Diversity of Prokaryotic Organisms

Chapter 11 Diversity of Prokaryotic Organisms

Diversity of Microbial Life

•Over 1 ______prokaryotic species exist

•Only about 6,000 described and classified

–850 genera

•Hard to culture and grow

–Therefore hard to study

•Most known about species closely associated with humans, especially pathogenic

•Many are extremely important ecologically

–Many not well described or understood

Many Changes in Classification Schemes

•Due to new discoveries, new information

–e.g. ______genes (rDNA)

•Some groups split

–e.g. Streptococcus split to become

•Streptococcus

•Enterococcus

•Lactococcus

•Some genera more closely related than previously thought

–e.g. Rhizobium and Rickettsia now in the same class

•Rhizobium is nitrogen-fixing bacteria, symbiotic with some plant roots

•Rickettsia is human pathogen, carried by ticks, obligate intracellular parasites

•We will focus on “groups” that have certain similarities

–Metabolic

–Ecophysiological

Metabolic and Ecophysiological Diversity

•______

–Anaerobic chemolitho(hetero)trophs

–Anaerobic chemoorgano(hetero)trophs

•Respirers

•Fermenters

–Anoxygenic photo(auto)trophs

•Aerobic, anaerobic

–Oxygenic photo(auto)trophs

•Aerobic, anaerobic

–[Aerobic chemolitho(hetero)trophs]

–Aerobic chemoorgano(hetero)trophs

•______

–Terrestrial

•Soil

•Plants

–Aquatic

–Animal hosts

•Skin

•Mucous membranes

•Intracellular parasites

–Extreme environments

•Archaea

Metabolic Diversity

•Anaerobic chemolithoautotrophs (“litho” = rock)

–Oxidize ______chemicals for ______

–Methanogens

•Oxidize H2 gas for energy, use CO2 as terminal electron acceptor

•Generate CH4 (methane) gas

•4 H2 + CO2 CH4 + 2 H2O

•______environments

–Packed and waterlogged soils

–Aquatic conditions with low dissolved O2

•Sewage, swamps, marine sediments, rice paddies

•Human and other animal intestines

Metabolic Diversity

•Anaerobic chemoorganoheterotrophs

–Anaerobic ______

•Oxidize ______chemicals for energy (e.g. glucose)

•Sulfate or sulfur reducing

–H2S produced turns water black in presence of iron

•e.g. Desulfovibrio

–Anaerobic ______

•End-products include characteristic acids and gases – may be good for identification

Metabolic Diversity

•Anaerobic fermenters: genus Clostridium

–Gram positive rods, endospore-forming

–Common in soil, anaerobic microenvironments

–Only ______O2 tolerant, resistant to other treatment

–Ferment sugars, cellulose, ethanol

•C. tetani – tetanus

•C. perfringens – gas gangrene, food poisoning

•C. botulinum – food poisoning (intoxication)

•Some species normal flora in intestinal tract

•Anaerobic fermenters: genus Propionobacterium

–Gram positive pleomorphic rods

–Produce ______acid

–Can also ferment lactic acid left from lactic acid bacteria

–Important in dairy industry

•Swiss cheese flavor, holes

Fermenting Bacteria

Metabolic Diversity

•Anaerobic fermenters: Lactic Acid bacteria

–Produce ______acid as major end-product of fermentation

–Catalase negative

–O2______

•Streptococcus spp – some pathogenic, chains of cocci

–S. pyogenes – strep throat, rheumatic fever, other

•Enterococcus spp – found in intestines, chains of cocci

•Lactococcus spp – make cheese, yogurt, chains of cocci

•Lactobacillus spp – single or loose chains of rods

–fermented milk products (yogurt)

–found in mouth, vagina

»lactic acid maintains beneficial acid environment

Metabolic Diversity

•______phototrophs use H2S (not H2O) for electron during ps

– no O2 evolves

–Purple bacteria – gram negative w/pigments making orange, red, purple Mostly anaerobic (some aerobic in dark)

•Purple sulfur bacteria

•Purple non-sulfur bacteria

–Green bacteria – gram negative, green or brown

•Green sulfur bacteria – strict anaerobes

•Green non-sulfur bacteria – some aerobic in dark

Metabolic Diversity

•______phototrophs – O2 evolves

–Primary producers

–Cyanobacteria (“blue-green algae”)

•> 60 genera

•Gram negative

•Freshwater, marine, soils, rock surfaces

•Some unicellular, some filamentous

•Some fix N2

–e.g. Anabena spp.

Metabolic Diversity – Aerobic Chemoorgano(hetero)trophs

•Obligate ______

–Genus Micrococcus

–Genus Mycobacterium

–Genus Pseudomonas

–Genera Thermus and Deinococcus

•______

–Genus Corynebacterium

–Family Enterobacteriaceae

Metabolic Diversity Obligate Aerobes

•Genus Micrococcus

–Gram positive cocci

–Soil, dust, skin, etc.

–Airborne, easily contaminate media

–Pigmented colonies

•e.g. M. luteus, yellow

–Tolerate arid conditions

–Grow in 7.5% NaCl

Metabolic Diversity Obligate Aerobes

•Genus Pseudomonas

–Gram negative rods

–Polar flagella, motile

–Often make pigments

–Most ______aerobes, some able to anaerobically respire w/nitrate

–Non-fermenting, oxidase positive

–Widespread

•Soil, water

–Some harmless, some pathogenic

•Plants and animals

–Biochemically diverse

•Grow on many substrates

–Plasmid mediated

•Important in breakdown of synthetics and hydrocarbons

–e.g. P. aeruginosa – opportunistic pathogen

–Grows in respirator water, (nutrient poor)

–Resistant to many antimicrobials

Metabolic Diversity Obligate Aerobes

•Genus Mycobacterium

–Gram pos., pleomorphic rods, often in chains

–Stain poorly due to waxy lipid in cell wall

–______

–Resistant to many antimicrobials (______wall)

–Widespread – saprophytes and pathogens

–e.g. M. tuberculosis – tuberculosis

–e.g. M. leprae - leprosy

Metabolic Diversity Obligate Aerobes

•Genera Thermus and Deinococcus

•Thermus spp.

–Thermophilic

–Heat-______enzymes

•T. aquaticus

•Source of ______polymerase, used in PCR molecular genetic techniques

•Deinococcus spp.

–Resistant to gamma ______

•D. radiodurans

•Survives dose that shatters human genome (lethal)!

•If genetically engineered, could they clean up radioactive waste?

Metabolic Diversity – Aerobic Chemoorgano(hetero)trophs

•Facultative Anaerobes

–Prefer ______respiration

–Will ferment if no O2 available

•Genus Corynebacterium

–Gram positive pleomorphic rods, often club-shaped (“koryne” = club)

•Often v-arrangements, or columns

–Some strict aerobes, most facultative anaerobes

–Soil, water, surface of plants

–Store phosphate granules as “volutin” = “metachromatic granules”

–e.g. C. diphtheriae - diphtheria

•Family Enterobacteriaceae

Metabolic Diversity Facultative Anaerobes

•Family Enterobacteriaceae

–“Enterics”, “enterobacteria”

–Gram negative rods

–Most live in intestinal tract, some in rich soils

–Some are ______flora

•Enterobacter, Klebsiella, Proteus, E. coli (most strains)

–Some are ______, causing diarrhea

•Shigella, Salmonella enteritidis, E. coli (some strains)

–Some are life-______

•Salmonella typhi – typhoid fever

•Yersinia pestis – bubonic and pneumonic plague

Metabolic Diversity Facultative Anaerobes

•Family Enterobacteriaceae

–Facultative anaerobes

–Ferment glucose

–~ 40 genera, distinguished with biochemical tests

–Many strains within species

–“______”, “fecal coliforms”

•If also ferment lactose

•Includes common intestinal flora, e.g. E. coli

•Easy to detect, testing water samples

•Indicator of fecal pollution in water

•High fecal pollution may also mean fecal-borne pathogens

Ecophysiological Diversity

•Prokaryotes show amazing diversity in ability to adapt to many habitats

•Terrestrial environments

–Soil

–Plants

•Aquatic environments

•Animal host environments

–Skin

–Mucous membranes

–Intracellular parasites

•Extreme environments

–Archaea

Ecophysiological Diversity Terrestrial Environments

•Soil inhabitants form ______stages

–Helps to survive daily and seasonal fluctuations in water and temperature

•______formers

–Gram positive rods

–Position of endospore used in identification

•e.g. Clostridium spp.

–Terminal endospore

•e.g. Bacillus spp.

–Central endospore

–B. stearothermophilus used as bioassay for autoclave function

–B. anthracis – anthrax

•Endospores in soil, animal hides, wool

•Agent of bioterrorism

•Endospores germinate on/in skin  disease

•Endospores inhaled  severe disease

•“Weaponizing” makes endospores lighter and easier to breathe

Endospores of Bacillus anthracis and Clostridium tetani

Ecophysiological Diversity Terrestrial Environments

•Soil inhabitants form resting stages

–Genus Streptomyces forms ______(spores)

–Gram positive

–Pattern of growth like ______

•Mass of filamentous hyphae

•Chains of conidia at tips

–Obligate aerobes

–Produce many extracellular enzymes

•Earthy odor of soil

–Make useful antibiotics

•Streptomycin

•Tetracycline

•Erythromycin

Ecophysiological Diversity Terrestrial Environments

•Bacteria associated with plants

–Several pathogenic, many not

–Genus Agrobacterium

•Gram negative rods

•Enter plant by wounds

•Cause plant tumors

•Transfer ______plasmid (tumor-inducing)

•Plasmid carries genes for growth hormone

• uncontrolled growth

•Plasmid used as vector to carry genes in genetic engineering

Ecophysiological Diversity Terrestrial Environments

•Bacteria associated with plants

–______-pathogenic

–Rhizobia

•Gram negative

•Group of N2-fixing bacteria

•Associated with legumes

–Pea/bean family

•Live inside nodules on roots

•Provide usable forms of Nitrogen for plant

•Reduces need for N fertilizer

•______

•e.g. Rhizobium, Sinorhizobium, Bradyrhizobium, others

Ecophysiological Diversity Aquatic Environments

•______bacteria

–Form chains within a protective sheath

•Prosthecate bacteria

–Form ______(stalks) with adhesive

•Bacteria with storage granules

•Bacteria that move by unusual methods

–______

–Coiled gram negative spirals

–Move like corkscrew

–Very thin, hard to see

–Fit through many small-pore filters

•Bacteria living on nutrients from other organisms

Ecophysiological Diversity Aquatic Environments

•Bacteria surviving in/on other organisms

•Genus Bdellovibrio (Greek “bdello” = ______)

•Highly motile, gram neg.

•Prey on E. coli and other G-neg

•Small curved rods (vibrios)

•Attacks with great speed, rotating

•Attaches, and digests hole in wall of prey

•Multiplies in space between wall and plasma membrane

•Prey cell lyses, and releases daughter vibrio cells

Ecophysiological Diversity Aquatic Environments

•Bioluminescent bacteria

•Genera Photobacterium and Vibrio

•Colonize light organ ______

•Provides contrast to throw fish or squid into shadow  camouflage

•Light confuses predators and prey in flashlight fish

•Luminescence catalyzed by enzyme luciferase

•e.g.Vibrio fischeri

Ecophysiological Diversity Animal Environments

•Bacteria of the skin

–Skin is dry, salty

•Some Staphylococcus spp thrive aerobically

•Propionic acid bacteria find microenvironments low in O2

–Staphylococcus spp.

•Gram positive cocci

•Facultative anaerobes

•Catalase positive

•e.g. S. aureus – wound infections, food poisoning

•e.g. S. epidermidis – normal flora of skin, opportunistic pathogen

Ecophysiological Diversity Animal Environments

•Bacteria of mucous membranes

–Intestinal, genitourinary, respiratory tracts

•Streptococcus spp. and Corynebacterium spp.

–Respiratory tract

•Bacteriodes spp.

–Small, strict anaerobes, Gram neg coccobacilli

–Mouth, intestinal tract and genital tract

–Infections after abdominal surgery

•Bifidobacterium spp.

–Gram pos, irregular rods, anaerobic fermenters

–Intestinal tract

–______of breast-fed babies, lower numbers in formula-fed

Ecophysiological Diversity Animal Environments

•Bacteria of mucous membranes

•Campylobacter spp. and Helicobacter spp.

–Gram neg, curved rods, microaerophiles

–Campylobacter diarrheal disease

–Helicobacter pylori stomach and duodenal ulcers

»Breaks down ______to ______ neutralizes stomach acid in microenvironment around cell

•Neisseria spp.

–Gram neg, kidney-bean-shaped cocci, in pairs (diplococci)

–Oral cavity, other mucous membranes

–Obligate aerobes, fastidious

–e.g. N. gonorrhoeae gonorrhea

–e.g. N. meningitidis meningitis

Ecophysiological Diversity Animal Environments

•Mycoplasma spp.

–______cell ______

–Small, pliable, pass ______bacterial filters

–Among ______of any life form

–Not susceptible to penicillin – WHY?

–M. pneumoniae pneumonia

•Fried-egg appearance on solid media

•Treponema spp. and Borrelia spp.

–Spirochetes of body fluids & mucous membranes

–Microaerophiles

–T. pallidum syphilis

•______been cultured

•Dependent on host cell

–B. burgdoferi Lyme disease

•Transmitted by ticks

•______chromosome!!

•Linear and circular plasmids!

Ecophysiological Diversity Animal Environments

•Obligate ______parasites

–Cannot reproduce outside eukaryotic cell

–Lost ability to make critical substances for growth

–Rely on host cell

–e.g. Rickettsia spp., Coxiella burnetii, Chlamydia spp.

•e.g. Rickettsia rickettsia – RockyMountain spotted fever, tickborne

•e.g. Coxiella burnetii – Q fever, survives outside cell, but cannot reproduce, transmit by inhalation

Ecophysiological Diversity Animal Environments

•Obligate intracellular parasites

–Chlamydia spp.

•Cell wall appears like gram negative, however, it has ______peptidoglycan

•Transmitted directly from person to person

•e.g. C. trachomatis eye infections & sexually transmitted disease

•e.g. C. psittaci  psittacosis, type of pneumonia

Life Cycle of Chlamydia spp.

•Life cycle:

–______body infects host cell

–Becomes ______body inside host cell & reproduces (1)

–Reticulate body becomes more dense (2, 3)  elementary body (4)

–Host cell ruptures and releases ______bodies to infect other host cells

Ecophysiological Diversity Extreme Environments

•Extreme ______

–High salt environments: salt lakes, soda lakes, brines for curing fish

–Grow in saturated salt solution (32% NaCl)

–Require minimum of 9%

–Aerobic or facultative anaerobes

–Some get energy from light

–Produce red/pink pigments  (picture)

–Shapes include rods, cocci, discs, triangles…

•______extreme ______

–Acid, hot environments

–e.g. Thermoplasma spp. optimal at pH 2

–e.g. Picrophilus spp. optimal at pH 1 !!!!!

Ecophysiological Diversity Extreme Environments

•Extreme ______

–Found in volcanic vents, fissures, hot springs, hydrothermal vents in deep sea

–Thought to be conditions like early earth

–Some methanogenic (other methanogens not extreme thermophiles)

–Some sulfur- and sulfate-reducing, obligate anaerobes

•Generate H2S (not H2O)

–Some oxidize H2 for energy

–Optimal temperatures 80°C  105°C !!!

–Upper growth range 90°C  113°C !!!