chapter 4: prokaryotic diversity · gram-negative and phototropic non-proteobacteria 2....

Chapter 4:

PROKARYOTIC DIVERSITY

3. Gram-negative and Phototropic Non-Proteobacteria

2. Proteobacteria

1. Prokaryote Habitats, Relationships & Biomes

4. Gram-Positive Bacteria

5. Deeply Branching Bacteria

6. Archaea

1. Prokaryote Habitats,

Relationships & Biomes

Important Metabolic Terminology

Oxygen tolerance/usage:

aerobic – requires or can use oxygen (O2)

anaerobic – does not require or cannot tolerate O2

Energy usage:

phototroph – uses light as an energy source

• all photosynthetic organisms

chemotroph – acquires energy from organic or inorganic molecules

• organotrophs – get energy from organic molecules

• lithotrophs – get energy from inorganic molecules

…more Important Terminology

Facultative vs Obligate (or Strict):

facultative – “able to, but not requiring”

• e.g., facultative anaerobes can survive w/ or w/o O2

obligate – “absolutely requires”

• e.g., obligate anaerobes cannot survive in O2

Carbon Source:

autotroph – uses CO2 as a carbon source

• e.g., photoautotrophs or chemoautotrophs

heterotroph – requires an organic carbon source

• e.g., chemoheterotroph – gets energy & carbon from organic molecules

Oligotrophs require few nutrients, the opposite of eutrophs or copiotrophs

Symbiotic Relationships

Symbiotic relationships (close, direct interactions) between

different organisms in nature are of several types:

• e.g., humans have beneficial

bacteria in their digestive

tracts that also benefit from

the food we eat (mutualism)

Microbiomes

All the microorganisms that inhabit a particular organism

or environment (e.g., human or soil microbiome):

Classification in the Bacterial Domain

We will look at important genera from a variety of bacterial groups

classified largely on staining & rRNA sequences (ribotyping):

Gram-negative Bacteria

• Proteobacteria

• Nonproteobacteria & Phototrophic Bacteria

Gram-positive Bacteria

• High G+C (Actinobacteria)

• Low G+C (Firmicutes)

Deeply Branching Bacteria

2. Proteobacteria

Alphaproteobacteria

Betaproteobacteria

Gammaproteobacteria

Deltaproteobacteria

Epsilonproteobacteria

Alphaproteobacteria

Pathogenic genera:

Rickettsia

Chlamydia

Rhizobium

• intracellular pathogens

• typhus, Rocky Mountain spotted fever

• C. trachomatis – most common STD

Most are oligotrophs:

• nitrogen fixation in soil

R. rickettsii

Rhizobium

Betaproteobacteria

Pathogenic genera:

Neisseria

Thiobacillus

Bordetella

• oxidize H2S to sulfate is soil

• important in sulfur cycle

• gonorrhea (N. gonorrheae)

• whooping cough (B. pertussis)

• meningococcal meningitis

(N. meningitidis)

N. meningitidis

Most are eutrophs:

Gammaproteobacteria

Escherichia

Pseudomonas

Salmonella

Largest & most diverse class of Proteobacteria, including many

enteric bacteria and human pathogens:

• E. coli

• opportunistic pathogens

• typhoid fever, foodborne

salmonellosisL. pneumophila

Vibrio

• cholera (V. cholerae)

Legionella

• legionnaires disease (L. pneumophila)

Deltaproteobacteria

Small class of Proteobacteria containing soil bacteria that

reduce sulfate (Desulfovibrio) and the Myxobacteria that form

unusual “fruiting bodies”:

Myxobacteria

Epsilonproteobacteria

Pathogenic genera:

Helicobacter

Campylobacter

• H. pylori – peptic ulcers

• various species cause

blood poisoning, intestinal

illness (e.g., C. jejuni)H. pylori

Smallest class of Proteobacteria containing microaerophilic

species that are typical helical or vibrioid in shape :

3. Gram-Negative & Phototropic

Non-Proteobacteria

Spirochetes

Treponema

Borrelia

• T. pallidum – syphilis

• B. burgdorferi – Lyme disease

Very thin, highly coiled bacteria

that are hard to see under the

microscope and harder to

culture:

The CFB Group

Grouped based on DNA similarity and includes the following

genera:

Cytophaga Fusobacterium Bacteroides

Bacteroides

• Some are potentially

pathogenic (Cytophaga,

Fusobacterium), others are

beneficial (Bacteroides)

• most are anaerobic rods

Sheath

Vegetativecell

Heterocyst

Akinete

Anabaena Oscillatora

Cyanobacteria

Gram-negative, oxygenic photoautotrophs

Anabaena

• carry out nitrogen fixation in non-photosynthetic heterocysts

• produce vast amounts of oxygen gas via photosynthesis, fix nitrogen (N2 NH4+)

Purple & Green Bacteria

Obligately anaerobic, anoxygenic photoautotrophs

• use organic molecules as a source of electrons (not H2O)

Green and Purple non-sulfur bacteria

Green and Purple sulfur bacteria

• use H2S as a source of electrons

• elemental sulfur is then released

(green sulfur bacteria) or forms

inclusions (purple sulfur bacteria)

4. Gram-Positive Bacteria

Classification of Gram-Positive Bacteria

Gram-positive bacteria are grouped based on DNA similarity:

Low G+C Gram-positive bacteria (Firmicutes)

• contains many serious pathogens

• characterized by branching filaments

High G+C Gram-positive bacteria (Actinomycetes)

• includes some pathogens

Actinobacteria (High G+C)

Streptomyces

Corynebacterium

Mycobacterium

• important soil bacteria, recycle nutrients

• many produce antibiotics (erythromycin, tetracycline)

• diphtheria (C. diphtheria)

• tuberculosis (M. tuberculosis), leprosy (M. leprae)

• contain mycolic acids in cell wall (stain acid-fast)

Bifidobacterium

• significant member of beneficial gut microbiota

C. diphtheria

Streptomyces

Firmicutes (Low G+C)…

Streptococcus

Staphylococcus

*Bacillus

*Clostridium *produce

endospores

• strep throat (S. pyogenes)

• MRSA (S. aureus)

• anthrax (B. anthracis)

• tetanus (C. tetani)

• botulism (C. botulinum)

C. difficile

S. pyogenes

S. aureus

• colitis (C. difficile)

Mycoplasma

• very small (less than 1 mm)

Lactobacillus

…more Firmicutes

• species used in fermented food products (e.g., yogurt, buttermilk, pickles)

• part of normal, healthy microbiota in human mouth, digestive tract, vagina

• no cell wall (stain Gram-negative)

• obligate intracellular pathogens

Mycoplasma

colonies

5. Deeply Branching Bacteria

Last Common Universal Ancestor

What Are “Deeply Branching Bacteria”?

Bacteria very close

to the base of the

phylogenetic tree:

• members of the

domain Bacteria

that diverged

very early, ~3.5

billion years ago

Genera of “Deeply Branching Bacteria”

Acetothermus

• deepest branching bacteria known to date

• thermophiles and hyperthermophiles

Aquifex

• adapted to harshest conditions on planet

(e.g., thermal oceanic vents that reach 138oC!)

Deinococcus

• D. radiodurans known as “Conan the

Bacterium” for the extremes of heat, UV,

radioactivity, etc, it can survive

D. radiodurans

6. Archaea

The Domain Archaea

Highly diverse group of prokaryotes first classified in 1977 by

Carl Woese and George Fox:

• cell walls made of material other than peptidoglycan

• have unusual membrane lipids

• much larger genomes that bacteria

• have metabolic processes, rRNA sequences and other features

more closely resembling eukaryotes

• e.g., initiate translation with methionine (as do eukaryotes) rather

than N-formyl methionine as do the Bacteria

Two Main Phyla

Crenarchaeota

• most are hyperthermophiles, some

acidophiles

Euryarchaeota

• includes the methanogens, halophiles, a few

thermophiles

**NO known archaeon causes disease in humans or animals!**

Other Phyla

• Korarchaeota, Nanoarchaeota, Thaumarchaeota

• based on environmental RNA

Sulfolobus

Key Terms for Chapter 4

• autotroph, heterotroph, oligotroph, eutroph

• facultative vs obligate

• aerobic vs anaerobic

• thermophile, halophile

• phototroph, chemotroph, organotroph, lithotroph

• symbiosis: mutualism, amensalism, commensalism,

neutralism, parasitism