Title: The Diversity of Prokaryotic Title: What is the ...… · From J. G. Holt (Ed.), The Shorter Bergey's Manual of Determinative Bacteriology, 8/e, 1977. Williams and Wilkins

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Speaker: Amit Dhingra

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Title: The Diversity of Prokaryotic

Organisms

Instructor: Consetta Helmick

The Diversity of Prokaryotic Organisms

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

Diversity of Prokaryotes

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


5 µm5 µm

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

a: © F. Widdel/Visuals Unlimited; b: © Ralph Robinson/Visuals Unlimited

(a) (b)

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 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



• 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)


1 µm10 µm


a: © Thomas Tottleben/Tottleben Scientific Company; b: © David M. Phillips/Visuals Unlimited

(a) (b)


• 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


5 µm


© John Walsh/Photo Researchers, Inc.

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


Sulfur granules

10 µm(b)(a)


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.

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


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


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

Cyanobacteria (continued...)

• Morphologically diverse

• Unicellular: cocci, rods,

spirals

• Multicellular: filamentous

associations: trichomes

•May be in sheath

•Motile trichomes glide

as unit

• May have gas vesicles for

vertical movement in water

Oxygenic Phototrophs

100 µm

15 µm(a)

(b)


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.


• 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



• 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


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 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


Multicellular

filament

Sulfur

granules

Cellular

septa

10 µm(a)

(b) 10 µm


a: Courtesy of J. T. Staley and J. P. Dalmasso; b: Courtesy of Dr. James Staley


• 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



• 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



• 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 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


• 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


• 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

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

•Bacillus, Clostridium most

common

•Gram-positive rods

•Bacillus include obligate and

facultative anaerobes

•Some medically important:

B. anthracis

Thriving in Terrestrial Environments


a: © Eric Grave/Photo Researchers, Inc.; b: © Soad Tabaqchali/Visuals Unlimited

5 µm5 µm(a) (b)

• 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



(a) (b)

a: Courtesy of Mary F. Lampe; b: © Patricia L. Grilione/Phototake

• 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


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.

• 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

•Allows bacteria to fix nitrogen


5 µm

(a)

(b)


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

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

Thriving in Aquatic Environments

Bacterial cells 10 µmSheath


Courtesy of J. T. Staley and J. P. Dalmasso

• 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



Bacterial prey

Bdellovibrios Bacterial prey

10 min

Cell wall

20 min

10 sec

Cytoplasmic

membrane

(b)1 µm(a)

Bdellovibrio

150–210 min

20 min

a: © Alfred Pasieka/Peter Arnold, Inc.

• 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



a: Courtesy of Amy Cheng Vollmer, Swarthmore College; b: © Kenneth Lucas/Biological Photo Service

(a) (b)

• 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

muds, anaerobic waters

•Leptospira are aerobes;

some free-living, others

inhabit animals

•L. interrogans causes

leptospirosis


Spirochetes

5 µm


Courtesy of Betsy L. Williams

• 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


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, Natrono-

bacterium, Natronococcus


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


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

1 µmDr. R. Rachel, and Prof. Dr. K.O. Stetter, University of Regensburg, Lehrstuhl fuer

Mikrobiologie, Regensburg, Germany



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


Documents

Title: The Diversity of Prokaryotic Title: What is the ...… · From J. G. Holt (Ed.), The Shorter Bergey's Manual of Determinative Bacteriology, 8/e, 1977. Williams and Wilkins