MICROBES OVERVIEW
DESCRIBE, REVIEW, DISCUSS, COMPARE
and IDENTIFY group of microbes
i.e. bacteria, fungi and virus.
INTRODUCTION
Taxonomy is the science of the classification
of organisms, with the goal of showing
relationships among organisms.
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Taxonomy also provides a means of
identifying organisms.
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THE STUDY OF PHYLOGENETIC RELATIONSHIPS
1. Phylogeny is the evolutionary history of a group of
organisms.
2. The taxonomic hierarchy shows evolutionary, or
phylogenetic, relationships among organisms.
3. Bacteria were separated into the Kingdom Prokaryotae
in 1968.
4. Living organisms were divided into five kingdoms in
1969.
HOW WOULD YOU CLASSIFY ?
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Taxanomy is the science of classifying microbes into
different groups based on their phenotype or genotype
characters.
Types of classification:
natural (introduced by Carolus Linnaeus reflecting
biological nature of an organism);
phenetic (based on similarities of biological and
morphological characters);
phylogenetic (considers differences and similarities of
evolutionary processess;
genotype (comparision of genetic similarity between
organisms using newer molecular techniques.)
THE THREE DOMAINS
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Living organisms are currently classified into three
domains. A domain can be divided into kingdoms.
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In this system, plants, animals, fungi, and protists
belong to the Domain Eukarya.
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Bacteria (with peptidoglycan) form a second domain.
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Archaea (with unusual cell walls) are placed in the
Domain Archaea.
A PHYLOGENETIC HIERARCHY
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Organisms are grouped into taxa according to
phylogenetic relationships (from a common
ancestor).
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Some of the information for eukaryotic
relationships is obtained from the fossil record.
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Prokaryotic relationships are determined by
rRNA sequencing.
CLASSIFICATION OF ORGANISMS
SCIENTIFIC NOMENCLATURE
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According to scientific nomenclature, each organism is
assigned two names, or a binomial: a genus and a specific
epithet, or species.
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Rules for the assignment of names to bacteria are
established by the International Committee on Systematic
Bacteriology.
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Rules for naming fungi and algae are published in the
International Code of Botanical Nomenclature.
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Rules for naming protozoa are found in the International
Code of Zoological Nomenclature.
THE TAXONOMIC HIERARCHY
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A eukaryotic species is a group of organisms
that interbreeds with each other but does not
breed with individuals of another species.
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Similar species are grouped into a genus;
similar genera are grouped into a family;
families, into an order; orders, into a class;
classes, into a phylum; phyla, into a kingdom;
and kingdoms, into a domain.
CLASSIFICATION OF PROKARYOTES
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Bergey’s Manual of Systematic Bacteriology is the standard
reference on bacterial classification.
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Prokaryotes are divided into two domain: Bacteria and Archaea.
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The classification is based on similarities in nucleotides
sequence.
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A prokaryotic species is defined simply as a population of cells
with similar characteristics
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A group of bacteria derived from a single cell is called a strain.
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Closely related strains constitute a bacterial species.
CLASSIFICATION OF EUKARYOTES
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Eukaryotic organisms may be classified into the Kingdom
Fungi, Plantae, or Animalia.
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Protists are mostly unicellular organisms; these organisms
are currently being assigned to kingdoms.
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Fungi are absorptive chemoheterotrophs that develop from
spores.
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Multicellular photoautotrophs are placed in the Kingdom
Plantae.
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Multicellular ingestive heterotrophs are classified as
Animalia.
CLASSIFICATION OF VIRUSES
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Viruses are not classified as part of any of three
domain.
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Viruses are not placed in a kingdom. They are not
composed of cells and cannot grow without a host
cell.
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A viral species is a population of viruses with
similar characteristics that occupies a particular
ecological niche.
THE PROKARYOTES:
DOMAINS BACTERIA AND
ARCHAEA
INTRODUCTION
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Bergey’s Manual categorizes bacteria into taxa
based on rRNA sequences.
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Bergey’s Manual lists identifying characteristics
such as Gram stain reaction, cellular
morphology, oxygen requirements, and
nutritional properties.
PROKARYOTIC GROUPS
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Prokaryotic organisms are classified into two
domains: Archaea and Bacteria.
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Both domains consist of prokaryotic cells.
DOMAIN BACTERIA
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Bacteria are essential to life on Earth.
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We should realize that without bacteria, much
of life as we know it would not be possible.
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In fact, all organisms made up of eukaryotic
cells probably evolved from bacterialike
organisms, which were some of the earlist
forms of life.
THE PROTEOBACTERIA
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Members of the phylum Proteobacteria are gram-negative.
Alphaproteobacteria includes nitrogen-fixing bacteria,
chemoautotrophs, and chemoheterotrophs.
The betaproteobacteria include chemoautotrophs and
chemoheterotrophs.
Pseudomonadales, Legionellales, Vibrionales,
Enterobacteriales, and Pasteurellales are classified as
gammaproteobacteria.
Purple and green photosynthetic bacteria are
photoautotrophs that use light energy and CO2 and do not
produce O2.
Myxococcus and Bdellovibrio in the deltaproteobacteria prey
on other bacteria.
Epsilonproteobacteria include Campylobacter and
Helicobacter.
THE NONPROTEOBACTERIA, GRAM-NEGATIVE
BACTERIA
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Several phyla of gram-negative bacteria are not
related phylogenetically to the Proteobacteria.
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Cyanobacteria are photoautotrophs that use
light energy and CO2 and do produce O2.
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Chemoheterotrophic examples are Chlamydia,
spirochetes, Bacteroides, and Fusobacterium.
THE GRAM-POSITIVE BACTERIA
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In Bergey’s Manual, gram-positive bacteria are
divided into those that have low G + C ratio and
those that have high G + C ratio.
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Low G + C gram-positive bacteria include common
soil bacteria, the lactic acid bacteria, and several
human pathogens.
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High G + C gram-positive bacteria include
mycobacteria, corynebacteria, and actinomycetes.
DOMAIN ARCHAEA
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Extreme halophiles, extreme thermophiles, and methanogens are
included in the archaea.
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Their cell walls lacked the peptidoglycan common to most bacteria.
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Most archaea are conventional morphology, that is, rods, cocci and
helixes, but some are of very unusual morphology
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Some are gram-positive, others gram-negative; some may divide by
binary fission, other by fragmentation or budding; a few lack cell
walls
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Organisms in this domain are physiologically diverse as well, ranging
from aerobic, to facultative anaerobic, to strictly anaerobic.
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Nutritionally, they include chemoautotrophs, photoautotrophs, and
chemoheterotrophs.
MICROBIAL DIVERSITY
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Few of the total number of different
prokaryotes have been isolated and identified.
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PCR can be used to uncover the presence of
bacteria that can’t be cultured in the
laboratory.
THE EUKARYOTES:
FUNGI, ALGAE, PROTOZOA,
AND HELMINTHS
FUNGI
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Mycology is the study of fungi.
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The number of serious fungal infections is
increasing.
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Fungi are aerobic or facultatively anaerobic
chemoheterotrophs.
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Most fungi are decomposers, and a few are
parasites of plants and animals.
CHARACTERISTICS OF FUNGI
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A fungal thallus consists of filaments of cells called hyphae; a
mass of hyphae is called a mycelium.
Yeasts are unicellular fungi. To reproduce, fission yeasts divide
symmetrically, whereas budding yeasts divide asymmetrically.
Buds that do not separate from the mother cell form
pseudohyphae.
Pathogenic dimorphic fungi are yeastlike at 37°C and moldlike
at 25°C.
Fungi are classified according to rRNA.
These spores can be produced asexually: sporangiospores and
conidia.
Sexual spores are usually produced in response to special
circumstances, often changes in the environment.
Fungi can grow in acidic, low-moisture, aerobic environments.
They are able to metabolize complex carbohydrates.
MEDICALLY IMPORTANT PHYLA OF FUNGI
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The Zygomycota have coenocytic hyphae and produce
sporangiospores and zygospores.
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The Ascomycota have septate hyphae and produce
ascospores and frequently conidia.
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Basidiomycota have septate hyphae and produce
basidiospores; some produce conidiospores.
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Teleomorphic fungi produce sexual and asexual spores;
anamorphic fungi produce asexual spores only.
FUNGAL DISEASES
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Systemic mycoses are fungal infections deep within the body
that affect many tissues and organs.
Subcutaneous mycoses are fungal infections beneath the
skin.
Cutaneous mycoses affect keratin-containing tissues such as
hair, nails, and skin.
Superficial mycoses are localized on hair shafts and
superficial skin cells.
Opportunistic mycoses are caused by normal microbiota or
fungi that are not usually pathogenic.
Opportunistic mycoses include Pneumocystis pneumonia;
aspergillosis, caused by Aspergillus; and candidiasis, caused
by Candida.
Opportunistic mycoses can infect any tissues. However, they
are usually systemic.
ECONOMIC EFFECTS OF FUNGI
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Saccharomyces and Trichoderma are used in the
production of foods.
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Fungi are used for the biological control of pests.
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Mold spoilage of fruits, grains, and vegetables is
more common than bacterial spoilage of these
products.
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Many fungi cause diseases in plants.
LICHENS
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A lichen is a mutualistic combination of an alga (or a
cyanobacterium) and a fungus.
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The alga photosynthesizes, providing carbohydrates for the
lichen; the fungus provides a holdfast.
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Lichens colonize habitats that are unsuitable for either the
alga or the fungus alone.
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Lichens may be classified on the basis of morphology as
crustose, foliose, or fruticose.
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Lichens are used for their pigments and as air quality
indicators.
ALGAE
Algae are unicellular, filamentous, or
multicellular (thallic).
 Most algae live in aquatic environments.
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CHARACTERISTICS OF ALGAE
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Algae are eukaryotic; most are photoautotrophs.
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The thallus (body) of multicellular algae usually consists of a
stipe, a holdfast, and blades.
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Algae reproduce asexually by cell division and fragmentation.
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Many algae reproduce sexually.
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Photoautotrophic algae produce oxygen.
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Algae are classified according to their structures and
pigments.
SELECTED PHYLA OF ALGAE
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Brown algae (kelp) may be harvested for algin.
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Red algae grow deeper in the ocean than other algae because their
red pigments can absorb the blue light that penetrates to deeper
levels.
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Green algae have cellulose and chlorophyll a and b and store starch.
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Diatoms are unicellular and have pectin and silica cell walls; some
produce a neurotoxin.
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Dinoflagellates produce neurotoxins that cause paralytic shellfish
poisoning and ciguatera.
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The oomycotes are heterotrophic; they include decomposers and
plant parasites.
ROLES OF ALGAE IN NATURE
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Algae are the primary producers in aquatic food chains.
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Planktonic algae produce most of the molecular oxygen
in the Earth’s atmosphere.
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Petroleum is the fossil remains of planktonic algae.
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Unicellular algae are symbionts in such animals as
Tridacna.
PROTOZOA
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Protozoa are unicellular, eukaryotic
chemoheterotrophs.
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Protozoa are found in soil and water and as
normal microbiota in animals.
CHARACTERISTICS OF PROTOZOA
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The vegetative form is called a trophozoite.
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Asexual reproduction is by fission, budding, or schizogony.
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Sexual reproduction is by conjugation.
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During ciliate conjugation, two haploid nuclei fuse to produce
a zygote.
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Some protozoa can produce a cyst that provides protection
during adverse environmental conditions.
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Protozoa have complex cells with a pellicle, a cytostome, and
an anal pore.
MEDICALLY IMPORTANT PHYLA OF PROTOZOA
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Archaezoa lack mitochondria and have flagella; they include
Trichomonas and Giardia.
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Microsporidia lack mitochondria and microtubules; microsporans
cause diarrhea in AIDS patients.
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Amoebozoa are amoeba; they include Entamoeba and
Acanthamoeba.
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Apicomplexa have apical organelles for penetrating host tissue; they
include Plasmodium and Cryptosporidium.
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Ciliophora move by means of cilia; Balantidium coli is the human
parasitic ciliate.
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Euglenozoa move by means of flagella and lack sexual reproduction;
they include Trypanosoma.
SLIME MOLDS
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Cellular slime molds resemble amoebas and
ingest bacteria by phagocytosis.
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Plasmodial slime molds consist of a
multinucleated mass of protoplasm that
engulfs organic debris and bacteria as it
moves.
HELMINTHS
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Parasitic flatworms belong to the Phylum
Platyhelminthes.
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Parasitic roundworms belong to the Phylum
Nematoda.
CHARACTERISTICS OF HELMINTHS
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Helminths are multicellular animals; a few are parasites
of humans.
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The anatomy and life cycle of parasitic helminths are
modified for parasitism.
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The adult stage of a parasitic helminth is found in the
definitive host.
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Each larval stage of a parasitic helminth requires an
intermediate host.
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Helminths can be monoecious or dioecious.
PLATYHELMINTHS
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Flatworms are dorsoventrally flattened animals; parasitic flatworms may
lack a digestive system.
Adult trematodes, or flukes, have an oral and ventral sucker with which they
attach to host tissue.
Eggs of trematodes hatch into free-swimming miracidia that enter the first
intermediate host; two generations of rediae develop in the first
intermediate host; the rediae become cercariae that bore out of the first
intermediate host and penetrate the second intermediate host; cercariae
encyst as metacercariae in the second intermediate host; after they are
ingested by the definitive host, the metacercariae develop into adults.
A cestode, or tapeworm, consists of a scolex (head) and proglottids.
Humans serve as the definitive host for the beef tapeworm, and cattle are
the intermediate host.
Humans serve as the definitive host and can be an intermediate host for the
pork tapeworm.
Humans serve as the intermediate host for Echinococcus granulosus; the
definitive hosts are dogs, wolves, and foxes.
NEMATODES
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Roundworms have a complete digestive system.
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The nematodes that infect humans with their eggs
are Enterobius vermicularis (pinworm) and Ascaris
lumbricoides.
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The nematodes that infect humans with their
larvae are Necator americanus, Trichinella spiralis,
and anisakine worms.
VIRUSES, VIROIDS, AND PRIONS
GENERAL CHARACTERISTICS OF VIRUSES
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Depending on one’s viewpoint, viruses may be regarded
as exceptionally complex aggregations of nonliving
chemicals or as exceptionally simple living microbes.
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Viruses contain a single type of nucleic acid (DNA or
RNA) and a protein coat, sometimes enclosed by an
envelope composed of lipids, proteins, and
carbohydrates.
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Viruses are obligatory intracellular parasites. They
multiply by using the host cell’s synthesizing machinery
to cause the synthesis of specialized elements that can
transfer the viral nucleic acid to other cells.
HOST RANGE
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Host range refers to the spectrum of host cells
in which a virus can multiply.
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Most viruses infect only specific types of cells
in one host species.
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Host range is determined by the specific
attachment site on the host cell’s surface and
the availability of host cellular factors.
VIRAL SIZE
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Viral size is ascertained by electron microscopy.
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Viruses range from 20 to 1000 nm in length.
VIRAL STRUCTURE
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A virion is a complete, fully developed viral
particle composed of nucleic acid surrounded
by a coat.
NUCLEIC ACID
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Viruses contain either DNA or RNA, never both,
and the nucleic acid may be single- or doublestranded, linear or circular, or divided into
several separate molecules.
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The proportion of nucleic acid in relation to
protein in viruses ranges from about 1% to
about 50%.
CAPSID AND ENVELOPE
The protein coat surrounding the nucleic acid of
a virus is called the capsid.
 The capsid is composed of subunits,
capsomeres, which can be a single type of
protein or several types.
 The capsid of some viruses is enclosed by an
envelope consisting of lipids, proteins, and
carbohydrates.
 Some envelopes are covered with
carbohydrate-protein complexes called spikes.
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GENERAL MORPHOLOGY
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Helical viruses (for example, Ebola virus) resemble long rods,
and their capsids are hollow cylinders surrounding the
nucleic acid.
Polyhedral viruses (for example, adenovirus) are many-sided.
Usually the capsid is an icosahedron.
Enveloped viruses are covered by an envelope and are
roughly spherical but highly pleomorphic. There are also
enveloped helical viruses (for example, influenza virus) and
enveloped polyhedral viruses (for example, Simplexvirus).
Complex viruses have complex structures. For example,
many bacteriophages have a polyhedral capsid with a helical
tail attached.
TAXONOMY OF VIRUSES
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Classification of viruses is based on type of
nucleic acid, strategy for replication, and
morphology.
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Virus family names end in -viridae; genus
names end in -virus.
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A viral species is a group of viruses sharing the
same genetic information and ecological niche.
ISOLATION, CULTIVATION, AND IDENTIFICATION
OF VIRUSES
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Viruses must be grown in living cells.
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The easiest viruses to grow are bacteriophages.
GROWING BACTERIOPHAGES IN THE
LABORATORY
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The plaque method mixes bacteriophages with
host bacteria and nutrient agar.
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After several viral multiplication cycles, the
bacteria in the area surrounding the original virus
are destroyed; the area of lysis is called a plaque.
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Each plaque originates with a single viral particle;
the concentration of viruses is given as plaqueforming units.
GROWING ANIMAL VIRUSES IN THE
LABORATORY
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Cultivation of some animal viruses requires whole animals.
Simian AIDS and feline AIDS provide models for studying
human AIDS.
Some animal viruses can be cultivated in embryonated eggs.
Cell cultures are cells growing in culture media in the
laboratory.
Primary cell lines and embryonic diploid cell lines grow for a
short time in vitro.
Continuous cell lines can be maintained in vitro indefinitely.
Viral growth can cause cytopathic effects in the cell culture.
VIRAL IDENTIFICATION
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Serological tests are used most often to identify
viruses.
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Viruses may be identified by RFLPs and PCR.
VIRAL MULTIPLICATION
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Viruses do not contain enzymes for energy
production or protein synthesis.
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For a virus to multiply, it must invade a host cell
and direct the host’s metabolic machinery to
produce viral enzymes and components.
MULTIPLICATION OF BACTERIOPHAGES
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During the lytic cycle, a phage causes the lysis and death of a host cell.
Some viruses can either cause lysis or have their DNA incorporated as a prophage into
the DNA of the host cell. The latter situation is called lysogeny.
During the attachment phase of the lytic cycle, sites on the phage’s tail fibers attach to
complementary receptor sites on the bacterial cell.
In penetration, phage lysozyme opens a portion of the bacterial cell wall, the tail sheath
contracts to force the tail core through the cell wall, and phage DNA enters the bacterial
cell. The capsid remains outside.
In biosynthesis, transcription of phage DNA produces mRNA coding for proteins necessary
for phage multiplication. Phage DNA is replicated, and capsid proteins are produced.
During the eclipse period, separate phage DNA and protein can be found.
During maturation, phage DNA and capsids are assembled into complete viruses.
During release, phage lysozyme breaks down the bacterial cell wall, and the new phages
are released.
During the lysogenic cycle, prophage genes are regulated by a repressor coded for by the
prophage. The prophage is replicated each time the cell divides.
Exposure to certain mutagens can lead to excision of the prophage and initiation of the
lytic cycle.
Because of lysogeny, lysogenic cells become immune to reinfection with the same phage
and may undergo phage conversion.
A lysogenic phage can transfer bacterial genes from one cell to another through
transduction. Any genes can be transferred in generalized transduction, and specific
genes can be transferred in specialized transduction.
MULTIPLICATION OF ANIMAL VIRUSES
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Animal viruses attach to the plasma membrane of the host cell.
Entry occurs by endocytosis or fusion.
Animal viruses are uncoated by viral or host cell enzymes.
The DNA of most DNA viruses is released into the nucleus of the host cell.
Transcription of viral DNA and translation produce viral DNA and, later, capsid
proteins. Capsid proteins are synthesized in the cytoplasm of the host cell.
DNA viruses include members of the families Adenoviridae, Poxviridae,
Herpesviridae, Papovaviridae, and Hepadnaviridae.
Multiplication of RNA viruses occurs in the cytoplasm of the host cell. RNAdependent RNA polymerase synthesizes a double-stranded RNA.
Picornaviridae + strand RNA acts as mRNA and directs the synthesis of RNAdependent RNA polymerase.
Togaviridae + strand RNA acts as a template for RNA-dependent RNA polymerase,
and mRNA is transcribed from a new – RNA strand.
Rhabdoviridae – strand RNA is a template for viral RNA-dependent RNA polymerase,
which transcribes mRNA.
Reoviridae are digested in host cell cytoplasm to release mRNA for viral biosynthesis.
Retroviridae reverse transcriptase (RNA-dependent DNA polymerase) transcribes
DNA from RNA.
After maturation, viruses are released. One method of release (and envelope
formation) is budding. nonenveloped viruses are released through ruptures in the
host cell membrane. *Animation: Viral Replication. The Microbiology Place.
VIRUSES AND CANCER
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The earliest relationship between cancer and
viruses was demonstrated in the early 1900s,
when chicken leukemia and chicken sarcoma
were transferred to healthy animals by cell-free
filtrates.
THE TRANSFORMATION OF NORMAL CELLS INTO
TUMOR CELLS
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When activated, oncogenes transform normal cells into cancerous
cells.
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Viruses capable of producing tumors are called oncogenic viruses.
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Several DNA viruses and retroviruses are oncogenic.
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The genetic material of oncogenic viruses becomes integrated into
the host cell’s DNA.
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Transformed cells lose contact inhibition, contain virus-specific
antigens (TSTA and T antigen), exhibit chromosome abnormalities,
and can produce tumors when injected into susceptible animals.
DNA ONCOGENIC VIRUSES
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Oncogenic viruses are found among the
Adenoviridae, Herpesviridae, Poxviridae, and
Papovaviridae.
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The EB virus, a herpesvirus, causes Burkitt’s
lymphoma and nasopharyngeal carcinoma.
Hepadnavirus causes liver cancer.
RNA ONCOGENIC VIRUSES
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Among the RNA viruses, only retroviruses seem to be
oncogenic.
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HTLV-1 and HTLV-2 have been associated with human
leukemia and lymphoma.
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The virus’s ability to produce tumors is related to the
production of reverse transcriptase. The DNA
synthesized from the viral RNA becomes incorporated as
a provirus into the host cell’s DNA.
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A provirus can remain latent, can produce viruses, or
can transform the host cell.
LATENT VIRAL INFECTIONS
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A latent viral infection is one in which the virus
remains in the host cell for long periods without
producing an infection.
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Examples are cold sores and shingles.
PERSISTENT VIRAL INFECTIONS
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Persistent viral infections are disease
processes that occur over a long period and are
generally fatal.
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Persistent viral infections are caused by
conventional viruses; viruses accumulate over
a long period.
PRIONS
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Prions are infectious proteins first discovered in
the 1980s.
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Prion diseases, such as CJD and mad cow disease,
all involve the degeneration of brain tissue.
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Prion diseases are the result of an altered protein;
the cause can be a mutation in the normal gene
for PrPC or contact with an altered protein (PrPSc).
*Animation: Prion Reproduction. The Microbiology
Place.
PLANT VIRUSES AND VIROIDS
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Plant viruses must enter plant hosts through
wounds or with invasive parasites, such as insects.
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Some plant viruses also multiply in insect (vector)
cells.
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Viroids are infectious pieces of RNA that cause
some plant diseases, such as potato spindle tuber
viroid disease.