PRELIM NOTES
Microbial Ecology
 Science that explores the interrelationship of
microorganisms with its biotic and abiotic environment
(Ernst Haeckel)
 Ecology “oikos” (dwelling place)
Microorganisms;
 Bacteria – cyanobacteria
 Archaea – all are microscopic, live in extremes
 Eukarya – fungi (yeast), protozoans
Environment affects the survival of the microorganism
 Abiotic components
 Nutrients, temperature, pH,
 Gases important for survival
 Biotic Components
 Living components
Microbial Ecology and its related fields
1. Zoology – animals are good environment for
microorganisms
- microbes benefit from animals such as in ruminant
- we also benefit from microbes by enhancing our digestion
2. Botany – microorganisms benefit plants
- Nitrogen fixation (N2→NO2→NO3) - absorbed by roots
3. Hydrology – marine and other aquatic environments
4. Current Environmental Concerns
 Biogeochemical cycles
 Bioenergetics – transfer of energy from one trophic
level to another
 Control of man-made pollution
Green House
 Maintains survival or thriving of plants
 Made up of plastic or glass
 Maintain warm temperature inside for plants
 Maintains warm temperature at night
 CO2 – main greenhouse gas
 Greenhouse gases trap radiation (at night time, traps
heat)
 Too much is bad!
Why is there a need to study microbial eco?
 It is a required course!
 The course is interesting
 To discover and understand the characteristics and
activities of microorganisms in their natural
environment
Relevance of Microbial Ecology  microscopic algae
1970s  Source of food
 Surge of interest – man more conscious of pollution  Cyanobacteria
 Man-made organics and industrial by-products that
degrade very slowly 2.Consumers
 Zooplankton: feed on phytoplankton
Principle of Microbial Infallibility 3.Decomposers
“No natural organic compound is totally resistant to  Fungi: exhibit extracellular digestion thru excreting
biodegradation provided that environmental conditions are enzymes
favorable.”  Mushrooms
>with the right organism and the right environmental  macroscopic organism as decomposers
conditions, everything can be degraded  extracellular digestion – secrete enzyme that
degrades
Biodegradation vs. Mineralization
Biodegradation Brief History of Microbiology
 Breakdown of complex substances to simpler ones A. Observation of Microorganisms
 Parent material does not exist anymore 1. Zacharias Jansen
 Degradation products may be more toxic  Invented the compound microscope
Mineralization 2. Anton van Leeuwenhoek
 Complex compounds to simpler minerals  “Father of Microbiology”
Xenobiotic substances  Observed “wee animalcules”
 “recalcitrant” substances  Did the first experiment on microecology
 Resist bio-degradation or are more metabolized 3. Ernst Karl Abbe
incompletely, accumulate in the environment  Introduced OIO
Examples;  Invented the Abbe condenser
1.Polychlorinated Biphenyls (PCB) 4. Paul Erlich
 Used as coolants in industry  Developed the precursor technique to gram staining
 Oil used in OIO  Discovered Arsphenamine (Salvarsan), a treatment for
 Results to thinning of egg shells and decrease syphilis
reproductive activity of birds 5. Hans Christian Gram
 Carcinogenic  Developed a staining method that later played a major
2.DDT (Dichlorodiphenyltrichloroethane) role in bacterial classification
 Colorless, odorless, tasteless organochloride used as  Gram staining; (+) Blue, (-)Pink
insecticide  Hucker’s modification of Gram Staining - used in
 Observed in human milk of lactating mothers living staining milk smears (allow Gram positive organisms
near Laguna Lake – indicates that it has seeped to remove stain from milk)
through the water table and had not been degraded *What has been modified?
Genetically Modified Organisms (GMO)
 Used in the degradation of xenobiotic substances B. Microorganisms as Living Entities
Microorganisms as co-habitants on Earth 1.Louis Pasteur
 Ubiquitous distribution  Refutation of the Theory of Spontaneous Generation
 Diverse metabolism  Fermentation and Pasteur Effect (wine and beer
 “The influence of the very small is very great indeed.” - industry)
Louis Pasteur  Pasteurization (UHT, HTST)
Dominant role in global ecology  Developed vaccines against anthrax and rabies
1.Producers 2.John Tyndall
 Phytoplankton: Maintains the optimum oxygen levels  Final blow to the Theory of Spontaneous Generation
of the atmosphere in the aquatic environments  Heat-resistant form (spores) of bacteria
*Tyndallization – address heat-resistant spores b. Specific inactivation of the gene or genes associated Structural Characters
3.Ferdinand Cohn with the suspected virulence trait should lead to a 1. Cell Wall
 Father of Modern Bacteriology measurable decrease in pathogenicity or virulence 2. Chloroplast
 Classification of Bacteria based on cell morphology c. Reversion or replacement of the mutated gene with 3 Kingdom System
 Discovered endospores in Bacillus subtilis the “wild type” gene should lead to a measurable (Ernst Heinrich Haeckel, 1866)
 Endospores are resistant to adverse environments decrease in pathogenicity  Degree of complexity (structural and physiological)
 Plantae and Animalia
C. Role of Microorganisms D. Microorganisms producing antimicrobial substances Multicellular; extensive cell differentiation
1. Microorganisms are cause of disease a. Alexander Fleming  Protista
a. Ignaz Semmelweis  Discovered lysozyme (enzyme against positive Unicellular, simple
 Father of Infection Control organisms)
 “childbed” fever (puerperal fever incidence and  “Miracle drug” benzylpenicillin (Penicillin G) from 5 Kingdom Systems
handwashing) Penicillium notatum (Robert Whittaker, 1969)
 Early pioneer of antiseptic procedures  Discovered bacteria developed resistance when  Cell type – prokaryotic and eukaryotic
b. Joseph Lister dosage of penicillin was low during short duration of Edward Chattun (1937)
 Antiseptic treatment  Coined the term “prokaryotic” – differentiated
 Surface sterilization of surgical instruments b. Selman Walksman nucleated from non-nucleated forms
 Phenol (carbolic acid) as disinfectant  Discovered streptomycin and 15 other antibiotics Robert Stanior (1961)
 Improved methods of asepsis and antisepsis  Albert Schatz, graduate student, co-discoverer  Coined nucleoplasm
c. Robert Koch  1952 Nobel Price  Level of organization:
 Direct demonstration of the role of bacteria in causing E. Role of Microorganism in Nature Solitary, colonial, unicellular, or multicellular
diseases a. Jacques Theophile Schloesing and Achille Munts  Nutritional Type:
 Identified causative agents of anthrax, cholera, and  Experiment on sewage passed through sand column – Photosynthetic, absorption, ingestion
tuberculosis high nitrate content
 Koch’s postulate-linked  Chloroform added to column→no nitrate 5 Kingdoms
Koch’s Postulate  Addition of garden soil to column after chloroform → 1. Monera
a. The same pathogen must be present in every case of high nitrate – Prokaryotes, algae (certain groups
disease  Conclusion: Nitrification caused by microorganisms –Prokaryotic organisms, most primitive
b. The pathogen must be isolated from the diseased host (bacteria) in soil 2. Protista
and grown in a pure culture b. Sergei Winogradsky –least homogenous; single-celled eukaryotes; solitary
c. The pathogen from the pure culture must cause the  Father of “Soil Microbiology” or colonial
disease when inoculated into healthy susceptible  Isolation and identification of nitrifying bacteria –all 3 types of nutrition
animals  Chemoautotrophy/Chemosynthesis – production of 3. Fungi
d. The pathogen must be isolated from the newly organic matter driven by chemical reactions –absorptive nutrition
infected animals and cultured again in the laboratory, *Winogradsky column - Aerobic nitrogen fixation –unicellular and multicellular eukaryotes with chitinous
after which it should be seen to be the same as the c. Martinus Beijerinck cell wall
original pathogen  Enrichment culture 4. Plantae
Reasons for limited applications of Koch’s Postulate  Isolated first pure cultures of many soil bacteria –multicellular organisms with walled, eukaryotic cells
–photosynthetic
1. Not all etiologic agents can be easily cultured using  Symbiotic and non-symbiotic nitrogen fixation
ordinary culture media 5. Animals
2. Some diseases have poor etiology –most complex, multicellular with complex cells;
CLASSIFICATION SYSTEMS
-Can be cause by more than one pathogen without cell walls
2 Kingdom Systems
3. One etiologic agent can be implicated in several (Carolus Linnaeus, 1735)
diseases 6 Kingdom system
Functional Characters
Modifications to Koch’s Postulate (Carl Woese, 1980s)
1. Energy source
–Emphasis on phylogeny and redefining kingdoms to
a. The phenotype or property under investigation (e.g. 2. Carbon Source – CO2
monophyletic groups
nucleic acid sequence of a putative pathogen) should 3. Growth factor requirement – inorganic minerals
be significantly –Monerans divided into 2 distinct Kingdoms (Eubacteria
4. Active movement
and Archeaobacteria)
–Blending of 5 kingdoms and 3 Domain System  Type Strain – organisms that was 1st described and 3. Metabolic Diversity
8 Kingdom System characterized, found in culture collection Type C-source E-source
(Cavalier and Smith) Chemoheterotrophs Org compd Org comp
 Ultrastructural characteristics (rRNA and other Intrasubspecific Ranks: Chemoautotrophs CO2 Inorg
molecular data)  Biovar – biotype; with special biochemical property Photoheterotrophs Org comp Light
Two empires  Serovar – Serotype; distinctive antigenic property Photoautotrophs CO2 light
1. Eukarya – Archezoa, Protozoa, Plantae, Chromista,  Pathovar – Pathotype; Pathogenic for certain hosts 4. Ecological Diversity
Fungi, Animalia  Phagovar – Phagotype; ability to be lysed by certain “Microorganisms are found in almost any type of habitat”
2. Bacteria – Archeaobacteria and Eubacteria bacteriophages 5. Behavioral Diversity
3 Domain System Classification Systems  Motility and taxis
Carl Woese, Otto Kandler and Mark Wheelis, 1990 1. Phenetic System  Sporulation
 rRNA sequences –groups organisms together based on mutual  Communication between cells – quorum sensing
 biochemical characteristics similarity of phenotypic characteristic overall similarity
 molecular characeristics 2. Phylogenetic / Phyletic Classification DOMAIN BACTERIA
Why the ribosomal RNA? –based on probable evolutionary relationships Proteobacteria
 Ancient molecule –molecular / genetic makeup of organisms is used  Largest and the most metabolically diverse phylum
 Functionally constant 3. Numerical Taxonomy  Constitute majority of bacteria that are of medical,
 Universally distributed –grouping by numerical methods of taxonomic units industrial, and agricultural significance
 Moderately well-conserved into taxa on the basis of their characteristics states  All are Gram negative
–info about the properties of the organisms is
Molecular Phylogenetic Tree  Diverse in oxygen requirement;
 Quantitative and objective converted into a suitable form for numerical analysis
 Anaerobic
 Tips of all branches are modern organisms –taxonomic distances in terms of number of
 Microaerophilic
 Presence of three evolutionary groups characters shared relative to number of characters
 Facultative aerobic
examined
 Eukaryotes are as ancient as prokaryotes  Wide range of cellular morphology;
MAJOR GROUP OF MICROORGANISMS
Revised Tree of Life  Straight and curved rods
Microbial Diversity
 No common ancestor  Spirilli
1. Morphological Diversity
 Evolved from primordial soup / menagerie  Cocci
–rods, cocci, spiral, star-shaped, square
 Early life – did not exist as distinct species – traded –bacteria size range; Thiomargarita (750um) to  Filamentous
genes promiscuously  Budding
Nanobacteria(0.02um)
Definition  Appendage forms
2. Structural Diversity
1. Taxonomy
 Gram positive – thick peptidoglycan,  Divided into 6 classes based on 16S rRNA gene
 Science of classifying organisms
 Gram negative – thin peptidoglycan sequences;
 Provides a universal language for all organisms 
 Diversity in flagella Alpha proteobacteria
Prokaryotic Flagella – flagellin, clockwise,  Beta proteobacteria
Components
counterclockwise, tumbling  Gamma proteobacteria
1. Classification – arrange of organisms into groups or
Eukaryotic flagella – whip-lash  Delta proteobacteria
taxa
*How is flagellin added?  Epsilon proteobacteria
2. Nomenclature – assignment of names
a. Monotrichous – one side  Zeta proteobacteria – only one species
3. Identification – process of determining that a particular
b. Amphitrichous – both sides  Species in different classes often have similar
isolate belongs to a recognized taxon
c. Lophotrichous – many on one side metabolism;
 Species – group of interbreeding or potentially
d. Petritrichous – all over  Phototrophy
interbreeding natural populations that are
Pili – pathogeneicty for some  Methylotrophy
reproductively isolated from other groups
Sexual Pili – conjugation
 Bacterial species – collection of strains that has the  Suggest horizontal gene transfer played a major role
 Production of spores in shaping metabolic diversity in the phylum
stable properties and differ significantly from other
Endospore for survival
strains  Sharing of metabolic traits in different classes
 Strain – a population that descends from a single →remind that phenotype & phylogeny provide
organisms / pure culture different views of prokaryotic diversity
 CLASS: ALPHA PROTEOBACTERIA  First identified and one of the few that is  Ammonia oxidizing bacteria
A. Order Rhizobiales culturable
1. Rhizobium – attach to host cell, initiate formation of  Uses: evolutionaty role of magnetism in CLASS: GAMA PROTEOBACTERIA
root nodules organisms, building models in bioremediation,  Largest and the most diverse class
2. Agrobacterium tumefaciens geobiochemical tracers  Include half of the characterized species in the
 attach to host cell  phylum
 crown gall disease (plasmids inserted) E. Order Caulobacterales  15 orders with more than 1500 characterized species
 Agrobacterium-mediated transformation 1. Caulobacter – asymmetric cell division  Include many well-known human pathogens
3. Methylobacterium  Stalked cell – non-motile for reproduction  Either respiratory or fermentative metabolism
 Forms pink-pigmented biofilms  Swarmer cells – motile, for dispersal, cannot  Members are often easy to grow in laboratory media,
 Methanol-carbon source reproduce can easily be isolated from variety of habitats
 Seen in toilets
 Bartonella henselae F. Order Sphingomonadales A. Order Enterobacteriales
 “cat scratch disease”  Ability to metabolize a wide range of organic 1. E. coli – universal inhabitants of human GI tract
 Formerly Ricketsiales because they are compounds including many aromatic compounds that 2. Salmonella – typhoid fever
intracellular pathogens transferre by arthropods are common environmental contaminants 3. Shigella – Bacillary dysenteriae
 Pelagibacter ubique  Widely studied as potential agents for bioremediation 4. Proteus – swarming phenotype urease – UTI in
 Most abundant bacteria on the face of the Earth  Easy to cultivate humans
 Present in the oceans  Sphingomonas wittichi 5. Enterobacter aerogenes – occasional cause of UTI
 25-50% of the bacterial population 6. Klebsiella pneumoniae – occasional pneumonia
CLASS: BETAPROTEOBACTERIA 7. Serratia marcescens – occasional contaminants in IV
B. Order Rickettsiales  Third largest class of Proteobacteria fluids
1. Ricketsia ricketsii  Immense amount of functional diversity B.Order Pseudomonales
Pseudomonas aeruginosa
 In tissue culture 1. Burkholderia cepacia
 Opportunistic pathogen  Opportunistic pathogen, nosocomial
 Rocky Mountain Spotted Fever
2. Rickettsia prowazeki  Secondary lung infection to immunocompromised  Naturally resistant to many widely-used antibiotics
 In human fibroblast typhus patients  Urinary and respiratory infections
 Closely associated with arthropod vectors (ticks, fleas,  Protects some plants  Secondary infections in burn patients & cystic fibrosis
lice, and mites)  Anti-fungal and antihematodal C.Order Vibrionales
1. Vibrio cholera – cholera
 Most are metabolically specialized – able to oxidize 2. Rhodocyclus
 Purple, non-sulfur bacteria 2. Vibro parahaemolyticus – major cause of gastroenteritis
only amino acids
3. Zooglea in Japan, isolated from seawater, shellfish and
 Aerobic wastewater treatment crustaceans
C. Order Rhodobacteralles
 Thick gelatinous capsules D.Order Pseudomonadales
1. Rhodobacter sphearoides – purple non-sulfur bacteria
1. Azotobacter and Azomonas – N fixers
2. Paracoccus denitrificans – used as a model to study  Aids in flocculation
2. Moraxella – conjunctiva
denitrification  Helps in cleaning water
3. Roseobacter – aerobic, anoxygenic phototroph; pink 4. Neisseria gonorrhea - serious human pathogen
F.Order Legionalles
pigmented bacteriochlorophyll 5. Neisseria meningitides - serious human pathogen
1. Legionella – found in streams, warm-water pipes
6. Chromobacterium violaceum
Legionella pneumophilia – pneumonia
D. Order Rhodospiralles  Pus-forming wounds of humans
2.Coxiella – Q fever transmitted via aerosols/ milk
1. Acetobacter – production of acetic acid  Violacein – antimicrobial and antioxidant
2. Guconobacter – production of acetic acid properties CLASS DELTA PROTEOBACTERIA
3. Azospirillum – obligately aerobic diazotroph 7. Thiobacillus denitrificans
– nitrogen fixer  With few phenotypic characteristics in common
 Oxidize reduced sulfur
4. Magnetospirillum magnetotaticum  Members are chemoorganotrophic
8. Methylophylus
 Synthesis of high quality single-domain magnetite 1. Desulfovibrio – bioremediation
 Grow on methanol and other C compounds but 2. Bdellovibrio
crystals not on CH4 3. Myxococcus
9. Nitrosomonas and Nitrospira
Members;  Membrane more resistant to osmotic lysis  B. megaterium – spore, very good source of antibiotic
1.Dissmilatory sulfate reducers Lypoglycans  B. polymyxa – polymyxin (antibiotic)
- use S instead of O2 as final electron acceptor  Resembles lipopolysaccharides (structure)  Bacitracin
- Desulfuromonas (Culture of S-reducer)  Enables them to attach to host cells  B. thuringensis – BT corn, ability to produce cyst, toxin
2.Predatory bacterium that kill insects
-feed on other bacteria FIRMICUTES 9.Staphylococcus
-Bdellovibrio 1. Lactobacillus S. aureus
 Feeds on other Gram negative  Probiotic  Natural microflora of the skin
 Goes to the periplasm of another bacteria and  In fermentation of milk products, yogurt  Pathogenic if it penetrates the skin
feeds on the org compound  Considered to be very resistant to very low pH  Pimples, boils, pneumonia, meningitis, arthritis
 Bdelloplast modify both cells of the host and the  Important in the GI tract; helps fight bad bacteria by  Can produce toxin that cause food poisoning
bacteria keeping the nutrients away from them ACTINOMYCETES
3.Aerobic, gliding bacteria 2.Streptococcus Nocardia
 With complex life cycle  Hemolysis of RBC  Normal microflora of healthy gingiva
 Myxococcus Streptococcus pyrogenes – cause strep throat  Feliodontal pockets
 Aggregate under unfavorable conditions to form S. mutans – dental plague  Infection through inhalation or traumatic introduction
mound cells 3.Enterococcus
 Develop into spores  From fecal matter Frankia
 Quorum sensing 4.Listeria  Nitrogen fixer that forms nodules
 Belong to Bacilliales  Not leguminous plants but other plants
CLASS: EPSILON PROTEOBACTERIA  Does not form spores  Casuarina, looks like a pine tree
 Fairly homogenous in phenotypes L. Monocytogenes
 Some members are chemolithotrophic while others  Major food borne diseases Streptomyces
are chemoorganotrophic of animal  Contaminants of ready-made foods such as cheese  Production of antibiotics
 Found to inhabit extreme environments as well as and sausages  Chloramphenicol, Neomycin
gastrointestinal tracts of animals  Meningitis  Complex secondary metabolism
1. Helicobacter – acute enteritis, ulcers 5.Heliobacter
2. Campylobacter – bloody diarrhea caused by  Recently discovered anoxygenic phototrophic bacteria Actinomyces
enterotoxin  Produce endospores  Soil ecology / soil bacteria
6.Clostridium  Able to degrade chitin and lignin
GRAM POSITIVE BACTERIA  Spore former  Opportunistic pathogen
 Most common in soil and sediment environments  Fecal matter  Cause abscess in mouth and GI tract
 Divided into three groups or lineages  From soil Mycobacterium
low % G+C (clostridial lineage) (firmacutes)  C.tetani
wall-less tenericutes  Rod-shaped, acid fast →mycolic acid on the surface
– deeply punctured wound because it is anaerobic of the cell
mycoplasmatales – mollicutes –soil bacteria high in fecal matter
 Phylogenetically related to clostridiales  Pleomorphic and may undergo branching or
 C. botulinum filamentous growth but do not form a true mycelium
 Lactobacillus, Streptococcus, Heliobacter, Clostridium, –canned goods with NaNO3
Epulopiscium, Bacillus, Staphylococcus  Two major groups; slow growing and fast growing
–botulinum toxin flaccid paralysis M. tuberculosis – slow growing, inhalation
 C. perfringes M. leprae – leprosy, inhalation
TENERICUTES / MYCOPLASMA –cause gas gangrene Gardnerella
 Eukaryotic host 7.Epulopiscium  Signal organisms of altered microflora; not the cause
 Wall-less bacteria; move phylogenetically related to  Giant bacteria 236um long of bacterial vaginosis
clostridiales  2000 fold layer in volume than ordinary bacteria  G. vaginalis is the only species
 Gram+  Isolated from gut of fish  Facultative anaerobic, non-spore forming, nonmotile
 Human pathogen: live in close association with plants  Closely related to Clostridium
and animals 8.Bacillus Propionibacterium & Corynebacterium
 Very small genome – most symbionts  B. anthacis – anthrax
 Anaerobes, ferment lactic acid, carbohydrates and
polyhydroxy alcohol to produce propionic acid, acetic
acid and CO2
 Propionibacterium – Swiss cheese
 Corynebacterium
–highly pleomorphic with no definite arrangement
–metachromatic granules in polar regions
–toxin secreted into skin or nasopharyngeal lesions
–Diphttheric lesion is often covered by pseudo
membrane composed of fibrin, bacteria and
inflammatory cells
 C.diptheriae – diphtheria
BACTEROIDETES
 More than 700 characterized species
 Gram negative, non-sporulating rods
 Aerobic, fermentative metabolism
 Gliding motility is widespread, non-motile, some
moved by flagella
 Four orders;
a. Order Bacteroides
 Normal commensals in the intestinal tract of humans
→numerically dominant bacteria in the colon
 Occasional pathogens → cause bacteremia
 Some genera are able to synthesize sphingolipid
→brain and nervous system
b. Order Cytophagales
 Long, slender gram negative rods, often with pointed
ends → several species are fish pathogens
 Move by gliding
 Degrade complex polysaccharides
 Cellulose decomposers
 Some species can degrade agar and chitin
 Cytophaga
 Degrade cellulose
 Fish is stressed
c. Flavobacteriales
 Abundant in marine waters including aquatic systems
in polar environments
 Some are psychrophilic or psychotolerant
Flavobacterium
 Freshwater and marine
 Food and food processing plants
 Frequently produce yellow pigments
 Rarely pathogenic except Flavobacterium
meningosepticum
Chlamydiae, Planctomycetes and Verrucomincrobia
 Same ancestors and are closely related groups 1. Thermotoga
 Found in a variety of habitats (soil and aquatic)  Rod-shaped and form a sheath-like envelope
 Associated with eukaryotic hosts  Species isolated from terrestrial hot springs and
marine hydrothermal vents
Chlamydia and relatives  Strong homology to hyperthermophilic archea
 Lacks peptidoglycan and with a protein cell wall 2. Thermodesulfubacterium
 Obligate intercellular parasites of animals  Thermophilic, sulfur reducer
 Exhibits a complete life cycle  Optimal growth T is 70°C
Chlamydia trachomatis  Strict anaerobe
 STD  Similar to Archaea lipids- ether linkage
 Trachoma, disease of the eye that causes blindness  But side chains have unique hydrocarbons and
Chlamydiophila pneumoniae some fatty acids
 Pneumonia 3. Aquificae
Chlamydia psittaci Aquifix pyrophilus
 Transmitted by birds  A blue filamentous bacterium
 people who work on aviaries  Grows optimally at 85 - 95°C
 Obligate chemoautotroph
PLANCTOMYCETES  Most thermophilic of all known bacteria
 Lack peptidoglycan and contain a protein cell wall  Can tolerate very low oxygen
 Free-living aquatic oligotrophs that divide by budding Hydrogenobacter thermophilus
 All members of the group contain internal membrane-  Grows at 75°C
defined compartmentalization  Oxidizes H2 using O2 microaerophilically
1. Planctomyces – appendage or stalk (thinner and not
bound by membrane) Deinococci and Relatives
2. Gemmeta – true nuclear envelope,  Members with atypical cell wall – stain G+
 double-membrane nucleus,  Some are radiation resistant
 circular DNA  Some members are thermophilic
 true unit membrane Deinococcis radiorans
 swarmer cells for disposal  extremely resistant to radiation
 stalk attaches cells  Red pigmented (carotenoids); resistant to radiation
because it has very efficient DNA repair mechanism
SPIROCHETES Thermus aquaticus
 helical cells with central axial filaments  Thermophilic heterotrophic rods
 exhibit corkscrew  Used as a source of heat-stable enzymes
1. Treponema pallidum – syphilis  Taq Polymerase
2. Leptospira – leptospirosis
3. Cristicpira – harmless parasites of freshwater and GREEN SULFUR BACTERIA
marine molluscs and gastropods  Motile or nonmotile anoxygenic phototrophic bacteria
4. Nitrospira – nitrogen fixation  With light harvesting pigments in clorosomes → also
contains carotenoids
HYPERTHERMOPHILIC BACTERIA  Obligate anaerobes reproduce by binary fission
 3 phyla; (Thermotogae, Thermodesulfobacteria and CYANOBACTERIA
Aquificae) that clusternear the root of the phylogenetic  Photosynthetic, oxygen-evolving bacteria
tree of bacteria  Can be divided into 2 groups
 Each group consists of one or two major genera  With chl a and phycobiliproteins
 Key physiological feature is hyperthermophily (optimal Oxychlorobacteria
growth at temperature usu. Above 80°C)  With chl a and b lacking phycobiliproteins
 Prochlorothrix, Acaryochloris
DOMAIN ARCHAEA
 Morphologically similar to bacteria
 Cell walls do not contain peptidoglycans
 Ether-linked membrane lipids
 5 phyla based on comparative sequences or
ribosomal proteins
1. Euryarcheaota
2. Crenarcheaota
3. Thaumarcheaota
4. Koraracheaota
5. Nanoarcheaota
 Ecology: found in extreme environments
EURYARCHEAOTA
 Large and physiologically diverse group
 Includes methanogens and many extremely halophilic
genera
 Methanogens are strict anaerobes while extreme
halophiles are obligate aerobes
A. Extreme halophiles
 Mesophilic, facultative anaerobes
 Require atleast 2M NaCl for growth
 Haloarcula
 Halobacterium – first studied before domain
Archaea
B. Methanogens
 Obligate litotrophs
 Extreme anaerobes
 Found in all type of anaerobic environments
 True methanogens when subjected to light-
fluorescence
Major Groups
1. Methanobacterium and relatives
 With pseudomurein in their cell wall
 Pseudomurein composed of methanochondroitin
2. Methanococcus and relatives
 Complete prototrophs
 Grow only on H2+CO2
 Sometimes CO and/or formate
 Killed by oxygen
3. Methanomicrobium and relatives
 Come in various shapes
 Require acetate for growth
 Use H2 +CO2, sometimes CO and/or formate
4. Methanophyrus and relatives
 hyperthermophile KORARCHAEOTA
5. Methanoscracina and relatives  Hyperthermophile
 Use methylated substances to form CH4  Have not yet been cultured
 used in waste-management Korarchaeum
 produce little biomass  Molecularly determined
 Genome sequence from metagenomic analysis
C.Sulfur-matabolizing group (Analysis of different kinds of DNA)
 members are thermophilic
1. Archaeoglobus NANOARCHAEOTA
 sulfate-reducing hyperthermophile  Parasitic archaea
 optimum growth 83°C  Occur singly, in pairs or up to 10 or more cells per
 can perform methanogenesis is reverse when sulfur is host
limiting  Hyperthermophilic
2.Thermoplasma
 lacks cell wall and resembles Mycoplasma 1.Nanoarhchaeum equitans
 unique cell membrane with lipoglycans and  Smallest
lipoproteins  1% volume of E.coli
 very small genome  Cannot be grown alone in a pure culture
 Genes for replication only
CRENARCHAEOTA  Optimum growth 78-98°C
 mostly hyperthermophiles→ species growing at
temperatures above boiling point of water THUMARCHAEOTA
 mostly have been isolated from geothermally heated  Initially thought to be a divergent lineage of
soil or waters containing S and H2S Crenarchaeota
 Inhabit undersea hot springs or hydrothermal vents  Become a distinct phylum after genome analysis of
 Generally are obligate anaerobes Nitrosopumilus maritimus
 Good model for early archaea or early life: Deep-see  Members have unique lipid-crenarchaeol
vent hypothesis  Growth temperature is very diverse – from polar seas
to 75°C
Sulfolubus and other relatives  Ubiquitos in soild and found throughout marine
 Generally facultative microaerophiles column from equator to polar seas
 Utilize sulfur oxidation or reduction 1.Nitrosophumilus maritimus
 All are acidothermophiles  Adapted to light under extreme nutrition limitation
 All are organotrophic  Ammonia-oxidizing bacteria – 100times lower
1.Sulfolubus  Very low ammonia concentration
 Oxidize Fe 2.Nitrososphaera viennensis
2.Thermoproteus  Wide range of ammonia concentration
 Neutral or slightly acidic hot springs  Urease activity (Used ammonia)
3.Pyridictium  Ammonia-oxidizing bacteria
 Optimum growth at 105°C, Maximum temp 115°C
 irregularly disk-shaped
 Attach to crystals of sulfur
 Composed of glycoproteins
4.Pyrolobus
 Optimum growth at 105°C, maximum 113°C
 Walls of the black smoker
 Can survive autoclaving