species. Their gametophyte is composed of
an upright “stem-like” structure on top of which are found the reproductive organs (gametangia). The
axis (cormus) bares leafy blades. They are
rudimentary structures with no stomata or veins and
are always one cell thick except for the midrib. The
leafy blades cells usually contain numerous
chloroplasts, except at the midrib. The ground
mounting is ensured by multicellular hairs named
rhizoids.

Figure 65 Female gametophytes holding the sporophytes.

The Mosses sporophyte develops on the female gametophyte. The sporophyte’s epidermis shows stomata.
It includes:
- A haustorial foot which anchors the sporophyte to the female gametophyte from which it absorbs
minerals and nutrients.
- A seta or stalk holding the capsule .
- The capsule. It is covered externally by a membranous or hairy hood called the calyptra. The apex
of the sporangium differentiates into a cap-like lid called the operculum, which separate from the
rest of the sporangium as cells torn apart. Cells breakage is precise, resulting in one or two rows
of complex teeth called peristome teeth. The teeth respond to humidity, bending outward when
the air is dry, and spores, therefore, are released.

Spore germination is immediate if the conditions are favorable. Each spore gives a branched and
chlorophyllous multicellular filament: the protonema (proto: primitive; nema: filament). On the backside
of the protonema appear the rhizoids; on its upperside appear buds that will be the starting point for
gametophytes.

57
 Figure 66 Moss sporophyte’s capsule
structure

Class of Hepaticopsida (Liverworts)

The liverworts are represented by around 6000 species. They grow in very humid environments. Their
gametophytes develop directly from spores. There are two groups according to their vegetative structure:
 The thalloid liverworts
 The leafy liverworts

Figure 67 Liverwort germination and growth.

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2.2.1 Thalloid liverworts (Marchantia polymorpha)

The best known species of thalloid liverworts are in the genus Marchantia.
The vegetative apparatus (thallus) is represented by
a creeping chlorophyllous thallus branched
dichotomously and fixed by rhizoids. The thallus, few
centimeters thick, is constituted by differentiated cells
formingfunctional groups, such as: chlroenchyma
(photosynthetic role) on the back or top side, pores and
air-carrying chambers (gas exchange), a ventral
parenchyma (reserve). The backside bears, in addition
to unicellular rhizoids, multicellular scales.
Figure 68 Diagram of a cross section in
Marchantia thallus.

2.2.2 Leafy liverwort

The vegetative apparatus is a creeping axis with dorso-ventral symmetry, with leaf-like structures and
rhizoids. “Leaves” of Liverworts, like in mosses, comprise a single layer of undifferentiated cells but do
not have a midrib. Many leafy liverworts, like Frullania, have two rows of equal-sized leaves and a third
row of smaller leaves along the lower surface of the gametophyte.

Figure 69 Leafy liverwort with prostrate branches, Frullania. A: ventral view of a

male. B: dorsal view of a female.

59
 Class Anthoceropsida (Hornworts)

Hornworts include few species (about 300). The gametophyte, in the

form of a rosette, bears on its dorsal side the archegonia and the
antheridia and on its ventral side unicellular rhizoids that anchor it to
the substrate. The sporophyte is composed of a foot (absence of seta
unlike the mosses and liverworts) and a long cylindrical capsule. The
epidermis of Hornworts sporophyte shows stomata. Several
sporophytes can grow on the same gametophyte. The cells of most
hornworts have large chloroplast with pyrenoid (like in green algae).
Their thalli have pores with underneath cavities and they are not
stomata with controlled openings.

Figure 70 Anthoceros, a hornowrts the

gametophyte holding the sporophyte

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3 Sub- kingdom of vascular plants

Organization of the vegetative organs in vascular plants

3.1.1 Roots

In addition to their anchor and absorption roles, roots can

sometimes store food and serve in asexual reproduction.
Two types of roots are found: taproot (one main principal
root and many secondary roots) and fibrous root
(numerous primary fine roots).

3.1.2 Stems

Functions of the stem are to produce and support new

leaves, branches, and flowers; to place them in
positions where they can function most efficiently; and
to transport materials to and from the roots.
Frequently, stems serve to store and transport food,
minerals and water (xylem and phloem), carry on
photosynthesis, and reproduce new plants.
The region of a stem where a leaf or leaves are attached
is called nod. The stem region between nodes is called
internode. Stems bears (terminal or axillary), branches
and flowers.

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3.1.3 Leaves

The leaves intercept light, exchange gases, and provide a site for photosynthesis. Some leaves also store
food and water, provide support, or form new plants.
A leaf usually has a flattened blade, and in most cases is attached to the twig by the petiole. Within each
leaves the vascular tissues form the veins. Each angle between the petiole and the stem is called axil and
contains a bud.
The arrangement of veins, venation, may be pinnate (one primary vein, and secondary veins branch from
the primary vein) or palmate (several primary veins fan out from the base of the blade) or parallel.

Phylum Pteridophyta

Pteridophytes (pteris: fern) have stems, leaves and roots (rhizophyta, rhizos : roots). They are vascular
cryptogams, without flowers or seeds but have conductive tissues (phloem and xylem elements
impregnated with lignin).
In general, the development cycle of Pteridophytes is very similar to the one of Bryophytes with one
important difference: the perennial plant dominating the cycle corresponds to the sporophyte. While the
gametophyte or prothallus is small and has a limited life. Like in Bryophytes, the gametophyte is directly
derived from the germination of a spore.

Like all vascular plants, Pteridophytes have three types of tissues: protective tissues that cover and
protect the external surface of the plant ; conductive tissues (Xylem and Phloem), surrounded by the
ground tissues.

62
The most primitive Pteridophytes (whisk fern) do not have leaves or roots. More complex groups (club
mosses, Horsetail…) have small leaves without petiole and with one vein, called microphylls. For the
most evolved (ferns), they have most developed leaves, called megaphylls, or fronds with petiole and
limbo with a network of veins and the leaves are inserted directly on rhizomes.
The fertile leaves holding the sporangia are called sporophylls.
Pteridophytes can be:
 Isosporic with identical spores that give one kind of prothallus bearing antheridia and archegonia.
 Heterosporic with microspores and megaspores that give two kinds of prothalli. One bears the
antheridia and the other the archegonia.

The phylum Pteridophyta has expanded greatly since the Paleozoic era (360 million years ago), several
groups have disappeared. The current representatives consist of four classes:
 Class Psilotopsida (Psilotum or whisk fern)
 Class Lycopodiopsida (Club mosses; Lycopodium and Selaginella )
 Class Sphenopsida (Equisetum or Horsetail)
 Class Filicopsida (Ferns)

63
3.2.1 Class of Psilotopsida (Whisk ferns)

The sporophyte is formed of upright green stems, branched

dichotomously, attached by a rhizome (underground stem)
with rhizoids. The stems are the main photosynthesic organs
since they have no “leaves”. They have enations, which are
green, leaflike, veinless, photosynthetic flaps of tissue. The
sporangia are trilocular (aggregated by three) and are borne on
short lateral branches directly on the stems. Psilotopsida are
isosporic.

Figure 71 Psilotum nudum sporophyte.

3.2.2 Class of Lycopodiopsida

The sporophyte is fixed to the ground by underground rhizomes holding roots. The branched stems carry
microphylls. The sporophylls bare sporangia grouped in conelike strobili.

3.2.2.1 Lycopodium (Club moss)

In Lycopodium the strobili are located at the tips of stems. Lycopodium are isosporic, they have one type
of sporophylls and produce one type of spores.

64
Figure 72 Lycopodium complanatum sporophyte.

65
3.2.2.2 Selaginella (Spike Moss)

Selaginella strobili are formed of microsporophylls where microspores are formed, and macrosporophylls
that produce macrospores after meiosis that develop respectively into male and female gametophytes.

Figure 73 Slelaginella sporophyte.

3.2.3 Class Sphenopsida (Equisetum or Horsetail)

66
Aerial stems of Equisetum or Horsetail grow from rhizomes bearing roots. The aerial stems have nodes,
internodes and ribs. Some species have separate fertile and sterile stems rising from the rhizome. The
chlorophyll vegetative stems bear small non photosynthetic leaves, the microphylls, arranged in whorls
on the nodes. In some species, lateral branches are inserted at the nodes. Fertile stems are not
photosynthetic and have at their end sporangia grouped in strobili. Equisetum is isosporic. The bisexual
gametophytes are green and independent.

Figure 74 Equisetum sp. Sporophyte

67
3.2.4 Class Filicopsida (Ferns)

The sporophyte of Ferns (e.g. Polypodium = Dryopteris) has an underground rhizome. The rhizome
carries on its backside adventitious roots. The large leaves or fronds are megaphylls. Ferns are the only
vascular cryptogam to have well-developed megaphylls. Commonly, the fronds are compound; that is, the
lamina is divided into leaflets, or pinnae, which are attached to the rachis, an extension of the leaf stalk,
or petiole. Fronds "emerge" by circinnate vernation, a nearly unique uncoiling process. The tips of
young fern fronds are called fiddleheads.

Sporangia are grouped in clusters called sori on the back side of the sporophylls. The sorus usually has a
protective layer termed indusium (plural: indusia). Most of the ferns are isosporic, others are heterosporic.

The gametophyte or prothallus, with a flattened, heart-shaped structure, has many rhizoids.

Figure 75 The fern Polypodium sp. structure.

68
 Phylum of Spermatophytes

The spermatophytes (sperma: seeds) or seed plants are plants with seeds or phanerogams (phaneros:
apparent). Seeds replace the spores in the developmental cycle. The male and female gametophytes are
very small and develop inside specialized organs in the sporophyte which gives them protection against
desiccation.. After fertilization, the ovule becomes a seed.

Figure 76 Evolution of the relation gametophyte/sporophyte in plants

All spermatophytes possess megaphylls, but they are transformed into needles or scales in some groups.
The spermatophytes are divided into two sub-phylum Gymnosperms and Angiosperms.

3.3.1 Sub-phylum of Gymnosperms

The name gymnosperm, which literally means “naked seed,” points to one of the principal characteristics
of plants belonging to this subphylum—namely, that their ovules and seeds are exposed on the surface of
modified leaves known as sporophylls. The ovule is not enclosed in an ovary. The seed is formed from
the ovule, but there is no fruit. They lack the specialized water-conducting vessels of flowering plants but
have tracheids,
Gymnosperms include four classes: Coniferopsida (conifers), Cycadopsida (cycads), Ginkgopsida
(maidenhair tree, or ginkgo), and Gnetopsida (gnetophytes).

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3.3.1.1 Class Cycadopsida (cycads)

The plants are fairly large with a short, stout, unbranched trunk. The trunk has a terminal crown of long,
leathery leaves giving it the appearance of palm tree . Cycads are dioecious: male and female reproductive
organs are found on separate plants.

Figure 77 Cycas sp.

3.3.1.2 Class Ginkgopsida

Essentially fossils, Ginkgoes are represented by a

single extant species, Ginkgo biloba. The veins
branch dichotomously, a unique leaf venation
pattern. A Ginkgo can always be identified from its
fan shaped leaves. Ginkgos are dioecious, with
separate male and female plants.

Trees can reach a large size (30 meters). Unlike

other gymnosperms, Ginkgo biloba loses its leaves
in autumn. This tree is often used as ornamental
plant in urban areas, because it resists well the air
Figure 78 Gingko biloba.
pollution and other environmental aggressions.

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3.3.1.3 Class Gnetopsida

They have some characteristics in common with Gymnosperms, and some with Angiosperms. They are
unique among Gymnosperm in having vessels in their xylem. Gnetopsida has three genus:
 Gnetum: shrubs or vines with large leathery leaves.
 Ephedra: much branched shrubs with scaly leaves.

Figure 79 Gnetum include climbing plants and Figure 80 Ephedra grow in arid regions, almost
everywhere in the world.
tropical trees.

 Welwitschia: Most of Welwitschia’s body is a long underground taproot. Its short, wide stem
forms a shallow disc from which two ribbon-like leaves extend.

Figure 81 Welwitschia mirabilis.

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3.3.1.4 Class Coniferopsida (conifers)

Conifers are the largest and most widespread among gymnosperms, e.g. Pine, Fir, Spruce, Larch, Cypress,
Redwood (sequoia), Juniper, Yew, etc.
They are named conifers because the reproductive organs are grouped inside unisexual cones composed
of scales. The leaves are either tough needles or scale-like well adapted to drought. The xylem of conifers
is composed of tracheids. Resin canals are found in stems and leaves, hence the appellation of resinous.
Most conifers are evergreen (the tree remains green by growing leaves all year long as other leaves fall
off) ; only a few are deciduous (lose their leaves at the end of their growing season, usually in autumn).
Conifers are generally monoecious (each tree hold both male and female cones) but some species are
dioecious.

Figure 82 Different type of female cones.

72
Figure 83 Pine tree Figure 84 Pine branch holding both male and female cones

3.3.2 Subphylum of Angiosperms

The main feature of angiosperms is the typical flower containing the reproductive organs. Angiosperms
are the most diverse group (about 240,000 species), and the most advanced of the Plant Kingdom. They
include both herbaceous and woody plants. In Angiosperms (angio: envelope and sperm: seed), the bi-
integumented ovule are enclosed in a protective envelop, the carpel, more or less closed in an ovary.
After fertilization, the ovary becomes a fruit and the ovule a seed. This group is characterized by a
particular mode of fertilization: the double fertilization. Wood is mainly comprising heterogeneous real
vessels and fibers.

73
A complete flower consists of four floral whorls inserted on the receptacle. These whorls are from the
outside to the inside:
 Sepals : mostly green , which together form the
calyx
 Petals: usually colored, which together
constitute the corolla.
The calyx and the corolla are the sterile protective parts
and do not have a reproductive role. Together they form
the perianth.
 Stamens: ♂ reproductive parts, which together
form the androecium.
 Carpels: ♀ reproductive parts, which together
form the gynoecium or pistil. Each carpel is
formed of a lower part, the ovary containing one
or more ovule, an upper part, the stigma which Figure 85 Flower parts
receives pollen grain. The pollination (transport of the pollen from the male organ to the female
organ) is insured by wind, animals or humans.

Angiosperms are divided into two classes: Liliopsida (Monocots, one cotyledon) and Magniliopsida
(Dicots, two cotyledons).

3.3.2.1 Class of Monocotyledons

Monocotyledons have the following characteristics:

 One cotyledon.
 Herbaceous plants (except palms...).
 Fibrous root system
 Number of floral parts by three (or multiple).
 Leaves with parallel veins.
 Conductive tissues of stems are numerous and scattered.

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3.3.2.2 Class of Dicotyledons

Dicotyledon plants are very diverse. Their main characteristics are:

 Two cotyledons.
 Herbaceous or woody plants.
 Taproot system usually present.
 Number of floral parts four or five (or multiple).
 Leaves with reticulate veins.
 The primary (primary growth) conductive tissues of the stem are arranged in a ring.
 Secondary tissues (wood, liber) and cambium.

Figure 86 Comparison between monocots and dicots plants.

75
 Chapter 6 Photosynthesis

1 Characteristics of the plant cell

Plant cells have some specific characteristics that differ from the animal cells. At the ultra-structural level,
the cell is surrounded by a cell wall; the cytoplasm encloses a large vacuole and plastids. Cellulose is the
main component of the cell wall. Starch is the main carbohydrate reserve. Chlorophylls, are the
photosynthetic pigments. They are light energy receptors necessary for photosynthesis and give the green
color to the plastids (chloroplasts) in which they are found. However, these criteria do not have an
absolute value and does not apply to all green plants.

2 Introduction to photosynthesis

During photosynthesis, plants, algae and photosynthetic bacteria capture light energy to synthesize
complex organic molecules (sugars) from simple inorganic elements (water and carbon dioxide), while
releasing the oxygen. Photosynthesis is carried out in the chloroplasts of plant cells or in specialized
regions of the cell membrane (thylakoids) of prokaryotes. Chlorophyll molecules absorb light energy to
synthesize energy-rich molecules ATP and NADPH used for plant metabolism (the light dependent
phase of photosynthesis). The chemical energy contained in these molecules allows, through a series of
reactions, the carbon sequestration from atmospheric carbon dioxide to form carbohydrates (the dark
phase or Calvin cycle). The overall reaction of photosynthesis is: 6 CO2 + 12 H2O → C6H12O6 + 6 H2O
+ 6 O2.

3 Places of photosynthesis

In eukaryotic cells, photosynthesis takes place in the chloroplasts of chlorophyll parenchyma of leaves
(mesophyll). Carbon dioxide enters the leaf and oxygen exits through the stomata. The water and minerals
collected from the roots flow through the stem by a conductive tissue (xylem) and reach the leaves by the
ribs. The sugars produced by photosynthesis, leave the leaves by the ribs and are carried by the conductive
tissue of the organic sap (phloem), to non-chlorophyllous organs. The reactions of the light dependent
phase of photosynthesis take place in the thylakoid membranes found inside the chloroplast. The reactions
of the dark phase take place in the stroma of the chloroplast.

76
4 The chloroplast structure

A chloroplast is wrapped by a double membrane. Inside, its cavity is filled with a dense liquid (stroma)
and it is crossed by membranous sacs called thylakoids. Stacks of thylakoids form grana (singular
granum), their membrane define a compartment, the thylakoid space. The thylakoids are interconnected
by stromal thylakoid (or intergranal thylakoids).

Figure 6 The illustrations represent successive magnifications from the leaf to the cell, then to the chloroplast (the
photosynthesis site). Gas exchanges between the mesophyll and the atmosphere take place at microscopic pores, the stomata.
The chloroplasts, found mainly in the mesophyll, are surrounded by a double membrane; they contain a dense liquid named
stroma. The thylakoid membrane isolates the stroma from the thylakoid space. The thylakoids forms stacks named grana.

5 Localization of the photosynthetic pigments

Chloroplasts contain pigments capable of absorbing photons (particles of light energy). The main
photosynthetic pigments are chlorophyll "a" and the accessory pigments are chlorophyll "b" and
carotenoids. These pigments absorb certain wavelengths (red, blue) more effectively than others.
Chlorophylls are integrated into the thylakoid membrane and are linked by membranous proteins.

77
Figure 7 Chloroplast and thylakoid diagrams.

Figure 8 Localization and structure of chlorophyll in plants.

78
6 Excitation of the chlorophyll

When the chlorophyll molecules (or other

pigmented molecules) absorb a photon of light, an
electron is excited and passes from one layer to
another, more distant from the atom nucleus. The
excited electron therefore has more energy. This
excited state is unstable and the molecule returns
to its initial state. In the thylakoid membranes of
chloroplasts, there are electron acceptors that
receive the excited electrons.

Figure 9 The green color of leaves: an interaction between the light and the
chloroplast. The chloroplast pigments absorb mainly red and blue light, the most
favorable wavelength for photosynthesis. They diffuse the majority of the green
light, giving the green color to the leaves.

7 Course of photosynthesis

Photosystems

A photosystem comprises a collecting antenna and a

reaction center. In the thylakoid membranes, photosynthetic
pigments form a complex antenna or antenna.
The antennas pigment molecules absorb light and transmit
the energy from a molecule to another until the reaction
center is reached. This center includes a pair of specialized
molecules of chlorophyll "a". These are the only molecules
that can transfer electrons to an electron acceptor. Figure 10 Light reception in a photosystem.

79
There are two photosystems: photosynthesis photosystems I and II, numbered in the order of their
discovery. They differ in the chlorophyll "a" molecule of the reaction center. Photosystem I “has" the
P700 reaction center ("P" stands for pigment and "700" optimal absorption peak in nanometers), which
means it does not absorb wavelengths longer than 700 nm and photosystem II has the center P680.

The chlorophyll "a" molecules of the reaction centers are identical except that they are associated with
different proteins. Both photosystems are connected by a chain of electron transport. They operate
simultaneously and continuously.

Light dependent phase (photochemical reactions)

During the photochemical reactions, the electrons excited by light are transmitted through a chain of
electron transport. There are 2 types of photochemical reactions: cyclic phosphorylation and acyclic
phosphorylation.

7.2.1 Cyclic phosphorylation

Photosystem I can operate independently of photosystem II. The molecules of the P700 reaction center
absorb light, the excited electron moves to a primary acceptor molecule that transfers its additional
electron to a secondary acceptor and so on along the electron transport chain. Finally, the electrons return
to the reaction center of photosystem I. This transfer of electrons is coupled to a proton pump from the
outside to the inside of the thylakoid membrane creating a proton motive force capable of producing
ATP from ADP and Pi. This ATP synthesis in chloroplast due to light is called phosphorylation.

80
 Figure 11 Cyclic electron transport.
7.2.2 Acyclic Phosphorylation

These reactions involve the two photosystems (I and II). There is production of O2, ATP and NADP+ is
reduced to NADH and H+. The NADP+ is the final electron acceptor and the electron donor is a water
molecule. The O2 is released into the atmosphere. Photosystem II absorbs light captured by molecules of
the antenna and pass to the molecules of the P680 reaction center which loses an electron. This excited
electron exits from P680 and passes into a chain of electron acceptors. The electron-deficient molecule of
P680 (oxidant) is capable of sensing and capturing the electrons from the electrons donor H2O. Photolysis
is the lysis, in the presence of light, of the molecule of H2O into ½O2 + 2H + +2ē.

The photooxidaton of 2 water molecules requires 4 photons and liberates 4 electrons, 4 protons and one
oxygen molecule: 2H2O O2 + 4H+ + 4 e-

The pairs of electrons pass from photosystem II to the photosystem I by an electron transport chain. This
passage generates a proton gradient or proton motive forces on both sides of the thylakoid membrane
which activate the ATP synthesis. Photosystem I is excited by a light photon. The excited electron is then
transmitted in a short chain of electron transport to NADP+. This can reduce the NADP+ into NADPH.
The electrons removed from the P700 molecule are replaced by those coming from photosystem II.

81
In conclusion, the photons picked up by the two photosystems allow the photolysis of water molecules.
Electrons will move continuously in one direction only, from water to NADP+ and a proton gradient that
allows the formation of
molecules rich in ATP
energy and NADPH. These
molecules are used in the
Calvin cycle. The O2 released
from chloroplasts cell fate
and eventually leaves
through the stomata.

Figure 12 Production of ATP and

NADPH + H+ through the acyclic
transport of electron during the
photochemical reactions.

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Figure 13 Acyclic Phosphorylation in the thylakoid membrane.

Dark phase: Calvin cycle

The Calvin takes place in the chloroplast stroma. This is the last step of photosynthesis where ATP and
NADPH, generated during the photochemical reactions, are used to fix and to reduce carbon dioxide in
the synthesis of simple sugars. The cycle takes place in three steps :

First step: CO2 fixation:

The Rubisco ( ribulose - bisphosphate - carboxylase ), an enzyme representing more than 40 % of soluble
protein in most leaves, plays a key role in the so-called C3 plants (most green plants such as trees, potato
and beet) . This enzyme fixes each of the 3 CO2 molecules (3x1C) to 1 molecule of ribulose 1,5-

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diphosphate (RUBP 3x5C), a 5-carbon sugar. 6 molecules of a 3 carbons product, the phosphoglyceric
acid (PGA 6x3C), are formed after passing through an unstable intermediate.
The first product of the cycle contains 3 carbon atoms, which is why the Calvin cycle is also known as the
C3 pathway.

Second step: Reduction

6 PGA molecules are reduced by 6 NADPH and 6 ATP to produce 6 molecules of glycerate 3-phosphate
(G3P).

Third step: Refreshing RUBP

One of the 6 G3P molecules leaves the cycle for the synthesis of sugars and other cellular materials. The
other 5 G3P molecules
remain in the cycle to
regenerate the RUBP
(initial reagent of the
cycle). The regeneration
of RUDP requires 3 ATP
molecules. The RUBP is
ready to receive CO2 and
the cycle starts again. A
carbon enters the cycle at
each time. The cycle
occurs three times,
producing one molecule
of glycerate 3 - phosphate
(G3P). Each time the
RUBP is regenerated.
Most of the fixed carbon
is converted into starch
and sucrose. Figure 14 The Calvin cycle.

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8 The different types of photosynthesis

Plants have various mechanisms carbon fixation step in photosynthesis. The photosynthesis type of plant
is determined by the number of carbon atoms of the organic molecule formed first when the CO2 is fixed.

The mechanism of C3 plants

The first step of the Calvin cycle consists of fixing a molecule of CO2 (carboxylation) on the ribulose 1,5-
diphosphate by the Rubisco , to give a compound of 3 carbon atoms , PGA. A large majority of plants,
including trees work under this mechanism. The CO2 fixed by Rubisco comes initially from the diffusion
of atmospheric CO2 through stomata, then in a dissolved form, through the leaf cells to the chloroplast
stroma.

The mechanism of C4 plants

Stomatal closure in a warm and dry atmosphere causes a lack of CO2 in the chlorenchyma. This problem
is solved by the so-called C4 as corn or sugar cane plants. These plants having this mechanism have
another enzyme fixing CO2, phosphoenolpyruvate carboxylase (PEP carboxylase) located in the leaf
mesophyll. Atmospheric CO2 binds first to phosphoenolpyruvate (PEP) to produce oxaloacetate, a 4-
carbon molecule in the mesophyll cells. The oxaloacetate is converted to malate (or aspartate, depending
on the species), which passes from the mesophyll cells to the bundle sheath cells. Malate is then
decarboxylated and CO2 enters into the Calvin cycle reacts with RUBP, where the Rubisco is present, to
form the PGA. The C4 pathway occurs in the mesophyll, but the Calvin cycle occurs in the bundle sheath.
Malate is then decarboxylated and the CO2 is transferred to RUBP of Calvin cycle. In Crassulaceae, the
stomata close during the day, which reduces water loss through transpiration.

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Figure 15 Leaf anatomy and photosynthesis pathway of C4 plants.

The mechanism of CAM plants (Crassulacean Acid Metabolism)

Many succulent plants sequester carbon through a process called crassulacean acid metabolism (CAM).
They differ from C4 plants by the fact that carbon sequestration is not separated in space (mesophyll /
bundle sheath), but over time (day / night).

CO2 fixation on phosphoenolpyruvate (PEP) and the production of oxaloacetate take place at night when
the stomata are open. The oxaloacetate is converted to malate which quickly is stored in the vacuole
overnight as malic acid. During the day, when the stomata are closed, malic acid is included in the vacuole
overnight as malic acid. During the day, when the stomata are closed, malic acid is included in the vacuole
and the CO2 is transferred to RUBP of Calvin cycle. In Crassulaceae, the stomata close during the day,
which reduces water loss through transpiration.

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 Figure 16 Comparison between C4 and CAM photosynthesis.

Figure 17 CAM metabolism

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 References

 Bidlack J.; Jansky S. and Stern K. R. Stern's Introductory Plant Biology. McGraw-Hill
Education. 2017
 Mauseth J.D. Botany: an introduction to Plant Biology. Jones & Bartlett Publishers. 2016
 Evert R.F. and Eichhorn S.E. Raven Biology of Plants, 8th edition. W.H. Freeman/Palgrave
Macmillan. 2013
 Solomon E. P., Berg L. and Martin D. W. Biology. 8th edition. 2008

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