DIVERSITY OF MICROORGANISMS Chlorobi, all of which utilize photochemical reaction centers (a

complex of proteins in which energy from the sun is converted in a

● Microorganisms are ubiquitous. Microbiologists have located
series of electron transfer reactions). Slide #8
them almost everywhere on the planet. Roundworms, for
example, are more abundant animals, native even to
Antarctica. Considering the ubiquity of microorganisms,
finding microorganisms is not hard except for the fact that
they can only be seen under microscopes.
● Bacteria, fungi and other single-celled organisms have been
discovered in ordinary areas (like the bathroom in your
house, for example) as well as in extreme locations (like
hydrothermal vents deep in the ocean).
The Amazing Diversity of Morphologies
● Although we do not base bacterial and archaeal taxonomy
on morphology because of predominance of a few common
shapes, several bacteria and archaea do come in a variety of
morphotypes.

● A New Discovery in One of the Original Eleven:

Zetaproteobacteria
● Novel classes can still be discovered within phyla that have been
known for decades, as evidenced by the discovery of the
● Comparison of the three domains Zetaproteobacteria by Emerson et al. (2007). These curved rods,
cultured from the Loihi Seamount, form “filamentous stalk-like
structures of iron oxyhydroxides” during their growth.

● Aquificales: Some Like It Very Hot!

● Fundamental differences, as well as similarities, occur
among the three domains Eukarya, Archaea, and
Bacteria. These similarities and differences have
helped decipher the relative position of the three
domains to each other in the tree of life. (Slide #5)
Diversity of Bacterial Groups
● Expansion of the Number of Bacterial Phyla
✔ Our knowledge of the diversity of bacteria has made
substantial leaps since the 1980s, from the 11 phyla in
Woese (1987) to the approximately 36 phyla
(Hugenholtz et al.1998; Hugenholtz 2002) to the 52
phyla identified by Rappe and Giovannoni (2003).
● Phototrophs: Critical Ecosystem Players
● Photosynthesis is critical to life on Earth, and many microorganisms
are phototrophic. Five bacterial phyla contain phototrophs:
Firmicutes, Proteobacteria, Chloroflexi, Cyanobacteria, and
● Thermophilic organisms are found not just within the Archaea but
also within the Bacteria. The phylum Aquificae, which branches
deeply within the Bacteria, contains the most thermophilic
bacterial genus, Aquifex, an obligate chemolithoautotrophic
bacterium. As electron donors, Aquifex uses sulfur, hydrogen, or
thiosulfate, and uses either nitrate or oxygen as electron
acceptors.
● Some theories of the origin of life suggest that early life was
thermophilic and used reduced substrates such as hydrogen.
Organisms such as the Aquificae that are thermophilic and utilize
hydrogen may shed light on lifestyles on early Earth.
● Nitrogen-Fixing Bacteria
● Nitrogen-fixing bacteria can participate in obligate or
facultative symbioses with a wide variety of eukaryotic hosts
across the animals, fungi, and plants. The diversity of
nitrogen-fixing bacteria is extensive and spans the
cyanobacteria, four subdivsions of the proteobacteria,
actinobacteria, firmicutes, Chromatiales (purple sulfur

1
 bacteria), Chlorobiales (green sulfur bacteria), and
spirochetes (Kneip et al. 2007). Slide #11
● The cyanobacterial partner in the lichen symbiosis (Section
6.4.2) brings nitrogen-fixing abilities to the partnership, as
well as photosynthetic capabilities. Cyanobacteria, such as
Nostoc spp. that live as symbiotic partners in lichens, have
more heterocysts as symbionts than as free-living bacteria.
● Interestingly, all nitrogen-fixing bacteria use the same
enzymatic reaction, based on the nitrogenase enzyme
complex, in a wide variety of symbiotic relationships
that provide eukaryotes with the key element,
nitrogen. These symbioses in plants are key to our
agricultural success and therefore can have large
economic impacts.
● At least 44 legume species in 12 genera have symbiotic
nitrogen-fixing bacteria (Sawada et al. 2003).
Additionally, nitrogen-fixing bacteria illustrate several
important ecological concepts: a range of obligate to
facultative symbiotic mutualisms across many
eukaryotic groups, nutrient cycling (i.e., nitrogen),
widespread diversity, and the importance of
microorganisms in the ecosystem.
● Epulopiscium: A Case of Extreme Polyploidy
● One of the largest bacteria known, Epulopiscium spp.,
some of the largest bacteria known, occur as
symbionts of surgeonfish and are famous for their size
(>600 μm) and mode of reproduction. This cigar-
shaped bacterium reproduces multiple offspring
intracellularly, a phenomenon that Angert (2005)
suggests evolved from endospore production.
● Many bacteria are small in size in order to increase
their access to environmental nutrients. If your
surface-to-volume ratio is high, then most of your
cytoplasm is always close to the source of the
nutrients, and diffusion is an effective tool for
distribution of needed resources.
● Mendell et al. (2008) suggest that the observed
extreme polyploidy may have evolved as part of the
symbiosis with the surgeonfish; larger Epulopiscium
cells are able to move more efficiently within the gut
to feed and also are able to escape ciliate predation
more effectively.
Discovery of Archaea as a Separate Domain
● In 1977, Carl Woese overturned one of the major dogmas of
biology
● The method Woese used to identify this “third form of life,” which
involved comparing the sequences of a particular molecule
central to cellular function, called ribosomal RNA
● Woese’s experimental discoveries were made in the context of his
search for a deep understanding of the process of evolution.
Archaeal Diversity
Archaea are most ecologically diverse of the three domains
● Psychrophiles- are organisms capable of growth and reproduction
in cold temperatures and are often xerophilic and halophilic as
well.
● Hyperthermophiles - are defined as microorganisms that
optimally grow at temperatures above 80°C (Stetter, 2013) or that
can grow at temperatures above 90°C (Adams and Kelly, 1998).
● Halophiles - are microorganisms that require certain
concentrations of salt to survive, and they are found in both
Eubacterial and Archaeal domains of life.
● Acidophiles or acidophilic - organisms are those that thrive under
highly acidic conditions (usually at pH 2.0 or below).
● Methanogens - are microorganisms that produce methane as a
metabolic byproduct in hypoxic conditions. They are prokaryotic
and belong to the domain Archaea. ... In marine sediments, the
biological production of methane, also termed methanogenesis, is
generally confined to where sulfates are depleted, below the top
layers.
● Archaea are also abundant in moderate habitats. - Open ocean,
soil, and surface of plant roots Surprisingly, the archaeal domain
lacks pathogens.
Archaeal Traits
The Archaea have unique key features, as well as traits shared by other
domains. Distinctive features of archaea, sometimes called “archaeal
signatures,” include:
● Cell membrane lipids
● Cell wall components
● Certain metabolic pathways
● Certain genome features
Archaea Traits
● Archaea domain contains single-celled organisms.
● Archaea are prokaryotic organisms and do not have a membrane-
bound nucleus.
● Lack internal cell organelles
● Archaea reproduce by binary fission
● One circular chromosome
● Use flagella to move around in their environment as do bacteria.
Archaea Lipids
● Are different from those of bacteria and eukaryotes
● Use L-glycerol, not D-glycerol
● Have ether (R–O–R) not ester (R–COO–R) links
● Are branched chains of lipid
o -Made from isoprenoid units
o -No unsaturations in lipids
● Can be more exotic in form
- Macrocyclic diether
- Tetraether – makes a single layer
- Cyclopentane rings
● Differ from Bacteria and Eukarya in having branched chain
hydrocarbons attached to glycerol by ether linkages polar
phospholipids, sulfolipids, glycolipids, and unique lipids are also
found in archaeal membranes
Archaeal Cell Walls and Other Characteristics
Archaea show distinctive versions of the cell wall.
Pseudopeptidoglycan in methanogens
- N-acetyltalosaminuronic acid
2
 - b(1,3) linkages instead of b(1,4) - Methanogens, halophiles, acidophiles, alkalinophiles
Phylum Crenarchaeota
▪ -Are therefore resistant to lysozyme
● Different types of cross-bridges
- Are therefore resistant to penicillin
● Other Archaea possess no cell wall at all.
- -Only an S-layer composed of protein
● Cell envelopes
- varied S layers attached to plasma membrane
- pseudomurein (peptidoglycan-like polymer)
- complex polysaccharides, proteins, or glycoproteins
found in some other species
- only Ignicoccus has outer membrane
● Chromosome - single (closed circular) molecule of double-
stranded DNA (one-third to one-half as much DNA per cell as
found in bacteria such as E. coli)
● Plasmids - these pieces of extrachromosomal DNA may make up
as much as 25-30% of cellular DNA ● hyperthermophiles (hydrothermal vents)

● Endospores - not formed ● most are strict anaerobes

● flagella- very long protein (flagellin) polymers that provide ● some are acidophiles
motility ● many are sulfur-dependent
● for some, used as electron acceptor in anaerobic respiration
● Pili- long thin protein polymers that act as cell "anchors" to
● for some, used as electron source
various surfaces and can assist in attaching archaeal cells to
facilitate DNA transfer from ● Grow throughout the ocean
Archaea Metabolic Pathways ● Abundance varies according to season and increases with depth
● Glucose is catabolized by several variants of the Entner-Doudoroff ● These uncultivated organisms are likely the predominant
(ED) and Embden-Meyerhoff-Parnas (EMP) pathways that rarely crenarchaeotes on Earth.
occur in bacteria.
● Psychrophilic species also grow in sea ice off Antarctica and in the
● The process of methanogenesis is unique to Archaea. marine benthos, or seafloor, sediment.
Archaeal Genomes
Unique features of Archaea ● The name Crenarchaeota means “scalloped archaea.” Are often
irregular in shape All crenarchaeotes synthesize a distinctive
● “Reverse gyrase” of hyperthermophiles tetraether lipid, called crenarchaeol. two best studied are
- Maintains positive supercoils Sulfolobus and Thermoproteus
● Similarities to bacteria
- Circular genome Genus Thermoproteus
- Gene size and density
- Presence of operons (what is an operon?)
● Similarities to eukaryotes ● long thin rod, bent or branched
- Presence of introns (what are introns?) ● thermoacidophiles
- RNA polymerase has TBP and TFIIB
- Presence of histone homologs ● cell walls composed of glycoprotein
Archaeal Taxonomy ● 70–97 °C pH 2.5–6.5
Two phyla based on Bergey’s Manual
● anaerobic metabolism
● lithotrophic on sulfur and hydrogen
● Euryarchaeota
● organotrophic on sugars, amino acids, alcohols, and organic acids
using elemental sulfur as electron acceptorautotrophic using CO
- Shows a wider range of temperature diversity or CO2 as carbon source
- Hyperthermophiles, thermophiles, mesophiles, and
psychrophiles
Genus Sulfolobus

● Crenarchaeota
● irregularly lobed, spherical shaped
● thermoacidophiles
- Shows a greater range of metabolism.
● cell walls contain lipoproteins and carbohydrates
● 70–80°C pH 2–3
● lithotrophic on sulfur using oxygen (usually) or ferric iron as
electron acceptor
● organotrophic on sugars and amino acids

Phylum Euryarchaeota

3

● Consists of many classes, orders, and
families
● Euryarchaeota means “broad-ranging
archaea.”
● Are dominated by methanogens
● All are poisoned by molecular oxygen and
therefore require complete anaerobiosis.
Euryarchaeota: Methanogens
● The methanogens include four classes.
- Thermophiles and mesophiles are found in all.
● They display an astonishing diversity of cell forms.
- Rods (single or filamentous), cocci, and spirals
● The methanogens have rigid cell walls made up of
pseudopeptidoglycan, proteins, or sulfated sugars.
● Filamentous methanogens form chains of large cells.
- Methanosaeta performs key functions in the treatment
of sewage waste.
- Traps bacteria into residual sludge
Anaerobic Habitats for Methanogens
● Methanogens grow in:
- Anaerobic soil of wetlands
- Especially rice paddies
- Landfills
- Digestive tracts of animals
- Termites
- Cattle
- Humans
- Marine benthic sediments
Euryarchaeota: Halophiles
Main inhabitants of high-salt environments are members of the class
Haloarchaea.
● Their photopigments color salterns, which are used for salt
production.
● Most are colored red by bacterioruberin, which protects them
from light.
● Halophilic archaea require at least 1.5M NaCl
Habitats for Haloarchaea- Different kinds of hypersaline habitats support
different species of haloarchaea.
● Thalassic lakes
● Athalassic lakes
● Solar salterns
● Brine pools beneath the ocean
● Alkaline soda lakes
● Antarctic brine lakes
● Underground salt deposits
● Salted foods
Euryarchaeota: Thermophiles
● Thermococcales
- Include Thermococcus and Pyrococcus
- Most are anaerobes. Use sulfur as a terminal electron
acceptor
● Archaeoglobus
o -Archeoglobales fulgidus
o -Reduces sulfate to sulfide
o -Runs methanogenesis in reverse
Euryarchaeota: Acidophiles
● Thermoplasmatales
● Include acidophiles (as well as thermophiles)
● Have no cell walls and no S-layers
● Thermoplasma acidophilum
● Metabolism is based on S0 respiration of organic molecules.
● Ferroplasma species
● Oxidize sulfur to sulfuric acid
● Generate pH values below pH 0
Protist Diversity
PROTISTS
 Protists represent a diverse group of unicellular eukaryotic
organisms, or multicellular eukaryotes that lack specialized
tissues. They are widespread, but most require liquid water.
 Protist is the informal name of the group of mostly unicellular
eukaryotes, but there are some colonial and multicellular species.
 Formerly classed in the Protista (or Protoctista) kingdom, protists
have now been dispersed within eukaryotic classification and the
term protist is an informal group name. Protozoa, which most
people think of as the animal-like protists, are heterotrophic,
motile, single-celled organisms.
Nutritional Methods of Protists
 PHOTOAUTOTROPH
o Protists that contain chloroplasts.
● HETEROTROPH
o Protists that absorb organic molecules of an aerobic
prokaryote.
● MIXOTROPH
o Protitsts that combine photosynthesis and
heterotophic nutrition
4

PHYLOGENETIC TREE OF PROTIST
SUPERGROUPS OF PROTISTS
● EXCAVATA
● SAR
● ARCHEAPLASTIDA
● UNIKONTA
EXCAVATA
● Some members of this supergroup have an “excavated” groove
on one side of the cell body.
● Two major clades (the parabasalids and diplomonads) have
highly reduced mitochondria; members of a third clade (the
euglenozoans) have flagella that differ in structure from those
of other organisms.
● Excavates include parasites such as Giardia, as well as many
predatory and photosynthetic species.
Diplomonads
● Diplomonads have reduced mitochondria called mitosomes.
These organelles lack functional electron transport chains and
hence cannot use oxygen to help extract energy from
carbohydrates and other organic molecules.
● Structurally, diplomonads have two equal-sized nuclei and
multiple flagella. Recall that eukaryotic flagella are extensions
of the cytoplasm, consisting of bundles of microtubules covered
by the cell’s plasma membrane.
Parabasalids
● Parabasalids also have reduced mitochondria; called
hydrogenosomes, these organelles generate some energy
anaerobically, releasing hydrogen gas as a by-product.
● The best-known parabasalid is Trichomonas vaginalis, a
sexually transmitted parasite that infects some 5 million people
each year. T. vaginalis travels along the mucus-coated lining of
the human reproductive and urinary tracts by moving its flagella
and by undulating part of its plasma membrane.
Euglenozoans
● Protists called euglenozoans belong to a diverse clade that
includes predatory heterotrophs, photosynthetic autotrophs,
mixotrophs, and parasites. The main morphological feature that
distinguishes protists in this clade is the presence of a rod with
either a spiral or a crystalline structure inside each of their
flagella.
Kinetoplastids
 Protists called kinetoplastids have a single, large
mitochondrion that contains an organized mass of
DNA called a kinetoplast. These protists include
species that feed on prokaryotes in freshwater,
marine, and moist terrestrial ecosystems, as well as
species that parasitize animals, plants, and other
protists.
 For example, kinetoplastids in the genus
Trypanosoma infect humans and cause sleeping
sickness, a neurological disease that is invariably
fatal if not treated. The infection occurs via the bite
of a vector (carrier) organism, the African tsetse fly.
Trypanosomes also cause Chaga’s disease, which is transmitted by
bloodsucking insects and can lead to congestive heart failure.
Euglenids
 A euglenid has a pocket at one end of the cell from
which one or two flagella emerge. Some euglenids
are mixotrophs: They perform photosynthesis when
sunlight is available, but when it is not, they can
become heterotrophic, absorbing organic nutrients
from their environment. Many other euglenids
engulf prey by phagocytosis.
SAR
● This supergroup contains (and is named after) three large and
very diverse clades: Stramenopila, Alveolata, and Rhizaria.
● SAR was proposed recently based on whole-genome DNA
sequence analyses. These studies have found that three major
clades of protists— the stramenopiles, alveolates, and
rhizarians—form a monophyletic supergroup. This supergroup
contains a large, extremely diverse collection of protists.
STRAMENOPHILES
● Stramenopiles include some of the most important
photosynthetic organisms on Earth.
● One major subgroup of SAR, the stramenopiles, includes some
of the most important photosynthetic organisms on the planet.
Their name (from the Latin stramen, straw, and pilos, hair)
refers to their characteristic flagellum, which has numerous
fine, hairlike projections.
5
Diatoms
 A key group of photosynthetic protists,
diatoms are unicellular algae that have a unique
glass-like wall made of silicon dioxide embedded in
an organic matrix.
 With an estimated 100,000 living species,
diatoms are a highly diverse group of protists. They
are among the most abundant photosynthetic
organisms both in the
ocean and in lakes: One bucket of water scooped
from the surface of the sea may contain millions of
these microscopic algae.
Golden Algae
 The characteristic color of golden algae results from
their yellow and brown carotenoids. The cells of
golden algae are typically biflagellated, with both
flagella attached near one end of the cell. Most
species are unicellular, but some are colonial.
 Many golden algae are components of freshwater
and marine plankton, communities of mostly
microscopic organisms that drift in currents near the
water’s surface. While all golden algae are
photosynthetic, some species are mixotrophic,
Brown Algae
 The largest and most complex algae are brown
algae. All are multicellular, and most are marine.
Brown algae are especially common along
temperate coasts that have cold-water currents.
They owe their characteristic brown or olive color to
the carotenoids in their plastids.
 Moreover, morphological and DNA data show that
these similarities evolved independently in the algal
and plant lineages and are thus analogous, not
homologous.
Alveolates
● Alveolates also include
photosynthetic species, as well as important
pathogens, such as Plasmodium, which
causes malaria. According to one current
hypothesis, stramenopiles and alveolates
originated by secondary endosymbiosis
when a heterotrophic protist engulfed a red alga.
● Members of the next subgroup of SAR, the alveolates, have
membrane-enclosed sacs (alveoli) just under the plasma
membrane.
● Alveolates are abundant in many habitats and include a wide
range of photosynthetic and heterotrophic protists.
Dinoflagellates
The cells of many dinoflagellates are reinforced by
cellulose plates. Two flagella located in grooves in this
“armor” make dinoflagellates (from the Greek dinos,
whirling) spin as they move through the waters of their
marine and freshwater communities.
Periods of explosive population growth (blooms) in
dinoflagellates sometimes cause a phenomenon called
“red tide
Apicomplexans
 Nearly all apicomplexans are parasites of animals—and virtually
all animal species examined so far are attacked by these
parasites. The parasites spread through their host as tiny
infectious cells called sporozoites.
 Most apicomplexans have intricate life cycles with both sexual
and asexual stages. Those life cycles often require two or more
host species for completion. For example,
Plasmodium, the parasite that causes malaria, lives
in both mosquitoes and humans.
Ciliates
 The ciliates are a large and varied group of protists
named for their use of cilia to move and feed. Most ciliates are
predators, typically of bacteria or of other protists.
 A distinctive feature of ciliates is the presence of two
types of nuclei: tiny micronuclei and large macronuclei. A cell has
one or more nuclei of each type.
Rhizarians
 The rhizarian subgroup of SAR includes many species of amoebas,
most of which have pseudopodia that are threadlike in shape.
Pseudopodia are extensions that can bulge from any portion of
the cell; they are used in movement and in the capture of prey.
 Many species in this group are amoebas, protists that move and
feed by means of pseudopodia, extensions that may bulge from
almost anywhere on the cell surface. As it moves, an amoeba
extends a pseudopodium and anchors the tip; more cytoplasm
then streams into the pseudopodium.
Radiolarians
 The protists called radiolarians have delicate, intricately
symmetrical internal skeletons that are generally made of
silica. The pseudopodia of these mostly marine protists
radiate from the central body and are reinforced by bundles
of microtubules.
 The microtubules are covered by a thin layer of cytoplasm, which
engulfs smaller microorganisms that become attached to the
pseudopodia.
Forams
 The protists called foraminiferans (from the Latin foramen, little
hole, and ferre, to bear), or forams, are named for their porous
shells, called tests.
 Foram tests consist of a single piece of organic
material that typically is hardened with calcium
carbonate. The pseudopodia that extend through the
pores function in swimming, test formation, and
feeding.
Cercozoans- Cercozoans are a large group of amoeboid
and flagellated protists that feed using threadlike
pseudopodia. Cercozoan protists are common inhabitants of marine,
freshwater, and soil ecosystems.
 Paulinella chromatophora, is an autotroph, deriving its energy
from light and its carbon from CO2. Paulinella appears to
represent an intriguing additional evolutionary example of a
eukaryotic lineage that obtained its photosynthetic apparatus
directly from a cyanobacterium.
Archaeaplastida - This supergroup of eukaryotes includes red algae and
green algae, along with plants. Red algae and green algae include unicellular
species, colonial species, and multicellular species (including the green alga
Volvox).
 Many of the large algae known informally as “seaweeds” are
multicellular red or green algae.
 Protists in Archaeplastida include key photosynthetic species that
form the base of the food web in many aquatic communities.
 Volvox, a multicellular freshwater green alga. This
alga has two types of differentiated cells, and so it is
considered multicellular rather than colonial. It resembles a
hollow ball whose wall is composed of hundreds of
biflagellated cells (see inset LM) embedded in a gelatinous
extracellular matrix; if isolated, these cells cannot reproduce.
Red Algae - Many of the 6,000 known species of red algae (rhodophytes,
from the Greek rhodos, red) are reddish, owing to the photosynthetic
pigment phycoerythrin, which masks the green of chlorophyll.
 Red algae reproduce sexually and have diverse life cycles in which
alternation of generations is common. However, unlike other
algae, red algae do not have flagellated gametes, so they depend
on water currents to bring gametes together for fertilization
6
7
Green Algae
 The grass-green chloroplasts of green algae have a structure and
pigment composition much like the chloroplasts of plants. Green
algae can be divided into two main groups, the charophytes and
the chlorophytes. The charophytes include the algae most closely
related to plants.
 The second group, the chlorophytes (from the Greek chloros,
green), includes more than 7,000 species. Most live in fresh
water, but there are also many marine and some terrestrial
species. The simplest chlorophytes are unicellular organisms such
as Chlamydomonas, which resemble gametes of more complex
chlorophytes.
 Zygnema, a common pond alga. This filamentous charophyte
features two star- shaped chloroplasts in each cell.
 Ulva, or sea lettuce. This multicellular, edible chlorophyte has
differentiated structures, such as its leaflike blades and a rootlike
holdfast that anchors the alga.
Caulerpa, an intertidal chlorophyte. The branched filaments lack crosswalls
and thus are multinucleate. In effect, the body of this alga is one huge”
supercell.”
Unikonta - This supergroup of eukaryotes includes amoebas that have lobe-
or tube-shaped pseudopodia, as well as animals, fungi, and non-amoeba
protists that are closely related to animals or fungi.
 According to one current hypothesis, the unikonts were the first
eukaryotic supergroup to diverge from all other eukaryotes;
however, this hypothesis has yet to be widely accepted.
Amoebozoans - The amoebozoan clade includes many species of amoebas
that have lobe- or tube-shaped pseudopodia rather than the threadlike
pseudopodia found in rhizarians. Amoebozoans include slime molds,
tubulinids, and entamoebas.
Slime Molds - Slime molds, or mycetozoans (from the Latin, meaning “fungus
animals”), once were thought to be fungi because, like fungi, they produce
fruiting bodies that aid in spore dispersal.
Algal Diversity
Algae
 Algae perform oxygenic photosynthesis, contain
chlorophyll, and are eukaryotes. It is estimated that 50%
of the oxygen produced in the world today is produced by
oxygenic phytoplankton, of which the algae are a major
part.
 One scientist estimates that the oxygen in one out of
every five breaths that a human draws is from one
particular alga, Prochlorococcus, which is very abundant in the
oceans.
 Two major groups are included within the algae: the red algae
(Rhodophyta) and the green algae (Chlorophyta).
 The green algae are most often found in freshwater habitats, but
are occasionally found in soil that is moist, in marine habitats, or
as part of some lichens.
 The bulk of red algae are marine, but some are found in
freshwater and terrestrial habitats. In contrast to green algae, the
red algae lack chlorophyll b, but do contain chlorophyll a and
phycobiliproteins (which green algae lack)
Fungal Diversity
Fungi - The number of fungal species is estimated to be > 1.5 million--of
which 75,000 have been described.
 Fungi decompose and recycle organic matter, breaking down
lignocellulose and other recalcitrant compounds.
 Wainright et. al (1993) suggested that fungi are more closely
related to animals than to plants.
What defines fungi as a group?
 Their eukaryotic nature, including a membrane-bound nucleus
and cytoplasmic organelles, sterol-containing membranes, 80S
ribosomes and cytoplasmic streaming.
 Heterotrophic metabolism: enzymes are secreted from hyphal
tips to break down complex organic matter that is then absorbed
from the environment through the cell wall and membrane.
 Growth as filaments, which increase in length at their tips, as
single-celled yeasts, or as both.
 Chitin and glucan containing cell walls.
 Haploid genome in many fungi.
 Asexual and sexual reproduction and the production of spores.
Phylogenetic Tree of Fungi
CHYTRIDS
 The fungi classified in the phylum
Chytridiomycota, called chytrids, are ubiquitous in
lakes and soil, and as described in several recent
metagenomic studies, more than 20 new clades of
chytrids have been found in hydrothermal vent
and other marine communities.
 Molecular evidence indicates that some
chytrid lineages diverged early in fungal evolution.
The fact that chytrids are unique among fungi in
having flagellated spores, called zoospores,
supports this hypothesis
 Chytrids, such as Batrachochytrium
dendrobatidis, have been suggested to be the
cause of the rapid decline of many amphibians
(Rodder et al. 2008)
ZYGOMYCETES
 There are approximately 1,000 known
species of zygomycetes, fungi in the phylum
Zygomycota. This diverse phylum includes
species of fast- growing molds responsible for
causing foods such as bread, peaches,
strawberries, and sweet potatoes to rot during
storage.
 Pilobolus aiming its sporangia. This
zygomycete decomposes animal dung. Its
spore- bearing hyphae bend toward light, where there are likely
to be openings in the vegetation through which spores may reach
fresh grass.
GLOMEROMYCETES
 The glomeromycetes, fungi assigned to the phylum
Glomeromycota, were formerly thought to be zygomycetes. The
glomeromycetes are an ecologically significant group in that
nearly all of them form arbuscular mycorrhizae.
 Arbuscular mycorrhizae. Most glomeromycetes form arbuscular
mycorrhizae with plant roots, supplying minerals and other
nutrients to the roots. This SEM depicts the branched hyphae—
an arbuscule—of Glomus mosseae bulging into a root cell by
pushing in the membrane (the root has been treated to remove
the cytoplasm).
ASCOMYCETES
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 Mycologists have described 65,000 species of ascomycetes, fungi

in the phylum Ascomycota, from a wide variety of marine,
freshwater, and terrestrial habitats. The defining feature of
ascomycetes is the production of spores (called ascospores) in
saclike asci (singular, ascus); thus, they are commonly called sac
fungi.
 Tuber melanosporum is a truffle species that forms
ectomycorrhizae with trees. The ascocarp grows underground.

BASIDIOMYCETES
 About 30,000 species, including mushrooms, puffballs, and shelf
fungi, are called basidiomycetes and are classified in the phylum
Basidiomycota. The club-like shape of the basidium also gives rise
to the common name club fungus.

Viral Diversity
Virus
 Viruses can be defined as obligate, intracellular parasites that
utilize the host cell machinery to manufacture proteins in order
to replicate. They are usually classified according to their nucleic
acid content, which can be double- or single-stranded DNA or
RNA, but not both, and by morphotype.
 Viruses can be lytic, resulting in lysis of the host cell; lysogenic,
where the viral genome is incorporated into the host genome,
creating a prophage; or pseudolysogenic, a less active lytic state
in which a nutrient-limited host cell still grows and divides.