Microorganism Taxonomy Classification and Characteristics

BIOL 2421 Lecture Notes
Microorganism Taxonomy and Organism Classification
Dr. Weis

Old classification: 5 Kingdoms

Monera (Prokaryotes) = Bacteria

Protista = Slime Molds, Protozoa, Unicellular Algae

Fungi = Molds, Yeasts, Mushrooms

Plantae = Multicellular Algae, Mosses, Plants

Animaliae = Insects, Worms, Vertebrates, Sponges

Further classification within the Kingdoms:

Species->Genus-> Family -> Order-> Class->Phylum-> Kingdom

For bacteria, there may be subspecies, strains, serotypes / serovar, and varieties that further classify a particular species.

Current Classification: 3 Domains (Super Kingdoms)

Archaea

Eubacteria

Eukarya

These new classification reflects genetic differences based on ribosomal RNA.

Archaea (Ancient Bacteria) and Eubacteria (True Bacteria) are still considered the Prokaryotes, a Greek name meaning before the [true] nucleus. Prokaryotes are the oldest, most abundant, and widely distributed group of organisms and can be found almost everywhere: soil, water, air, and even in extreme environments. They are generally single celled organisms with no internal membrane bound organelles and a singular circular chromosome. However, the two Domain groups differ in the structure of their plasma membrane and cell wall.

Prokaryotic Reproduction = Asexual Reproduction

A. Binary Fission

* DNA replicated, attached to cytoplasmic membrane of cell wall

* cell growth occurs

* cross wall divides

* daughter cells form, may or may not separate

cell wall division and daughter separation leads to arrangement of cells

Possible Cocci arrangement after division

^ pairs

^ chains

^ tetrads

^ cubes

^ clusters

Possible Rod arrangement after division

^ separate

^ longitudinal pairs

^ chains

B. Snapping Division

* Inner cell wall divides

* Daughter cell attached by a portion of the outer cell wall to create a hinged appearance

C. Budding

* Out growth from original cell

D. Reproductive Spore formation

* Clone of original cell at end of filament

Domain of Archaea:

No known human pathogens

Plasma membrane consists of a glycerol bonded to branched fatty acids.

Cell wall does not contain peptidoglycan or muramic acid.

Unicellular organisms are adapted to extreme environments.

Asexual reproduction

Pleomorphic shapes

Examples include two Phyla: Crenarchaeota and Euryarchaeota

Extremophiles

a) Thermophiles, which grow at temperatures of 45°C or above

Hyperthermophiles prefer temperatures above 80ºC

Found in hot springs, ocean geysers

b) Halophiles, which grow in salty environments containing at least 9% NaCl. 20% NaCl is optimal; found in the Dead Sea

c) Psychrophiles: cold loving, found in Antarctic Sea

d) Acidophiles: acid loving microbes, pH < 5; found in Sulfur springs

e) Alkaliphiles: basic loving microbes; pH >9; found in soda lakes

Methanogens

Largest group of Archaea bacteria

Grow in anaerobic conditions using CO2 to generate methane gas

Domain of Bacteria

Plasma membrane similar to Eukaryotes in that the glycerol is bonded to a straight chained fatty acids.

Cell wall composed of a peptidoglycan, a protein-carbohydrate polymer that contains muramic acid.

Reproduce primarily by binary fission (asexual reproduction)

Unicellular

Domain of Eukaryotes

Organelles: Membranous and Nonmembranous

Plasma membrane: phospholipid bilayer with proteins and other fats

Cell wall (if present): polysaccharides depending on organism

Fungi – chitin

Plants and Algae – cellulose, pectins

Vertebrates- no cell wall

Compare and Contrast of Two Major Super Kingdoms: Eukarya and Prokarya

Structure	Eukaryotes	Prokaryotes
DNA	Enclosed in membrane Multiple chromosomes Associated with histones DNA in nucleus	Not enclosed in membrane One circular chromosome No histones, other proteins used in small amounts DNA in nucleoid region
Organelles	Most are enclosed in a membrane	Not enclosed in a membrane
Ribosomes	Free in cytoplasm; small 70S	Free or bound; large 80S
Cell Walls	Chitin, cellulose, pectin	Peptidoglycan
Division	Mitosis Sexual and Asexual Reproduction	Binary Fission Asexual reproduction
Cytosol	Water / electrolytes	Water / electrolytes
Motility	Flagella	Flagella
Additional processes	Cilia	Pili

Specific Types of Microorganisms

A. Bacterium, Bacteria:

Prokaryotic

Unicellular

Several Shapes:

Coccus (spherical), Bacillus (Rod like), Spiral (Corkscrew)

Others are modified versions: Coccobacillus, pleomorphic

Most beneficial, some pathogenic

Photosynthetic or derive nutrition from environment

B. Other organisms now classified as Bacteria: Rickettsia, Chlamydia, Mycoplasma

Prokaryotic

Progressively smaller in size

Most are pathogenic

Rickettsia use arthropod vectors such as ticks

Rocky Mountain Spotted Fever, Ehrlichia, Cat Scratch Fever

Chlamydia infects living tissues, primarily open body cavities

Chlamydia

Mycoplasmas have no cell walls, smallest of all the bacteria

Leprosy, Tuberculosis

C. Fungus, Fungi

Eukaryotic

Unicellular = yeast

Multicellular = molds, mushrooms

Use preformed organic matter in environment for nutrition via hyphae

Cell wall contains chitin

Most beneficial in decomposition

Some pathogenic (external and internal)

Examples: Ringworm, Cryptococcus, Blastomycosis

D. Protozoa

Eukaryotic

Unicellular

Lack cell wall

Classified based on movement (ciliates, flagellates, pseduopods)

Photosynthetic or absorb/ingest/recycle nutrients from decomposing organisms

Pathogenic if access nutrients from living organisms

Examples: Amoebas, Trypanosomes, Giardia, Coccidia

E. Viruses

Acellular

Nucleic acid core of EITHER DNA or RNA (not both)

Protein coat surrounds nucleic acid core

+ /- lipid membrane envelope

Primary function is to reproduce/replicate, only in living tissues

Not considered living organisms, outside host are inert

Multiply in host cells, destroying cells in process -> tissue degradation

Bacterial Taxonomy Overview

Additional classifications of bacteria using various microscopy techniques in the DNA sequencing of RNA have given microbiologists the following phylogenic groups for bacteria:

Bacterial Groups	Example
Thematogales	Thermatoga maritima
Green Nonsulfur Bacteria	Chlorflexus aurantiacus
Green Sulfur Bacteria	Chlorobium limicola
Flavobacteria	Flavobacterium litoralis
Bacteriodes	Bacteriodes fragilis
Fusobacteria	Fusobacterium ulcerans
Cyanobacteria	Oscillatora sp.
Planctomycetes	Chlamydia trachomatis
Spirochetes	Borrelia burgdorferi
High Gram Positives	Mycobacterium tuberculosis
Low Gram Positives	Staphylococcus aureus
Є proteobacteria	Helicobacter pylori
δ proteobacteria	Myxococcus xanthus
ά proteobacteria	Rickettsia reickettsii
γ proteobacteria	Vibrio cholerae
β proteobacteria	Alcaligenes denitrificans

Recall that Genus and species are used to identify the bacterial organism.

Other subtypes may be identified based on strain number, serotype/serovars, varieties, etc.

Bergey’s Manual is the current reference for bacterial groups. Other organisms have nomenclature based on specific publications.

Bacterial Taxonomy

I. Deeply Branching

Autotrophic

Anaerobic

Resistant to radiation

II. Phototrophic

Autotrophic

Grouped based on pigment

* Blue algae

* Green algae

* Purple/Red algae

III. Gram Positive Bacteria

A. Low G+C

1. Clostridia

G + bacillus, obligate anaerobe, endospores, toxins

2. Mycoplasmas

no cell wall, appear G negative pleomorphic filamentous

sterols in cell membrane

colonize respiratory and uritogenital tracts

smallest free living cells

3. Gram Positive Rods [Low G+C]

a) Bacillus

facultative anaerobe

endospore

motile via flagella

Dz: Food poisoning, Anthrax

b) Listeria

psychrophilic

Dz: food poisoning, infection in immunosuppressed

c) Lactobacillus

normal gut inhabitant

used in food industry [active yogurt culture]

4. Gram Positive Cocci [Low G+C]

a) Streptococcus, Enterococcus

Dz: toxin formation, affects numerous body systems

b) Staphylococcus

normal skin flora

Dz: food poisoning, blood poisoning

B. High G+C

1. Actinobacteria

a) Corynebacterium

facultative anaerobe

pleomorphic rod

snapping division

metochromic granules

Dz: diphtheria

b) Mycobacterium

aerobic

straight to curved rods

slow growth on media

cell wall contains mycolic acid => Acid Fast Stain

Dz: TB, leprosy

c) Actinomycetes

i) Actinomyces

normal inhabitant of the mouth

Dz: Actinomyces

ii) Nocardia

found in environment

Dz: lesions in heart

iii) Streptomyces

environmental recycler

used to produce antibiotics: CHPC, Tetracycline

IV. Gram Negative Proteobacteria

A. Alpha

1. Nonpathogenic: Environmental nitrogen fixers

2. Pathogenic

a) Rickettsia: aerobic gram – rod; RMSF

b) Brucella: coccobacillus; Reproductive abortions

c) Ehrlichia: tickborne ; Ehrlichiosis

B. Beta

1. Nonpathogenic: Environmental nitrogen or sulfur fixers

2. Pathogenic

a) Neisseria: diplococcus, inhabit mucus membranes

Dz: gonorrhea, meningitis

b) Bordetella: coccobacillus; inhabit respiratory tract

Dz: pertussis [whooping cough]

c) Burkholderia: respiratory inhabitant

d) Spirillum: causative agent of rat bite fever

C. Gamma

1. Nonpathogenic: Environment by products sulfur or methane

2. Pathogenic

a) Legionella: found in standing water; Legionellosis pneumonia

b) Coxiella: causative agent of Q fever

c) Enterobacteriaceae

i E. coli

ii. Salmonella

iii Shigella

iv Proteus

v Yersinia

vi. Enterobacter

vii Serratia

d) Pseudomonads : gram neg rod, aerobic, flagella

i Pseudomonas

D. Delta

1. Nonpathogenic: Environmental recyclers, H2S production

2. Pathogenic: all other gram neg bacteria

E. Epsilon

Pathogenic

a) Campylobacter: GI inflammation

b) Heliobacter: GI ulcer

F. Others

Chlamydia gram negative cocci; STD

Spirochetes helical shape

Treponema: STD syphilis

Borrela : tick borne dz à Lyme Disease

Bacteriodes gram neg rod, facultative anaerobe, normal GI flora