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Home , Korarchaeota, Oligotroph, Organotroph, Phototroph

Chapter 4: PROKARYOTIC DIVERSITY

1. , Relationships & Biomes 2. 3. Gram-negative and Phototropic Non-Proteobacteria 4. Gram-Positive 5. Deeply Branching Bacteria 6. 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: – uses light as an source • all photosynthetic

– acquires energy from organic or inorganic molecules

• – get energy from organic molecules

• – get energy from inorganic molecules …more Important Terminology Source:

– uses CO2 as a carbon source • e.g., photoautotrophs or chemoautotrophs – requires an organic carbon source • e.g., chemoheterotroph – gets energy & carbon from organic molecules require few , the opposite of eutrophs or 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 Symbiotic Relationships

Symbiotic relationships (close, direct interactions) between different organisms in are of several types:

• e.g., humans have beneficial bacteria in their digestive tracts that also benefit from the food we eat () Microbiomes All the that inhabit a particular or environment (e.g., human or microbiome): Classification in the Bacterial 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 () • Low G+C () Deeply Branching Bacteria 2. Proteobacteria

Alphaproteobacteria

Betaproteobacteria Gammaproteobacteria

Deltaproteobacteria

Epsilonproteobacteria Alphaproteobacteria

Most are oligotrophs: Rhizobium Rhizobium • in soil

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

Thiobacillus • oxidize H S to sulfate is soil 2 Pathogenic genera: • important in cycle Neisseria • gonorrhea (N. gonorrheae) • meningococcal meningitis (N. meningitidis)

Bordetella • whooping cough (B. pertussis)

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

Myxobacteria Epsilonproteobacteria

Smallest class of Proteobacteria containing microaerophilic 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 3. Gram-Negative & Phototropic Non-Proteobacteria 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 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 Gram-negative, oxygenic photoautotrophs

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

Anabaena • carry out nitrogen fixation in non-photosynthetic heterocysts

Vegetative cell Sheath Heterocyst

Akinete

Anabaena Oscillatora & Green Bacteria

Obligately anaerobic, anoxygenic photoautotrophs

Green and Purple non-sulfur bacteria

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

Green and

• use H2S as a source of electrons

• elemental sulfur is then released () 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

High G+C Gram-positive bacteria (Actinomycetes)

• characterized by branching filaments

• includes some pathogens 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 (stain acid-fast) • tuberculosis (M. tuberculosis), leprosy (M. leprae)

Streptomyces Bifidobacterium • significant member of beneficial gut microbiota 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) …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 5. Deeply Branching Bacteria 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 Genera of “Deeply Branching Bacteria” Acetothermus • deepest branching bacteria known to date D. radiodurans • and

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 6. Archaea The Domain Archaea

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

• have metabolic processes, rRNA sequences and other features more closely resembling • 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 Two Main Phyla Sulfolobus

• most are hyperthermophiles, some • includes the , , a few thermophiles

Other Phyla • Korarchaeota, , • based on environmental RNA **NO known archaeon causes disease in humans or !** Key Terms for Chapter 4

• aerobic vs anaerobic • facultative vs obligate • phototroph, chemotroph, , • autotroph, heterotroph, , eutroph • : mutualism, amensalism, , neutralism, • ,