3/9/2020

Chapter 4: PROKARYOTIC DIVERSITY

1. Prokaryote Habitats, Relationships & Biomes 2. Proteobacteria 3. Gram-negative and Phototropic Non-Proteobacteria 4. Gram-Positive Bacteria 5. Deeply Branching Bacteria 6. Archaea

1

1. Prokaryote Habitats, Relationships & Biomes

2

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

3

1 3/9/2020

…more Important Terminology 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 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 4

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)

5

Microbiomes All the microorganisms that inhabit a particular organism or environment (e.g., human or soil microbiome):

6

2 3/9/2020

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

7

2. Proteobacteria

Alphaproteobacteria

Betaproteobacteria Gammaproteobacteria

Deltaproteobacteria

Epsilonproteobacteria

8

Alphaproteobacteria

Most are oligotrophs: Rhizobium Rhizobium • nitrogen fixation in soil

Pathogenic genera: Rickettsia • intracellular pathogens • typhus, Rocky Mountain spotted fever Chlamydia R. rickettsii • C. trachomatis – most common STD 9

3 3/9/2020

Betaproteobacteria Most are eutrophs:

Thiobacillus

• oxidize H2S to sulfate is soil Pathogenic genera: • important in sulfur cycle Neisseria • gonorrhea (N. gonorrheae) • meningococcal meningitis (N. meningitidis)

Bordetella • whooping cough (B. pertussis)

N. meningitidis 10

Gammaproteobacteria

Largest & most diverse class of Proteobacteria, including many enteric bacteria and human pathogens:

Escherichia Vibrio • E. coli • cholera (V. cholerae) Legionella

• legionnaires disease (L. pneumophila)

Pseudomonas • opportunistic pathogens

Salmonella • typhoid fever, foodborne L. pneumophila salmonellosis 11

Deltaproteobacteria Small class of Proteobacteria containing soil bacteria that reduce sulfate (Desulfovibrio) and the Myxobacteria that form unusual “fruiting bodies”:

Myxobacteria 12

4 3/9/2020

Epsilonproteobacteria

Smallest class of Proteobacteria containing microaerophilic species that are typical helical or vibrioid in shape :

Pathogenic genera:

Helicobacter • H. pylori – peptic ulcers

Campylobacter • various species cause blood poisoning, intestinal illness (e.g., C. jejuni) H. pylori 13

3. Gram-Negative & Phototropic Non-Proteobacteria

14

Spirochetes Very thin, highly coiled bacteria that are hard to see under the microscope and harder to culture:

Treponema • T. pallidum – syphilis

Borrelia • B. burgdorferi – Lyme disease

15

5 3/9/2020

The CFB Group Grouped based on DNA similarity and includes the following genera: Cytophaga Fusobacterium Bacteroides

• most are anaerobic rods

• Some are potentially pathogenic (Cytophaga, Fusobacterium), others are beneficial (Bacteroides) Bacteroides 16

Cyanobacteria Gram-negative, oxygenic photoautotrophs

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

Anabaena • carry out nitrogen fixation in non-photosynthetic heterocysts

Vegetative cell Sheath Heterocyst

Akinete

Anabaena Oscillatora 17

Purple & Green Bacteria

Obligately anaerobic, anoxygenic photoautotrophs

Green and Purple non-sulfur bacteria

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

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)

18

6 3/9/2020

4. Gram-Positive Bacteria

19

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

High G+C Gram-positive bacteria (Actinomycetes)

• characterized by branching filaments

• includes some pathogens

20

Actinobacteria (High G+C)

Streptomyces

• important soil bacteria, recycle nutrients • many produce antibiotics (erythromycin, tetracycline)

Corynebacterium C. diphtheria • diphtheria (C. diphtheria)

Mycobacterium • contain mycolic acids in cell wall (stain acid-fast) • tuberculosis (M. tuberculosis), leprosy (M. leprae)

Streptomyces Bifidobacterium • significant member of beneficial gut microbiota 21

7 3/9/2020

Firmicutes (Low G+C)…

Streptococcus S. pyogenes • strep throat (S. pyogenes)

Staphylococcus • MRSA (S. aureus) S. aureus

C. difficile *Bacillus • anthrax (B. anthracis) *Clostridium *produce • tetanus (C. tetani) endospores • botulism (C. botulinum) • colitis (C. difficile) 22

…more Firmicutes Lactobacillus

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

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

colonies Mycoplasma

• very small (less than 1 mm)

• no cell wall (stain Gram-negative)

• obligate intracellular pathogens

Mycoplasma 23

5. Deeply Branching Bacteria

24

8 3/9/2020

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

Last Common Universal Ancestor

25

Genera of “Deeply Branching Bacteria” Acetothermus • deepest branching bacteria known to date D. radiodurans • 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

26

6. Archaea

27

9 3/9/2020

The Domain Archaea

Highly diverse group of prokaryotes first classified in 1977 by Carl Woese and George Fox:

• 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

• cell walls made of material other than peptidoglycan • have unusual membrane lipids • much larger genomes that bacteria

28

Two Main Phyla Sulfolobus Crenarchaeota

• most are hyperthermophiles, some acidophiles Euryarchaeota • includes the methanogens, halophiles, a few thermophiles

Other Phyla • Korarchaeota, Nanoarchaeota, Thaumarchaeota • based on environmental RNA **NO known archaeon causes disease in humans or animals!**

29

Key Terms for Chapter 4

• aerobic vs anaerobic • facultative vs obligate • phototroph, chemotroph, organotroph, lithotroph • autotroph, heterotroph, oligotroph, eutroph • symbiosis: mutualism, amensalism, commensalism, neutralism, parasitism • thermophile, halophile

30

10