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Title: The Diversity of Prokaryotic
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Organisms
Speaker:
Amit
Dhingra
Instructor: Consetta Helmick
Created by: (remove if same as speaker)
online.wsu.edu
The Diversity of Prokaryotic
Organisms
Diversity of Prokaryotes
 Scientists just beginning to understand vast
diversity of microbial life
 Only ~6,000 of estimated million species of
prokaryotes described
• 950 genera
 Vast majority have
not been isolated
 New molecular
techniques aiding
in discovery,
characterization
Diversity of Prokaryotes
 Prokaryotes are
metabolically diverse
• Numerous
approaches to
harvesting energy to
produce ATP
Anaerobic Chemotrophs
 Atmosphere anoxic for first ~1.5 billion years that
prokaryotes inhabited earth
• Early chemotrophs likely used anaerobic respiration
•Terminal electron acceptors like abundant CO2 or S
• Others may have used fermentation
•Passed electrons to organic molecule like pyruvate
 Today anaerobic habitats common
•
•
•
•
Aerobes contribute by depleting O2
Mud, tightly packed soil limit diffusion of gases
Aquatic environments can become limiting
Human body (especially intestinal tract)
•Also anaerobic microenvironments in skin, oral cavity
Anaerobic Chemotrophs
 Anaerobic Chemolithotrophs (continued…)
• Methanogens are group of methane-producing archaea
•Oxidize H2 gas to generate ATP
•Alternatives include formate, methanol, acetate
•CO2 as terminal electron acceptor
•Smaller energy yield than other electron acceptors
•Very sensitive to O2
•Sewage, swamps, marine
sediments, rice paddies,
digestive tracts
•Cows produce ~10 ft3/day
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(a)
5 µm
(b)
a: © F. Widdel/Visuals Unlimited; b: © Ralph Robinson/Visuals Unlimited
5 µm
Anaerobic Chemotrophs
 Anaerobic Chemoorganotrophs—Respiration
• Chemoorganotrophs oxidize organic compounds (e.g.,
glucose) to obtain energy
•Anaerobes often use sulfur, sulfate as electron acceptor
• Sulfur- and Sulfate-Reducing Bacteria
•Produce hydrogen sulfide (rotten-egg smell)
•H2S is corrosive to metals
•Important in sulfur cycle
•At least a dozen recognized genera
•Desulfovibrio most studied
•Gram-negative curved rods
•Some archaea
Anaerobic Chemotrophs
 Anaerobic Chemoorganotrophs—Fermentation
• Numerous anaerobic bacteria ferment
•ATP via substrate-level phosphorylation
•Many different organic energy sources, end products
• Clostridium are Gram-positive, endospore-forming rods
•Common in soils; vegetative cells live in anaerobic
microenvironments created by aerobes consuming O2
•Endospores tolerate O2, survive long periods of heat,
drying, chemicals, irradiation;
•Germinate when conditions improve
•Diverse metabolism; some cause diseases
Anaerobic Chemotrophs
 Anaerobic Chemoorganotrophs—Fermentation
• Lactic Acid Bacteria: produce lactic acid
•Most can grow in aerobic environments; only ferment
•Lack catalase
•Streptococcus inhabit oral cavity; normal microbiota
•Some pathogenic (e.g., β-hemolytic S. pyogenes)
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10 µm
(b)
a: © Thomas Tottleben/Tottleben Scientific Company; b: © David M. Phillips/Visuals Unlimited
1 µm
Anaerobic Chemotrophs
 Anaerobic Chemoorganotrophs—Fermentation
• Lactic Acid Bacteria (continued…)
•Lactococcus species used to make cheese, yogurt
•Enterococcus inhabit human, animal intestinal tract
•Lactobacillus rod-shaped, common in mouth, vagina
•Break down glycogen deposited in vaginal lining
•Resulting low pH helps
prevent vaginal infections
•Also present in
decomposing materials
•Important in production
of fermented foods
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5 µm
© John Walsh/Photo Researchers, Inc.
Anoxygenic Phototrophs
 Earliest photosynthesizers likely anoxygenic
phototrophs
• Use hydrogen sulfide or organic compounds (not water)
to make NADPH; do not generate O2
• Modern-day phylogenetically diverse
•Live in bogs, lakes, upper layers of mud
•Little or no O2, but light penetrates
•Different photosystems than plants, algae, cyanobacteria
•Use unique bacteriochlorophyll
•Absorb wavelengths that penetrate deeper
Anoxygenic Phototrophs
 Purple Bacteria
• Purple Sulfur Bacteria (continued…)
•Representatives include Chromatium, Thiospirillum,
Thiodictyon
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Sulfur granules
(a)
(b)
10 µm
a: Courtesy of Dr. Heinrich Kaltwasser. From ASM News 53(2): Cover, 187.; b: From M. P. Starr et al (Eds.), The Prokaryotes. Springer-Verlag.
Anoxygenic Phototrophs
 Purple Bacteria (continued...)
• Purple Non-Sulfur Bacteria
•Moist soils, bogs, paddy fields
•Preferentially use organic molecules instead of H2S as
source of electrons
•Lack gas vesicles
•May store sulfur; granules form outside cell
•Remarkably diverse metabolism
•Many use H2 or H2S (like purple sulfur bacteria)
•Most can grow aerobically in absence of light using
chemotrophic metabolism
•Representatives include Rhodobacter,
Rhodopseudomonas
Anoxygenic Phototrophs
 Green Bacteria
• Gram-negative; typically green or brownish
• Green Sulfur Bacteria:
•Habitats similar to purple sulfur bacteria
•Form granules outside of cell
•Accessory pigments located in chlorosomes
•Lack flagella
•May have gas vesicles
•Strict anaerobes
•None are chemotrophic
•Representatives include
Chlorobium, Pelodictyon
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Sulfur granules
5 µm
From J. G. Holt (Ed.), The Shorter Bergey's Manual of Determinative Bacteriology,
8/e, 1977. Williams and Wilkins Co.,Baltimore
Oxygenic Phototrophs
 Cyanobacteria (continued...)
• Morphologically diverse
• Unicellular: cocci, rods,
spirals
• Multicellular: filamentous
associations: trichomes
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•May be in sheath
•Motile trichomes glide
as unit
(a)
15 µm
(b)
100 µm
• May have gas vesicles for
vertical movement in water
a: Courtesy of Isao Inouye, University of Tsukuba, Mark A. Shneegurt, Wichita State University and Cyanosite
(www. cyanosite.bio.purdue.edu/index.html); b: © M. I. Walker/Photo Researchers, inc.
Oxygenic Phototrophs
 Cyanobacteria (continued...)
• Large numbers can accumulate in freshwater habitats
•Called a bloom
•Sunny, hot weather can lyse cells, create scum
• Photosystems like those in chloroplasts of algae,
plants, which evolved from
ancestral cyanobacteria
• Also have phycobiliproteins
•Absorb additional
wavelengths
Oxygenic Phototrophs
 Cyanobacteria (continued...)
• Nitrogen-fixing cyanobacteria critical ecologically
•Incorporate N2 and CO2 into organic material
•Form usable by other organisms
•Nitrogenase destroyed by O2, must be protected
•Anabaena form specialized heterocysts
•Lack photosystem II
•A. azollae fixes N2 in
special sac of fern
•Synechococcus fix
N2 in dark
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Heterocyst
10 µm
Courtesy of Roger Burks, University of California Riverside, Mark A. Schneegurt, Wichita State University and Cyanosite
(www.cyanosite.bio.purdue.edu/index.html)
Aerobic Chemolithotrophs
 Aerobic chemolithotrophs gain energy by
oxidizing reduced inorganic chemicals
• Sulfur-oxidizing bacteria: Gram-negative rods, spirals
•Energy from oxidation of sulfur, sulfur compounds
including H2S, thiosulfate
•Important in sulfur cycle
•Filamentous and unicellular lifestyles
Aerobic Chemolithotrophs
 Aerobic chemolithotrophs (continued...)
• Filamentous Sulfur Oxidizers
•Beggiatoa, Thiothrix: sulfur
springs, sewage-polluted
waters, surface of marine
and freshwater sediments
•Store sulfur as intracellular
granules
•Beggiatoa filaments move by
gliding motility
•Thiothrix filaments immobile;
progeny cells detach, move
via gliding motility
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Multicellular
filament
Sulfur
granules
Cellular
septa
(a)
(b)
10 µm
10 µm
a: Courtesy of J. T. Staley and J. P. Dalmasso; b: Courtesy of Dr. James Staley
Aerobic Chemolithotrophs
 Aerobic chemolithotrophs (continued...)
• Unicellular Sulfur Oxidizers
•Acidithiobacillus: terrestrial and aquatic habitats
•Oxidize metal sulfides, can be used for bioleaching
•E.g., oxidation of gold sulfide produces sulfuric acid;
lower pH converts metal
to soluble form
•Can oxidize sulfur in fuels to
sulfate; removal helps
prevent acid rain
•Can produce damaging
acid runoff as low as pH 1.0
Aerobic Chemolithotrophs
 Aerobic chemolithotrophs (continued...)
• Nitrifiers are diverse group of Gram-negatives
•Oxidize inorganic nitrogen compounds for energy
•Concern to farmers using ammonium nitrogen
•Can deplete water of O2 if wastes high in ammonia
•Two groups; usually grow in close association
•Ammonia oxidizers: Nitrosomonas, Nitrosococcus
•Nitrite oxidizers: Nitrobacter, Nitrococcus
Aerobic Chemolithotrophs
 Aerobic chemolithotrophs (continued...)
• Hydrogen-Oxidizing Bacteria
•Aquifex, Hydrogenobactera among few hydrogen-oxidizing
bacteria that are obligate chemolithotrophs
•Thermophillic; typically inhabit hot springs
•Some Aquifex have maximum growth at 95ºC
•Deeply branching in phylogenetic tree, believed one of
earliest bacterial forms to exist on earth
•O2 requirements low, possibly available early on in
certain niches due to photochemical processes that
split water
Aerobic Chemoorganotrophs
 Aerobic chemoorganotrophs oxidize organic
compounds for energy
• Some inhabit specific environments, others ubiquitous
• Obligate Aerobes
• Micrococcus: Gram-positive cocci
•Found in soil, dust
particles, inanimate
objects, skin
•Pigmented colonies
•Tolerate dry, salty
conditions
Aerobic Chemoorganotrophs
• Obligate Aerobes
• Mycobacterium are acid-fast bacteria
•Mycolic acid in cell wall prevents Gram-staining
•Special staining used; resist destaining
•Generally pleomorphic rods
•Notable pathogens: M. tuberculosis, M. leprae
•More resistant to disinfectants, differ in susceptibility to
antimicrobial drugs
•Related Nocardia species also acid-fast
Aerobic Chemoorganotrophs
• Obligate Aerobes (continued…)
• Pseudomonas: Gram-negative rods; oxidase positive
•Motile by polar flagella; often produce pigments
•Most are strict aerobes; no fermentation
•Extreme metabolic diversity important in degradation
•Ability sometimes from plasmids
•Widespread: soil, water
•Most harmless
•Some pathogens:
P. aeruginosa common
opportunistic pathogen
Aerobic Chemoorganotrophs
• Obligate Aerobes (continued…)
• Family Enterobacteriaceae: enterics or enterobacteria
are Gram-negative rods typically found in intestinal tract
of humans, other animals; some thrive in soil
•Facultative anaerobes that ferment glucose
•Normal intestinal microbiota include Enterobacter,
Klebsiella, Proteus, most E. coli strains
•Those that cause diarrheal disease include Shigella,
Salmonella enterica, and some E. coli strains
•Life-threatening systemic diseases include typhoid fever
(Salmonella enterica serotype Thyphi) and bubonic and
pneumonic plague (Yersinia pestis)
•Lactose fermenters termed coliforms
Ecophysiological Diversity
Thriving in Terrestrial Environments
 Soils pose variety of challenges
• Wet and dry, warm and cold, abundant to sparse
nutrients
• Bacteria that form a resting stage
• Endospore-formers most resistant
to environmental extremes
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•Bacillus, Clostridium most
common
•Gram-positive rods
•Bacillus include obligate and
facultative anaerobes
•Some medically important:
B. anthracis
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5 µm
(b)
5 µm
a: © Eric Grave/Photo Researchers, Inc.; b: © Soad Tabaqchali/Visuals Unlimited
Thriving in Terrestrial Environments
• Bacteria that form a resting stage (continued...)
• Myxobacteria: group of aerobic Gram-negative rods that
includes Chondromyces, Myxococcus, Stigmatella
•Favorable conditions: secrete slime layer, form swarm
•Nutrients depleted: cells congregate into fruiting body
•Cells differentiate, form dormant microcysts
•Microcysts resist heat, drying, radiation
•Degraders of
complex organic
substances
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(a)
(b)
a: Courtesy of Mary F. Lampe; b: © Patricia L. Grilione/Phototake
Thriving in Terrestrial Environments
• Bacteria that form a resting stage (continued...)
• Streptomyces: aerobic Gram-positive bacteria
•Growth resembles fungi: form mass of branching hyphae
called mycelium
•Chains of spores (conidia) develop at tips
•Conidia resistant to drying;
easily spread by air currents
•Produce extracellular
enzymes; also geosmins,
medically useful antibiotics
including streptomycin,
tetracycline, erythromycin
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5 µm
From S.T. Williams, M.E. Sharpe and J.G. Holt (Eds.), Bergey’s Manual of Systematic
Bacteriology, Vol. 4, Figure 29.3, p. 2454 © 1989 Williams
and Wilkins Co., Baltimore. Micrograph from T. Cross, University of Bradford, Bradford, U.K.
Thriving in Terrestrial Environments
• Bacteria That Associate with Plants (continued…)
• Rhizobia: Gram-negative rods that often fix nitrogen
•Includes Rhizobium, Sinorhizobium, Bradyrhizobium,
Mesorhizobium, Azorhizobium
•Live in nodules on roots of
legumes
•Plants synthesize leghemoglobin,
which binds and controls O2 levels
to yield microaerobic conditions
(a)
•Allows bacteria to fix nitrogen
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(b)
5 µm
a: © John D. Cunningham/Visuals Unlimited; b: From N. R. Krieg and J. G
Holt (Eds.), Bergey’s Manual of Systematic Bacteriology, Vol. 1,1984.
Williams and Wilkins Co., Baltimore
Thriving in Aquatic Environments
 Aquatic environments lack steady nutrient supply
• Sheathed bacteria form chains of cells within tube
•Sheaths protect, help bacteria attach to solid objects
•Often seen streaming from rocks in water polluted by
nutrient-rich effluents; may clog pipes
•Include Gram-negative
rods Sphaerotilus,
Leptothrix
•Motile swarmer cells
exit open end of
sheath, move to new
surface, attach
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Sheath
Bacterial cells
Courtesy of J. T. Staley and J. P. Dalmasso
10 µm
Thriving in Aquatic Environments
• Bacteria That Derive Nutrients from Other Organisms
• Bdellovibrio: highly motile Gram-negative curved rods
•Prey on E. coli and other Gram-negatives
•Strikes forcefully; prey propelled short distance
•Parasite attaches, rotates, secretes digestive enzymes;
forms hole in cell wall of prey
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Bdellovibrios
Bacterial prey
Bacterial prey
10 min
20 min
Cell wall
Cytoplasmic
membrane
10 sec
Bdellovibrio
150–210 min
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1 µm
(b)
a: © Alfred Pasieka/Peter Arnold, Inc.
20 min
Thriving in Aquatic Environments
• Bacteria That Derive Nutrients from Other Organisms
• Bioluminescent bacteria: Photobacterium, Vibrio
•Symbiotic relationships with certain fish, squid
•Help with camouflage, confuse predators and prey
•Gram-negative rods (Vibrio are curved rods)
•Facultative anaerobes; not all are bioluminescent
•Some pathogenic: V. cholerae; V. parahaemolyticus
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(a)
(b)
a: Courtesy of Amy Cheng Vollmer, Swarthmore College; b: © Kenneth Lucas/Biological Photo Service
Thriving in Aquatic Environments
• Bacteria That Move by Unusual Mechanisms
• Spirochetes: group of Gram-negatives with spiral shape
•Flexible cell wall
•Endoflagella or axial filament contained within periplasm
allows corkscrew-like motion
•Able to move through viscous environments like mud
•Spirochaeta thrive in
Spirochetes
muds, anaerobic waters
•Leptospira are aerobes;
some free-living, others
inhabit animals
•L. interrogans causes
leptospirosis
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5 µm
Courtesy of Betsy L. Williams
Thriving in Aquatic Environments
• Bacteria That Form Storage Granules
• Spirillum: Gram-negative spiral-shaped microaerophilic
bacteria
•S. volutans stores phosphate as volutin granules
•Metachromatic granules
• Sulfur-Oxidizing, Nitrate-Reducing Marine Bacteria
•Some store sulfur (energy source) and nitrate (terminal
electron acceptor), which may not coexist
•Thioploca species form long sheaths; cells shuttle
between sulfur-rich sediments and nitrate-rich water
•Thiomargarita namibiensis cells have nitrate storage
vacuole occupying ~ 98% of cell; cell diameter can reach
3/4 mm
Archaea That Thrive in Extreme Conditions
 Characterized Archaea thrive in extremes
• High heat, acidity, alkalinity, salinity
• Methanogens are exception
Archaea That Thrive in Extreme Conditions
 Extreme Halophiles: salt lakes, soda lakes, brines
• Most can grow in 32% NaCl; require at least 9% NaCl
• Produce pigments; seen as red patches on salted fish,
pink blooms in salt water ponds
• Aerobic or facultatively anaerobic chemoheterotrophs
• Some obtain additional energy from light via
bacteriorhodopsin, which expels protons from cell
•Proton gradient can drive
flagella, ATP synthesis
• Variety of shapes: rods,
cocci, discs, triangles
• Includes Halobacterium,
Halorubrum, Natronobacterium, Natronococcus
Archaea That Thrive in Extreme Conditions
 Extreme Thermophiles
• Found near volcanic vents and fissures that release
sulfurous gases, other hot vapors
•Believed to closely mimic earth’s early environment
• Others in hydrothermal vents in deep sea, hot springs
• Methane-Generating Hyperthermophiles
•Methanothermus species grow optimally at 84ºC, as high
as 97ºC
•Oxidize H2 using CO2 as terminal electron acceptor
Archaea That Thrive in Extreme Conditions
 Extreme Thermophiles (continued...)
• Sulfur-Reducing Hyperthermophiles
•Obligate anaerobes; oxidize organic compounds, H2
•Sulfur as terminal electron acceptor; generate H2S
•Sulfur hot springs, hydrothermal vents
•Pyrolobus fumarii from “black smoker” 3,650 m deep in
Atlantic Ocean; grows between 90–113ºC
•Pyrodictium occultum cannot
grow below 82ºC; 105ºC is
optimum
•“Strain 121” grows at 121ºC;
related to Pyrodictium
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1 µm
Dr. R. Rachel, and Prof. Dr. K.O. Stetter, University of Regensburg, Lehrstuhl fuer
Mikrobiologie, Regensburg, Germany
Archaea That Thrive in Extreme Conditions
 Extreme Thermophiles (continued...)
• Nanoarchaea: Nanoarcheota is new phylum
•Nanoarchaeum equitans grows as 400 nm spheres
attached to sulfur-reducing hyperthermophile Ignococcus,
presumably parasitizing
• Sulfur Oxidizers: Sulfolobus species at surface of acidic
sulfur-containing hot springs
•Obligate aerobes
•Oxidize sulfur compounds
•Generate sulfuric acid
•Thermoacidophilic: grow
above 50ºC and pH 1–6