630 Microbiology for Teachers

Bacterial Diversity

Proteobacteria (Kingdom I)

• Purple Phototrophic Bacteria
  • Gram-negative rods (1.5-4 x 4-40 µm), spirals, ovoid, bean-shaped; some rods motile (via polar flagella)
  • strictly anaerobic anoxygenic phototrophs that use the Calvin cycle for CO₂ fixation; have bacteriochlorophylls and use reduced molecules such as hydrogen sulfide, sulfur, thiosulfate or hydrogen as electron source for generation of NADH and NADPH:
    • purple sulfur bacteria - Chromatium, Halorhodospira, Thiocapsa, Thiococcus, Thiopedia,Thiospirillum are photolithoautotrophs and often form sulfur granules inside their cells
    • purple nonsulfur bacteria - Rhodobacter, Rhodocyclus, Rhodobacter Rhodopseudomonas, Rhodophila are photoorganotrophs
  • found in anaerobic, sulfide-rich zones of lakes and lake muds
• Nitrifying Bacteria - Nitrobacter, Nitrosomonas
  • Gram-negative rods (0.8-1 x 1-2 µm), coccoid (0.2-1 µm), spiral (0.3-0.4 µm in diameter), lobular (1-1.5 µm); may have extensive membrane complexes in cytoplasm
  • aerobic lithotrophs which use carbon dioxide or carbonate as carbon source (via Calvin cycle) and derive energy by oxidizing inorganic compounds containing reduced nitrogen (NH4+, nitrite-)
  • found in soil, sewage treatment systems, freshwater, and marine habitats
• Sulfur- and Iron-Oxidizing Bacteria - Thiobacillus, Beggiatoa, Thioploca, Thiothrix
  • Gram-negative rods (0.8-1 x 1-2 µm), coccoid (0.2-1 µm), spiral (0.3-0.4 µm in diameter), lobular (1-1.5 µm); may have extensive membrane complexes in cytoplasm; or filamentous with gliding motility (Beggiatoa
  • aerobic lithotrophs use carbon dioxide or carbonate as carbon source (via Calvin cycle) and derive energy by oxidizing inorganic compounds containing reduced sulfur (Thiobacillus, Thiomicrospora) and/or reduced sulfur and iron (Thiobacillus ferroxidans)
  • found in soil, sewage treatment systems, freshwater, and marine habitats, especially sulfur springs
• Hydrogen-Oxidizing Bacteria - Alcaligenes
  • Gram-negative rods (0.8-1 x 1-2 µm), coccoid (0.2-1 µm), spiral (0.3-0.4 µm in diameter), lobular (1-1.5 µm); may have extensive membrane complexes in cytoplasm
  • aerobic lithotrophs which use carbon dioxide or carbonate as carbon source (via Calvin cycle) and derive energy by oxidizing inorganic compounds containing reduced hydrogen (generally hydrogen)
  • found in soil, sewage treatment systems, freshwater, and marine habitats
• Methanotrophs and Methyltrophs - Methlyosinus, Methylcoccus
  • Gram-negative motile rods (Methylmonas), nonmotile cocci (Methylcoccus) or motile vibrios (Methylosinus); possess sterols
  • aerobic organotrophs; generate energy by oxidizing methane (or methyl groups)
  • widespread in nature in soil and water
• Pseudomonas and the Pseudomonads- Pseudomonas, Agrobacterium, Rhizobium, Zymomonas
  • Gram-negative straight or slightly curved rods (0.5 x 1.5 to 1.4 x 6 µm); motile (polar flagella)
  • aerobic and facultative aerobic organotrophs; respiratory (non-fermentative) metabolism that utilizes the Entner-Doudoroff pathway for carbohydrate oxidation (Zymomonas uses the Entner-Doudoroff pathway for oxidation of glucose to ethanol); versatile use of carbon and energy sources, including use of nitrate as final electron acceptor via anaerobic respiration; Rhizobia are aerobic organisms which live inside other organisms
  • free-living to parasitic in animals (Pseudomonas) and plants (Pseudomonas, Xanthomonas); Rhizobium is a plant symbiote; Zymomonas is found in soil and water; occasionally present in pyogenic infections of humans and animals
• Acetic Acid Bacteria (Acetobacteraceae) - Acetobacter, Gluconobacter
  • Gram-negative straight or curved rods and cocci (0.3 x 2 to 0.9 x 20 µm); motile - polar (Gluconobacter) or peritrichous (Acetobacter) flagella
  • aerobic respiratory organotrophs; derive energy by oxidizing ethanol to acetic acid
  • free-living, important in the food industry as vinegar producers
• Free-Living Aerobic Nitrogen-Fixing Bacteria - Azotobacter, Azomonas
  • Gram-negative, large, rod to pear-shaped (2-4 µm in diameter)
  • aerobic or microaerophilic organotrophic nitrogen-fixers; use organic and amino acids as carbon and energy source, not carbohydrate; Azotobacter has fastest rate of oxygen-uptake of any known organism
  • free-living terrestrial nitrogen-fixers, including Azospirillum, Azotobacter, Azomonas
• Neisseria, Chromobacterium, and Relatives - Neisseria, Chromobacterium
  • Gram-negative cocci (Neisseria) or rod-coccoid; generally nonmotile (Moraxella and Acinetobacter possess "twitching" motility); Chromobacterium violaceum has bright purple pigment
  • aerobic respiratory (non-fermentative) organotrophs; oxidase positive; versatile carbon and energy sources; Chromobacterium ferments a variety of carbohydrates and produces a violet-colored pigment (violacein) when grown in the presence of tryptophan
  • isolated from animals (Neisseria are generally parasitic, some Branhamella are symbiotic with humans) or from soil and water (Acinetobacter); Chromobacterium and Acinetobacter are occasionally present in pyogenic infections of humans and animals
• Enteric Bacteria - Escherichia, Salmonella, Proteus, Enterobacter
  • Gram-negative, straight rods (0.3-1 x 1-6 µm); nonmotile to motile (peritrichous flagella)
  • facultative aerobes; oxidase negative; diverse (including fermentative) organotrophic catabolism
  • normal flora and/or parasitic on mammals, birds and plants
• Vibrio and Photobacterium - Vibrio, Photobacterium
  • Gram-negative curved rods (0.3-1 x 1-6 µm); nonmotile to motile (peritrichous or polar flagella)
  • facultative aerobes; oxidase positive; diverse (fermentative) organotrophic catabolism
  • typically aquatic (freshwater or marine) free-living; Vibrio cholerae and Vibrio parahemolyticus are parasitic on animals, especially humans; Photobacterium is bioluminescent
• Rickettsias -Coxiella, Rickettsia, Rochalimaea
  • Gram-negative rod, coccoid, pleomorphic (0.3-0.7 x 1-2 µm); nonmotile
  • aerobic organotrophs; Coxiella oxidize glucose; Rickettsia do not oxidize glucose or organic acids, but obtain ATP from oxidation of glutamate or glutamine, which they obtain from the host cell (there is some suggestion that they also obtain NAD+ and coenzyme A from the host cell), and they replicate in the cytoplasm of the host cell until it is loaded with parasites
  • pathogens - transmitted to humans by arthropods; Rickettsia are obligate intracellular parasites; Rochalimaea grow attached to outside of host cell cytoplasmic membrane
• Spirilla - Spirilum, Bdellovibrio, Campylobacter
  • Gram-negative; helical to vibrioid (curved = helical but not long enough to encompass one full helical turn; 0.2 x 1.4 to 1.7 x 60 µm); motile via flagella (Spirillum, Aquaspirillum) or nonmotile (Spirosomaceae, Microcyclus)
  • aerobic, microaerophilic or facultative aerobic organotrophs; use organic and amino acids as carbon/energy source, not carbohydrate
  • free-living (freshwater - Spirillum, Aquaspirillum; marine - Oceanospirillum), soil (some nitrogen-fixers - Azospirillum), parasitic (animals - Campylobacter; bacteria - Bdellovibrio) 
• Sheathed Proteobacteria - Sphaerotilus, Leptothrix
  • Gram-negative; filamentous - chains of cells surrounded by hollow tubelike structure (sheath) used for surface attachment (frequently have holdfasts), nutrient adsorption and protection from predators; unicellular elements (swarmers) generally motile by subpolar flagella, some nonmotile (Crenothrix)
  • aerobic metal oxidizers; precipitate iron or manganese on sheath; Lepthothrix oxidizes manganese, Sphaerotilus doesn't
  • freshwater (flowing) habitats; polluted streams and activated sludge
• Budding and Prosthecate/Stalked Bacteria - Hyphomicrobium, Caulobacter
  • Gram-negative rods (0.5-1 x 1-3 µm); mobile by flagella; heterogeneous group, but reproduce by budding and/or possess a prostheca (cytoplasmic extrusions such as stalks, hyphae, or other appendages); motile by flagella; Hyphomicrobium - stalks & budding; Caulobacter - stalk with holdfast; reproduces by budding
  • generally aerobic organotrophs (Rhodomicrobium is an exception ... it is phototrophic)
  • frequently found in nutrient-poor freshwater habitats
• Gliding Myxoacteria - Myxococcus, Stigmatella
  • Gram-negative rods (0.6-0.9 x 3-8 µm) with gliding motility and production of fruiting bodies (50-500 µm tall) which contain myxospores (Myxococcus, Chondromyces)
  • aerobic respiratory organotrophs; micropredators which kill other bacteria with antibiotics, then secrete enzymes to dissolve them
  • found worldwide in soil, decaying plant material and animal dung; most abundant in warm areas; also found in arctic tundra
• Sulfate- and Sulfur-Reducing Bacteria - Desulfovibrio, Desulfobacter, Desulfuromonas
  • Gram-negative (although some are Gram-positive endospore formers); straight, curved, or helical rods (0.5-1.5 x 3-10 µm)
  • anaerobic dissimilatory organotrophic bacteria which use sulfate or sulfur as electron acceptors in anaerobic respiration of organic compounds such as acetate, which they oxidize via an acetyl-CoA pathway; when they have a source of hydrogen and carbon dioxide, but no organic compounds, they can use hydrogenase to generate energy during lithotrophic growth
  • thrive in fresh water sediments and sewage digestors; important in sulfur cycle; combat acid rain

Gram-Positive Bacteria (Kingdom II)

• Nonsporulating, Low GC, Gram-Positive Bacteria (plus Lactic Acid Bacteria) - Staphylococcus, Micrococcus, Streptococcus, Lactobacillus
  • Gram-positive, nonmotile cocci (0.2-2.5 µm), single or in variable-sized clusters (Staphylococcus, Micrococcus) or in chains (Streptococcus) or Gram-positive, usually nonmotile bacilli (0.8 x 2 µm - Lactobacillus) single or in variable-sized clusters; nonsporulating
  • aerobic organotrophs (Micrococcus); facultatively aerobic or microaerophilic aerobic organotrophs (Staphylococcus, Streptococcus, Leuconostoc); anaerobic organotrophs (Lactobacillus) that lack porphyrins (no cytochromes) so must obtain energy exclusively by substrate-level phosphorylation; lactic acid bacteria are:
    • homofermentative - produce lactic acid as sole product of fermentative metabolism (Streptococcus, Pediococcus, Enterococcus, Lactococcus, some Lactobacillus species)
    • heterofermentative - produce other products (ethanol, etc.) in addition to lactic acid (Leuconostoc, some Lactobacillus species)
  • free in nature, normal flora, parasites (Staphylococcus, Streptococcus); many lactic acid bacteria (Lactobacillus, Streptococcus, Leuconostoc) are useful in food production because of the lactic acid they generate
• Endospore-Forming Gram-Positive Rods and Cocci (plus Homoacetogenic Bacteria and Heliobacteria) - Bacillus, Clostridium, Sporosarcina, Heliobacterium
  • Gram-positive endosporeforming bacilli (0.3-2.2 x 1.2-6 µm); usually motile by peritrichous flagella (Bacillus, Clostridium) or Gram-positive gliding rod and motile spirilla (Heliobacterium - two species produce endospores) or actively motile rods (Heliobacillus) or cocci in tetrads or packets of 8 or more cells (Sporocarcina)
  • physiology is highly variable:
    • facultatively aerobic (Bacillus)
    • microaerophilic (Sporolactobacillus); anaerobic (Clostridium, Desulfotomaculum, Sporosarcina - lack catalase)
    • obligately anaerobic organotrophs; produce acetate as the sole product of sugar fermentation (to produce 2 acetates plus 2CO₂ and H₂) coupled with reduction of carbon dioxide (via the acetyl-CoA pathway) to form a third acetate ... thus the name homoacetogenic (the sole or only product of sugar catabolism is acetate); may also grow lithotrophically using hydrogen as an energy source (same acetyl-CoA pathway as above) (Acetobacterium, Clostridium, Desulfotomaculum)
    • obligately anaerobic phototrophs (have bacteriochlorophyll g), but can utilize acetate, pyruvate, lactate or butyrate as carbon sources for organotrophic growth (Heliobacterium)
    • ubiquitous in nature (soil); Heliobacterium is found in tropical soils, especially rice paddies; Bacillus and Clostridium are important in food spoilage, infectious disease
• Cell Wall-Less, Low GC, Gram-Positive Bacteria: The Mycoplasmas - Mycoplasma, Spiroplasma
  • Gram-negative pleomorphic (0.1-0.25 x 3-150 µm); lack cell wall, possess sterols; most are non-motile, some have "gliding" motion
  • facultatively aerobic or obligately anaerobic organotrophs; Mycoplasmataceae require steroids, Acholeplasmataceae do not
  • ubiquitous parasites (may have arisen from Clostridium or Gram-positive Archaea)
• High GC, Gram-Positive Bacteria: Coryneform and Propionic Acid Bacteria - Corynebacterium, Arthrobacter, Propionibacterium
  • Gram-positive; nonmotile straight or slightly curved bacilli, sometimes with swellings (club-shaped ... Coryneforms); or Gram-positive pleomorphic, nonsporulating bacilli (0.8 x 2 µm ... Propionibacterium)
  • aerobic organotrophs (Coryneforms); anaerobic, organotrophic versatile fermenters (Propionibacterium)
  • animal or plant pathogens or normal microbiota (Corynebacterium) or soil saprophytes which mineralize soil contaminants (Arthrobacter); Propionibacterium grows free in nature, normal flora and is useful in food production (swiss cheese)
• High GC, Gram-Positive Bacteria: Mycobacterium
  • Gram-positive (weakly), slightly curved or straight rods (0.2-0.6 x 1-10 µm); cell walls have long-chain waxes containing mycolic acids (acid-fast)
  • aerobic organotrophs; growth slow or very slow
  • important as pathogens
• Filamentous, High GC, Gram-Positive Bacteria: The Actinomycetes - Streptomyces, Actinomyces
  • Nocardioforms
    • Gram-variable; Nocardia develop a highly branched substrate mycelium (hyphae 0.5-1.2 µm in diameter) that breaks up into rods and cocci, form aerial hyphae, and produce conidia; others may (Nocardioides) or may not (Rhodococcus) form aerial hyphae or produce conidia
    • mesophilic, aerobic organotrophs; Nocardia degrades hydrocarbons
    • world-wide in soil and water; mostly free-living; Nocardia is pathogenic
  • Actinomycetes with Multilocular Sporangia
    • Gram-positive; 0.5-2 µm diameter hyphae; clusters of coccoid spores, some motile via tufts of flagella (Dermatophilus), others non-motile (Frankia)
    • facultatively anaerobic or microaerophilic organotrophs (non-fermentative)
    • Dermatophilus is parasitic, causes streptothrichosis; Frankia is symbiotic with roots of non-leguminous plants (Alder trees) and fixes nitrogen
  • Actinoplanetes
    • Gram-positive, extensive branched, non-fragmenting substrate mycelium with 0.2-2.6 µm diameter hyphae; highly colored; motile spores formed in sporangia (3-20 x 6-30 µm, spherical-cylindrical, very irregular) on sporangiophores
    • mesophilic aerobic organotrophic decomposers
    • found in soil (forest litter to beach sand), freshwater and marine habitats; important in mineralization of organics (Pilimelia) and production of gentamicin (Micromonospora)
  • Streptomyces and Related Genera
    • Gram-positive; aerial hyphae (0.5-2 µm diameter) which form chains of motile conidio-spores; mycelium does not undergo fragmentation; variety of colors
    • aerobic mesophiles with flexible organotrophic metabolism; degrade chitin, cellulose, pectin, keratin, etc.
    • abundant soil microbes (up to 20% of total) which are responsible for the odor of soil (geosmin) and are important in mineralization; Streptomyces also produce antibiotics (antifungals -amphotericin B and nystatin; ribosome active antibacterials - streptomycin, neomycin, erythromycin, tetracycline, chloramphenicol); some cause diseases such as actinomycetoma
  • Maduromycetes
    • Gram-positive; aerial mycelia with non-fragmenting mycelium which forms pairs or short chains of arthrospores; some form sporangia
    • aerobic organotrophs; most mesophilic, some thermophilic
    • parasitic - Actinomadura causes actinomycetomas in humans
  • Thermonospora and Related Genera
    • Gram-positive; variable morphology; single heat-sensitive spores on aerial mycelium and/or substrate mycelium
    • aerobic thermophilic (40-48C) organotrophs
    • high temperature habitats (compost piles, haystacks, etc.)
  • Thermoactinomycetes
    • Gram-positive; hyphae (0.4-0.8 µm diameter) in substrate mycelium; single endospores (heat resistant) on both aerial and substrate mycelia
    • aerobic thermophilic (45-60C) organotrophs
    • Thermoactinomyces vulgaris is one of the causative agents of farmer's lung disease (allergic disease of respiratory system)
  • Other Genera
    • "catch-all" category for Actinomycete genera whose characteristics are different from those found above
    • current members include: Glycomyces, Kibdelosporangium, Kitasatosporia, Saccharothrix, Pasteuria

Cyanobacteria, Prochlorophytes, and Chloroplasts (Kingdom III)

• Cyanobacteria - Synechococcus, Oscillatoria, Nostoc
  • Gram-negative; 1-10 µm diameter, unicellular (Anacystis, Synechococcus, Pleurocapsa) or filamentous (Anabena, Nostoc, Oscillatoria); gliding motility; some have gas vesicles for vertical movement in water
  • aerobic oxygenic photolithotrophs with chlorophyll a plus phycobiliproteins which use water as electron source for generation of NADH and NADPH and generate oxygen; heterocystous cyanobacteria (Anabena, Nostoc) have heterocysts which facilitate nitrogen-fixation
  • responsible for most of the oxygen in the atmosphere and for some of the nitrogen-fixation; very good at symbiotic relationships (e.g., the "algae" in most lichens are Cyanobacteria); ecology, etc.
• Prochlorophytes and Chloroplasts - Prochloron, Prochlorothrix
  • Gram-negative; 8-10 µm diameter, spherical (Prochloron) with extensive thylakoid membrane system (because it closely resembles them, and is frequently endosymbiotic, some think Prochloron is the precursor of chloroplasts); filamentous (Prochlorothrix) with meager thylakoid membrane development
  • aerobic oxygenic photolithotrophs with chlorophyll a or b (but lack phycobiliproteins); picoplankton is ~1 µm in diameter and has only chlorophyll b)
  • endosymbionts of marine invertebrates

Chlamydias (Kingdom IV) - Chlamydia

• Gram-negative coccoid (0.2-1.5 µm); non-motile; no peptidoglycan
• aerobic organotrophs; most limited catabolic and biosynthetic capabilities of any known organism; no energy-generating system - obtain ATP and metabolic intermediates from host cell (energy parasites); replicate via binary fission of reticulate bodies, which then differentiate into small, dense cell forms called elementary bodies, which are specialized for transmission to a new host
• pathogens - obligate intracellular parasites; life cycle involves elementary and reticulate bodies)

Planctomyces/Pirella (Kingdom V) - Planctomyces, Pirella

• Gram-negative ovoid bacterium with a slender stalk, pili and a flagellum; cell wall contains protein instead of peptidoglycan; reproduces by budding and expresses a life cycle
• facultatively aerobic organotrophs that ferment or respire sugars
• aquatic habitats ... freshwater or marine

Bacteroides/Flavobacteria (Kingdom VI) - Bacteroides, Flavobacterium, Cytophaga

• Gram-negative straight, curved or helical rods (0.5 x 0.5-10 µm); nonmotile or motile via flagella (Bacteroides) or yellow pigmented rods (Flavobacterium) or rods with gliding motility (Cytophaga)
• aerobic organotrophs (Cytophaga) or anaerobic organotrophs (Bacteroides)
• found in soil and rotting logs, etc. (Cytophaga); symbiotic in the oral cavity and/or intestinal tract of humans and other animals, rumen of cattle, etc. (Bacteroides); aquatic environments, in foods and food-processing plants (Flavobacterium)

Green Sulfur Bacteria (Kingdom VII) - Chlorobium, Prosthechloris, Chlorochromatium

• Gram-negative nonmotile rods, cocci or spirals (0.5-1.1 µm wide or diameter) often form sulfur granules outside their cells
• obligately anaerobic photolithotrophs which have bacteriochlorophylls in chlorosomes and use reduced molecules such as hydrogen sulfide, sulfur, thiosulfate or hydrogen as electron source for generation of NADH and NADPH
• found in anaerobic, sulfide-rich zones of lakes and lake muds

Tightly Coiled Bacteria: The Spirochetes (Kingdom VIII) - Spirochaeta, Treponema, Cristispira, Leptospira, Borrelia

• Gram-negative; helical, long and slender (0.1-5 x 0.75-250 µm); motile via axial filaments
• aerobic, microaerophilic, facultatively aerobic, or anaerobic organotrophs; catabolize carbohydrates, amino acids or lipids
• free-living (Spirochaeta), symbiotic (Cristispira), or parasitic (Treponema, Borrelia, Leptospira)

Deinococci (Kingdom IX) - Dienococcus, Thermus

• Gram-Positive, but Deinococcus has an outer membrane and is not phylogenetically related to other Gram-positive bacteria
• aerobic organotroph that is highly resistant to radiation damage; the best-known representative of the thermophilic genusThermus is Thermus aquaticus, the bacterium from which Taq polymerase is derived
• free in nature, especially near radioactive materials (Dienococcus) or in hot springs (Thermus)

Green Nonsulfur Bacteria (Kingdom X) - Chloroflexus, Thermomicrobium

• Gram-negative motile (gliding) filamentous bacteria
• thermophilic obligately anaerobic phototrophs (Chloroflexus) which have bacteriochlorophylls in chlorosomes and use reduced molecules such as hydrogen sulfide, sulfur, thiosulfate or hydrogen as electron source for generation of NADH and NADPH, but can also grow lithotrophically or organotrophically under appropriate conditions; or thermophilic aerobic organotrophs (Thermomicrobium) with no glycerol and neither ester- nor ether-linkages in their membrane lipids
• found in anaerobic, sulfide-rich zones of lakes and lake muds

Thermotoga (Kingdom XI)

• Gram-negative rod with a sheath-like envelope (hence the term "toga" in the name)
• thermophilic anaerobic fermenters (organotrophs)
• grows around benthic hydrothermal vents and continental hot springs

Thermodesulfobacterium (Kingdom XII)

• Gram-negative bacillus with ether-linked lipids (very Archaea-like!)
• thermophilic sulfate-reducing organotroph with an optimum growth temperature of 70C (most thermophilic of all known sulfate-reducing bacteria)
• grows in high-temperature areas near hot springs, etc.

Aquifex and Relatives (Kingdom XIII)

• Gram-negative bacillus
• hyperthermophilic (optimum temperature for growth is 85C, but can grow up to 95C ... most thermophilic of all known bacteria) aerobic (one of the few aerobic hyperthermophiles known) lithotroph (reverse TCA cycle) that oxidizes hydrogen, sulfur or thiosulfate and uses oxygen (microaerophilic growth) or nitrate (anaerobic growth) as terminal electron acceptors
• submarine volcanic hot spring bacterium; most ancient branch of the bacterial phylogenetic tree