Download microbes overview

Microbial overview
Prokaryotes
Archaea
Bacteria
Eukaryotes
(microbial Protists)
Fungi
Algae
Protozoa
Viruses
How would you classify ?
• 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.)
Linnaeus Classification
1.
2.
3.
4.
5.
6.
7.
8.
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
1. PROKARYOTES
Prokaryotes (evolved between 3-4 billion years ago) are the original
inhabitants of the planet
• Prokaryotes can be distinguished from eukaryotes in terms of their
size, cell structure, and molecular make-up
• Most prokaryotes are simple cells lacking extensive, complex,
internal membrane systems
• Prokaryotes are divided into: Bacteria and Archaea
• Bacteria can be classified as Gram negative or Gram positive
• Many prokaryotes are motile
• Some bacteria form resistant endospores to survive harsh
environment in a dormant stage
1.1 The Archaea Ch.20 Prescott
• The Archaea are best known for growing in restricted
habitats e.g. Hypersaline or high temperature
• Many have special structural, chemical, and metabolic
adaptations that enable them to grow in extreme
environments
• Divided into 2 phyla: Crenarchaeota (extremely
thermophyllic and many acidophiles and sulfur
dependent; anaerobes e.g. Thermoproteus or Gramnegative aerobes Sulfobolus
• and Euryarchaeota (diverse phylum: 5 major
physiologic groups)
• Metanogenic and sulfate-reducing archae have cofactors
that paticipate in methanogenesis
Euryarchaeota contd.
5 major physiologic groups:
• The Metanogens (strict anaerobes,
e.g.Methanobacterium, Methanococcus – Refer p. 507 of
Prescott);
• The Halobacteria ( gram negative or positive,
chemoorganotrophs dependent on high salt content e.g.
Halobacterium salinarum; has bacteriorhodopsin
protein that can trap light energy without chlorophyll;
• The Thermoplasms ( thermoacidophiles, pleomorphic
lacking cell wall e.g. Thermoplasma growing in refuse
piles of coal mines);
• Extremely Thermophillic So- Metabolizers (e.g anaerobic,
motile, flagellate, Thermococcus that reduces sulfur to
sulfide;
• Sulfate-Reducing Euryarchaeota ( irregular gram
negative coccoid anaerobic cells e.g. Archaeoglobus in
marine aera.
1.2 Bacteria (Denococci and Non proteobacteria
Gram negatives, Ch.21 Prescott)
• Deeply branching very old group e.g. Aquifex,
Thermotoga
• Photosynthetic bacteria and Cyanobacteria are
different distinct groups
• Chlamydiae bacteria obligate parasites
• Many have gliding motility and useful for
bacteria that digest insoluble nutrients or move
over the surfaces of moist, solid substrata
• Phyla in this group: 1. Aquificae and
Thermotogae; 2. Deinococcus-Thermus;
• 3. Photosynthetic bacteria; 4. Planctomycetes;
5. Chlamydiae; 6. Spirochaetes; Bactereoidetes
1.2.1 Aquificae
• Aquificae and Thermotoga bacterial
thermophilles
• Aquificae oldest branch of bacteria e.g. Aquifex
and Hydrogenobacter – thermophilic
chemolithoautotrophs, gram negative rods.
(Chemolithoautotroph or mixotroph– a microbe
that oxidizes inorganic compounds to drive both
energy and electrons)
• Thermotoga e.g. Thermotoga sp.-gram negative
rods with an outer sheath-like envelope (togaouter garment p.520 Prescott); hasgenes for
sugar degradation
1.2.2 Deinococcus-Thermus
• Phylum Deinococcus-Thermus has class
Deinococci with orders Deinococcales and
Thermales
• Deinococcus sp.
- gram negative spherical or rod shaped
and associated in pairs or tetrads;
- aerobic producing acids from a few
sugars;
- have resistance to dessication and
rediation
1.2.3 Photosynthetic bacteria
• 3 groups of gram-negative bacteria: the purple bacteria; the green
bacteria; cyanobacteria, having pigments chlorophyll and
bacteriophyll
• Cyanobacteria are able to carry out oxygenic photosynthesis,
having photosystems I and II and use water as electron donor to
release oxygen;
• dominate aerated freshwater and marine microbial communities
absorbing red and blue light; e.g. Cyanobacteria sp – unicellular
varying in shape and appearence;
• move by gliding motility (Refer to Prescott p. 525 for Cyanobacterial
cell structure);
• can develop symbiotic relationships with other organisms like lichen,
fungi, protozoa, nitrogen-fixing bacteria;
• reproduce by binary fission;
• phycobilisomes contain light –harvesting pigments phycocyanin and
phycoerythrin
Photosynthetic bacteria contd.
• Purple bacteria ( gamma proteobacteria,
Bergey’s Manual) and the green bacteria e.g.
Chlorobium sp. have only one photosystem and
use anoxygenic photosynthesis.
• Because they cannot use water as electron
source, they employ reduced molecules such as
hydrogen sulfide, sulfur, hydrogen, and organic
matter as their electron source for the reduction
of NAD(P)+ to NAD(P)H
1.3 Other Phyla
Planctomycetes – gram negative
• Have compartmentalized cells lacking
peptidoglycan; role in anaerobic ammonia
oxidation e.g. Candidatus Brocadia
anammoxidans
Chlamydiae – gram negative
• Non motile, coccoid, gram-negative reproducing
within the cytoplasmic vacoules by
phagocytosing the attached elementary bodies
of host cells to form reticulate bodies that can
cause disease. They are energy parasites
Other Phyla contd.
Spirochaetes – gram neagative
• Slender, long, helical, gram-negative bacteria that are
motile because of their axial filament underlying an outer
membrane e.g. Myxotrichia paradoxa; Treponema
(cause syphilus), Borrelia burgdorferi (cause Lyme
disease)
Bacteroidetes e.g. Bacteroides, Cytophaga, Flexibacter
spp – gram negative
• Are obligately anaerobic,gram negative,
chemoheterotrophic, nonsporing, motile/nonmotile rods
of various shapes;some intestinal symbiotants, others
can cause disease; gliding motility; cytophagas degrade
proteins and carbohydrates and active in mineralization
of organic matter and produce yellow to orange colonies.
1.4 The Proteobacteria
• The phylum Proteobacteria is the largest bacterial group
with more than 500 genera and 2000 species
• Many species are Gram negative serving as
scavengers in ecosystem or as disease agents.
Escherichia coli is a major experimental organism
studied in many labs
• These bacteria are very diverse in their metabolism and
life styles ranging from obligate parasites to free-living
existence in soil and aquatic habitats
• Chemolithotrophic bacteria obtain energy and electrons
by oxidation of inorganic compounds
• Some Proteobacteria produce specialized structures
such as buds or complex fruiting bodies.
1.4.1 Classes of Proteobacteria
(Bauman Ch 11, p. 334)
5 classes- the alpha-, beta-, gamma-, delta-, and
epsilonproteobacteria
Alphaproteobacteria – aerobes, attached to hosts by cell
extensions (prosthecae); Azospirillum and Rhizobium
are nitrogen fixers
• Some members, e.g. Nitrobacter, are nitrifying bacteria
that oxidize NH3 to NO3 by a process called nitrification
• Most purple nonsulfur phototrophs are in this group
• Pathogenic bacteria include Rickettsia (typhus), Brucella
(brucellosis), Ehrlichia (ehlichiosis)
• Beneficial bacteria include Acetobacter and Caulobacter
which synthesize acetic acid; Agrobacterum is used in
genetic recombination in plants
Classes of Proteobacteria contd.
Betaproteobacteria
• Include nitrifying Nitrosomonas and pathogenic species,
Neisseria (gonorrhea), Bordetella (whooping cough),
Burkholderia (colonizes lungs)
• Thiobacillus (ecologically important), Zoogloea (sewage
treatment), and Spirillum
Gammaproteobacteria – largest class
• Include purple sulfur bacteria – obligate anaerobes that
oxidize hydrogen sulfide to sulfur
• intracellular pathogens (Legionella, Coxiella),
• methane oxodizers (Methylococcus),
• facultative anaerobes that utilize glycolysis and the
pentose phosphate pathway (Escherichia coli),
• and pseudomonads (pathogenic Pseudomonas,
nitrogen-fixing Azotobacter and Azomonas)
Classes of Proteobacteria contd.
Deltaproteobacteria
• Include Desulfovibrio (important in the sulfur cycle and in
corrosion of pipes); Bdellovibrio (pathogenic to bacteria);
• and myxobacteria – gram negative, soil-dwelling
bacteria forming stalked fruiting bodies containing
resistant, dormant myxospores; common worldwide in
the soils having decaying plant material or dung
Epsilonproteobacteria
• Gram-negative rods, vibrios, or spiral
• Include important human pathogens (Campylobacter,
curved rods, causes blood poisoning; Helicobacter
spirals, cause ulcers)
1.5 Low G+C Gram-positive bacteria
(Ch 11 Bauman)
• Classified within phylum Firmicutes, which include 3 groups:
clostridia, mycoplasmas, other low G+C gram-positive bacilli and
cocci
• Bacilli and cocci important to humans and industry
• Bacillus contain species that cause anthrax (B.anthracis) and food
poisoning (endospores of B.cereus contaminate rice and ingestion
cause nausea, vomiting, abdominal cramping), besides beneficial Bt
toxin bacteria (B.thuringiensis- caterpillar biopesticide)
• Listeria sp. causes meningitis in fetus and contaminate milk and
meat products (L.monocytogenes - does not produce endospores
and continues to reproduce under refrigeration)
• Lactobacillus (non-sporing-forming rods) is used to produce yogurt
and pickles; it inhibits growth of pathogens – microbial antagonism.
• Streptococcus cause strep throat and other diseases (scarlet fever,
wound infections, pneumonia, & inner ear, blood, kidney diseases)
• Staphylococcus causes a number of human diseases (bacteremia,
pneumonia, wound infections, food poisoning, and diseases of
joints, bones, heart, and blood. S. aureus grows harmlessly on the
skin in clusters.
1.5 Clostridia & Mycoplasma
Clostridia
• Clostridium pathogenic bacteria causing gangrene,
tetanus, botulism, and diarrhea
• Epulopiscium and Veillonella found in dental plaque
Mycoplasmas
• Gram-positive (previously under gram negative category
until neucleic acid sequences proved similarity with gram
positive organisms) , pleomorphic, facultative anaerobes
and obligate anaerobes lacking cell walls and stain pink
in gram stain
• Show distinct “bull’s eye - fried egg” appearence when
grown in solid media
• Usually associated with pneumonia and urinary tract
infections
1.6 High G+C Gram-Positive Bacteria
• Include Corynebacterium, Mycobacterium and
Actinomycetes that have a G+C ratio > 50% in the
phylum Actinobacteria, which have species with rodshaped cells
• Corynebacterium store phosphates in metachromatic
granules. C. diptheria causes diphtheria
• Mycobacterium cause tuberculosis and leporosy. It has
unique resistant cell walls containing mycolic acids.
Hence, acid fast stain (for penetrating waxy cell walls) is
used for its identification
• Actinomycetes resemble fungi as they produce spores
and form filaments; important genera: Actinomyces
found in human mouths; Nocardia useful in degradation
of pollutants; and Streptomyces produces antibiotics
2. Algae [Ch 12, Bauman]
ALGAE
• Reproduce by alternation of generations (haploid and diploid thalli)
• Large algae attach to substrates by leaf-like blades or stem-like stipes
• Division Chlorophyta containd green algae that are similar to land plants
and some taxanomists place them in kingdom Plantae e.g. Codium (marine
used in seasoning pepper); Trebouxia (in lichens); Prototheca (colorless
cauce skin rashes)
• Rhodophyta (red algae) contain pigment phycoerythrin and agar or
carrageenan cell walls, substances used as thickening agents, e.g.
Geledium, Chondrus – used as thickening agent in ice cream, toothpaste,
salad, syrup, and snack foods
• Phaeophyta (brown algae) contain xanthophylls, and oils. Cell walls
composed of alginic acid, another thickening agent. Spore motile having
one ‘hairy’ flagellum and one whiplike flagellum
• Chrysophyta (the golden algae, yellow-green algae, and diatoms –
contain chrysolaminarin, a storage product
• The silica cell walls of diatoms are arranged in nesting halves called
frustules. Organic gardeners use diatomaceous earth, composed of dead
diatoms, as a pesticide ageanst harmful insects and worms. It is also used
in polishing compounds, detergents, paint removers, and reflective paints
3. Protozoa
• Classified into 7 groups: alveolates, cercozoa, radiolaria,
amoebozoa, eglenozoa, diplomods, and parabasalids,
• Protozoa are eukaryotic, unicelular organisms lacking cell walls;
Most are chemoautotrophs
• In the life cycle, trophozoite is the feeding stage; cyst resting stage.
A few undergo sexual stage by forming gametocytes that fuse to
form zygotes
• Alveolates have small cavities (alveoli) beneath cell walls. They also
have tubular mitochondrial cristae or folds; Imp. groups: Ciliates –
Vorticella (create whirlpool current during feeding); Balantidium
(human pathogen; Didinium (Paramecium predator);
Apicomplexans – Plasmodium (cause malaria); Dinoflagellates
(freshwater and marine photoautotrophs, producing light via
metabolic reactions e.g. ‘red tide’in sea) – Gymnodinium and
Gonyaulax produce ‘neurotoxins’.
• Cercozoa – amoebae, moving and feeding by pseudopodia. Major
taxon- foraminifera (fossil species forming thick layers of limestone
Egyptian pyramids built of such limestone)
Protozoa contd.
• Radiolaria – amoebae with threadlike pseudopodia; have ornate
shells composed of silica; dead bodies settle at bottom of ocean and
form ooze that is dispersed hundred of meters thick
• Amoebozoa – have lobe-shaped pseudopodia; are slime molds
(lacking cell wall and are phagocytes); 2 groups : plasmodial molds
(acellular slime molds e.g. Physarium phagocytizing organic debris
in the forest and bacteria; cellular slime molds e.g. haploid
Dictyostelium that phagocytize bacteria, yeasts, dung, and decaying
vegetation
• Eglenozoa – share characteristics of both plants and animals; 2
groups: euglenids are photoautotrophic having chlorophyll a and b,
and carotene; movement by flagella and by flowing,contracting, and
expanding their cytoplasm or ‘squirming movement’ e.g. Euglena sp;
kinetoplastids have a single large mitochondrion with unique
mitochondrial DNA (kinetoplast); mostly intracellular and some
pathogenic e.g. Trypanosoma and Leishmania cause fatal diseases
in animals and humans.
Plant cell
Protozoa contd.
• Dilpomonadida – lack several organelles of a
cell; have 2 equal-sized nuclei and mutiple
flagella; Giardia – diarrhea-causing pathogen
spread by ingestion of food
• Parabasala – lack mitochondria and have a
single nucleus a parabasal body (a Golgi bodylike structure); Trychonympha inhabits guts of
termites assisting in didestion of wood;
Trichomonas cause sterility in raised acidic pH of
human vagina
3. PREVIEW OF EUKARYOTES
• Eukaryotes differ from prokaryote cells in having a
variety of complex membranous organelles in the
cytoplasm matrix and genetic material within membrane
–delimited nuclei
• Each organelle has a distintive structure directly related
to specific functions
• A cytoskeleton composed of microtubles,
microfilamentsa and intermediate filaments helps give
eukaryotic cells shape; the cytoskeleton is also involved
in cell movements, intracellular transport, and
reproduction
• When eukaryotes reproduce, genetic material is
distributed between cells by mitosis and meiosis
• Despite great differences between eukaryotes and
prokaryotes with respect to morphology, they are similar
on the biochemical level.
3. PREVIEW OF THE FUNGI (EUMYCOTA )
Fungi widely distributed and are both beneficial and
harmful
They are mostly associated with moist environment and
exist as filamentous hyphae which collectively is termed
as mycelium
They digest insoluble organic matter by exoenzymes and
absorb the solubilized nutrients
Their reproductive structures incluse: sporangia forming
asexual spores and gametangia forming sexual gametes
Fungal systematics include 8 subdivisions:
Chytriodomycetes, Zygomycota, Ascomycota,
Basidiomycota, Urediniomycetes, Ustilaginomycetes,
Glomeromycota, and Microsporidia
3.1 Eumycota
The Chytriodomycetes are terrestrial and aquatic that
reproduce by motile zoospores with single, posterior,
whiplike flagella e.g. Pythium, Phytophthora spp.
The Zygomycota are coenocytic molds forming resting
zygospores in which zygotes are formed e.g. Black
bread mold Rhizopus nigricans
The Ascomycota (32,000 known species of molds and
yeasts [unicellular]) form zygotes within sac-like
structures called asci (singular ascus) occuring in sexual
ascocarp fruiting bodies. The ascus contains 2-8
ascospores
They reproduce asexually by coniodospores e.g.
Penicillium
Economic importance of ascomycetes
•
•
•
•
•
Economic importance of ascomycetes include:
Underground edible mushrooms truffles grow as
mycorrhizae in association with oak trees(Tuber
melanosporum priced at $500 per pound); ascocarps of
common morel (Morchella esculenta)
Claviceps purpurea growing on grains produces
lysergic acid diethylamide (LSD) which causes abortions
in cattle and hallucinations in humans;
Penicillium mold source of penicillin;
Saccharomyces ferments sugar to produce alcohol and
CO2 gas, used in bakery and brewery industries;
Pink bread mold Neurospora, has been important
tool in genetics and biochemistry;
Many ascomycetes partner with green algae to form
lichens
Fungi (Deuteromycetes)
• Taxanomists in the middle of 20th century created the
division Deuteromycota to contain collection of fungi
whose sexual stages are unknown
• These fungi do not produce sexual spores or sexual
spores have not been observed
• Recently, analysis of rRNA sequences revealed that
most deuteromycetes in fact belong to division
Ascomycota
• Modern taxanomists have abandoned Deuteromycota as
a formal taxon, but many medical lab technologists
continue to refer “deuteromycetes” as a tradisional name
• Most deuteromycetes are terresterial saprobes,
pathogens of plants, or pathogens of other fungi.
Trichophyton causes ringworm and Aspergillus, allergies
in humans,
3.2 Fungi
•
Basidiomycota (22,000 known soecies) possess
dikaryotic hyphae, one of each mating type. The hyphae
divide uniquely, forming basidiocarps within which clubshaped basidia (sin. basidium) can be found. The
basidia bear 2-4 basidiospores.
•
They are mostly cosmopolitan in nature found
growing in fields and woods as visible basidiocarps of
mushrooms, puffballs, stinkhorns, jelly fungi, bird’s nest
fungi (Crucibulum). Poisonous mushrooms are
sometimes as toadstools e.g Amanita muscaria
•
Economic importance of basidiomycetes Refer Ch 12
of Bauman’s book: edible mushrooms e.g. Agaricus
and Cortinellis; Important decomposers that digest
plant material and return nutrients to the soil; Many
produce hallucinatory chemicals or toxins;
Basidiomycete yeast Cryptococcus neoformans causes
fungal meningitis.
Fungi contd,
Urediniomycetes (rusts in plants) and
Ustilaginomycetes (smuts)include important
plant pathogens, whereas the Glomeromycota
form mycorrhizae (vascular plant roots forming
associations with fungi) that enhance plant
nutrient uptake
Some members of Microsporidia are considered
as pathogens for humans e.g Nosema and
Microsporodium. They are similar to
zygomycetes and are obligatory parasites in
insects e.g. Nosema infecting silkworms and
honey bees, and grasshoppers
5. Preview of Viruses
Viruses are simple, acellular entities (obligate intracellular
parasites) reproducing only within living cells
Structurally, all viruses have a nucleocapsid composed of a
nucleic acid genome surrounded by a protein capsid
Some viruses have a membranous envelope that lies
outside the nucleocapsid
The nucleic acid of virus can be RNA or DNA, single
stranded or double stranded, linear or circular
Capsids may hace a helical, icoshedral, or complex
symmetry. They are constructed of protomers [individual
subunits of a virus capsid] that self assemble through
noncovalent bonds
5.1 General replication in viruses
Each virus has unique aspects to its life cycle but
the generalised pattern of replication consists
of 5 steps:
1. Attachment to the host cell
2. Entry into the host cell
3. Synthesis of viral nucleic acids and proteins
within the host cell
4. Self assembly of virons[ sin. virion- a complete
virus particlerepresenting the extracellular
phase of the virus life cycle]] within the host
cell
5. Release of virions from the host cells
5.2 Culturing viruses
• Viruses are cultured by inoculating living hosts or cell
cultures with a virion preparation
• Purification depends on their large size relative to cell
components, high protein content and great stability
• The virus concentration may be determined from the
virion count or from the number of infectious units
• Viruses are classified on the basis of their nucleic acid’s
characteristics, reproductive strategy, capsid symmetry,
and the presence or absence of an envelope
5.3 Viral associations
Types of eukaryotic viruses:
• Causing cancer viruses
•
Plant viruses and plant diseases [most plant viruses have an RNA genome
and may be helical or icosahedral]
•
Animal viruses and diseases [e.g. Parvoviruses, retroviruses]
•
Mycoviruses from higher fungi have isometric capsids and dsRNA, whereas
lower fungi may have either dsRNA or dsDNA genomes
•
Insect viruses produce inclusion bodies that aid in their trasmission
Baculoviruses and other viruses are finding uses in biological control of
insects
Viral associations contd.
• Viriods are infectious agents simpler than
existing viruses. In plants they are short strands
of infectious RNA
• Virusoids are infectious RNAs that encode one
or more gene products and require a helper
virus for replication
• Prions are small proteinaceous agents
associated with degenerative nervous system
disorders e.g. Fatal familial insomnia, bovine
spongiform encaphalopathy. The precise nature
of prions is unclear.
Review questions
Give the Linneaus classification of the following microbes:
1. That turns milk sour
2. That ferments sugar
3. That carries out exygenic photosynthesis
4. That is found in the human intestine
5. That carries out nitrification
6. That is used in genetic recombination in plants
7. That is a methane oxidizer
8. That is used as diatomaceous earth
9. That were used as limestone for building the Egyptian
pyramids
10. Is an edible mushroom