ch 10 classification and bacterial diversity

what is classification

The organization of organisms into groups based on shared characteristics and evolutionary relationships.

Binomial nomenclature

A unique, two-part scientific name for each species, usually Latinized; written as Genus species, with the genus capitalized and species lowercase, and both italicized when typed.

Linnaean classification ranks

Kingdom → Phylum → Class → Order → Family → Genus → Species.

Bacterial strain

A variation or specific type within a bacterial species.

Three domains of life

Bacteria and Archaea are prokaryotic; Eukarya includes all eukaryotes. Viruses use a separate classification system.

Early bacterial classification

bacteria were initially grouped by morphology, staining reactions such as Gram-positive or Gram-negative, and nutritional requirements.

Bergey's Manual of Determinative Bacteriology (1923)

classified bacteria mainly by phenotype and was organized into four volumes.

Bergey's Manual of Systematics of Archaea and Bacteria (1984)

Organized microorganisms according to evolutionary relationships and was published in five volumes.

Modern microbial classification

Molecular genetics, including 16S rRNA gene sequences, helps determine evolutionary relationships. Classification continues to change as new species are described.

General characteristics of Archaea

Unicellular prokaryotes that are more closely related to eukaryotes than to Bacteria; may be bacillus, coccus, spiral, square, or triangular; can be aerobic or anaerobic and autotrophic or heterotrophic.

Archaeal cell walls and membranes

Archaea do not have true peptidoglycan; some have pseudomurein, most have proteinaceous S-layers, and their membrane lipids differ from those of bacteria.

Archaeal DNA

Usually a single, double-stranded circular DNA molecule; Archaea have histone proteins similar to those in eukaryotes.

Archaea and extreme environments

Many are extremophiles adapted to extreme heat, cold, acidity, alkalinity, or salinity, but Archaea also occur in ordinary environments, especially oceans. Some are difficult to culture in the laboratory.

Major archaeal phyla

Euryarchaeota and Crenarchaeota.

Minor archaeal phyla

Korarchaeota, Thaumarchaeota, and Nanoarchaeota.

Euryarchaeota

The most diverse archaeal group in the notes; includes extreme halophiles and methanogens. Examples: Halobacterium, Methanobacterium, and Methanococcus.

Methanogens

Archaea that generate methane; found in environments such as hot springs, marshes, and cow guts, according to the notes.

Crenarchaeota

Mostly extreme thermophiles; many are anaerobic and use sulfur compounds in redox reactions. Examples: Thermoproteus and Sulfolobus.

Korarchaeota

Thermophiles associated with hydrothermal vents.

Thaumarchaeota

Ammonia (NH₄⁺/NH₃) oxidizers; formerly grouped with Crenarchaeota as mesophiles.

Nanoarchaeota

Hyperthermophiles that form a symbiotic association with another archaeon; have an extremely small genome, approximately 490 kb, according to the notes.

General characteristics of Bacteria

Unicellular prokaryotes classified into many phyla; the notes list 30–50 phyla.

Major Gram-positive bacterial phyla

Actinobacteria, Firmicutes, and Tenericutes; the notes also highlight GC content as a way to group them.

Major Gram-negative bacterial phyla

Proteobacteria, Cyanobacteria, Chlorobi, Chloroflexi, Deinococcus-Thermus, Planctomycetes, Chlamydiae, Spirochaetae, and Bacteroidetes.

Gram-positive bacteria

Most are chemoheterotrophs; some are important pathogens, while others have industrial uses. The amount of GC content in DNA is used to group these phyla.

Actinobacteria

Gram-positive group with high GC content, characterized by aerobic, filamentous forms that structurally resemble fungi.

Actinobacteria: Key genera and significance

Streptomyces produces antibiotics such as streptomycin, erythromycin, and tetracycline; Mycobacterium has waxy cell walls requiring acid-fast staining (causes tuberculosis and leprosy); Propionibacterium is linked to Swiss cheese production and acne.

Firmicutes

Gram-positive group with low GC content; includes endospore-forming and non-endospore-forming bacteria.

Endospore-forming Firmicutes

Clostridium species are obligate anaerobes associated with botulism, tetanus, gas gangrene, and C. difficile infection.

Bacillus anthracis is associated with anthrax; Bacillus species are also associated with antibiotics such as bacitracin and polymyxin and with biological insect control

Non-endospore-forming Firmicutes

Lactic acid bacteria are used in foods such as yogurt. Streptococcus species can be identified by hemolysis on blood agar and include bacteria associated with strep throat, scarlet fever, and pneumococcal pneumonia. Staphylococcus includes MRSA.

Tenericutes

Gram-positive group listed as having low GC content; bacteria are very small and lack a cell wall. Some cause respiratory diseases.

Proteobacteria

The largest bacterial phylum , containing about one-third of known bacterial species. Members have diverse morphology and physiology but share 16S rRNA sequences. Many are important Gram-negative bacteria.

Photosynthetic Proteobacteria

Include purple sulfur and purple non-sulfur bacteria.

the ancestor of Proteobacteria was photosynthetic; these bacteria may be facultative or obligate anaerobes and occur in lake mud, sediments, and salt marshes.

Nitrifying bacteria

Aerobic bacteria that obtain energy from nitrogen compounds and carbon from CO₂; important in the nitrogen cycle in terrestrial, marine, and freshwater habitats.

Iron- and sulfur-oxidizing Proteobacteria

Obtain energy by oxidizing iron or sulfur; some are extreme acidophiles that can produce sulfuric acid. They can contribute to acid mine drainage, releasing heavy metals into the environment.

Habitats include sulfur springs, marine sediments, hydrothermal vents, bogs, and iron springs.

Hydrogen-oxidizing Proteobacteria

Obtain energy by oxidizing hydrogen (H₂), using O₂ as the electron acceptor; obtain carbon from organic compounds.

Nitrogen-fixing Proteobacteria

Convert nitrogen gas (N₂) into ammonium (NH₄⁺); may live freely in soil or symbiotically with plant roots. Agrobacterium enters plant cells and causes nodules and is used in genetic engineering.

Methanotrophic Proteobacteria

strict aerobes that use methane as an energy and carbon source; found in marshes, sewage sludge, and animal intestines.

Sulfate- and sulfur-reducing Proteobacteria

Anaerobic bacteria found in mud; important in the sulfur cycle.

Enteric Proteobacteria

Facultative anaerobes that can ferment sugars without oxygen and are distinguished by biochemical characteristics. Examples: Escherichia coli, Serratia, Salmonella, and Yersinia.

Vibrio and related genera

Facultative anaerobes, some of which are bioluminescent; identified by biochemical characteristics. Example: Vibrio cholerae.

Pseudomonads

Use a wide range of organic compounds for carbon and energy and are important in the carbon cycle; some cause food spoilage or infections.

Example: Pseudomonas aeruginosa can cause secondary infections in wounds and burns.

Acetic acid bacteria

Gram-negative aerobes that convert ethanol into acetic acid; some can further convert it to CO₂ and H₂O, and some can produce cellulose.

Stalked and budding Proteobacteria

Aquatic bacteria with thin cytoplasmic extensions called prosthecae that increase surface area for nutrient absorption; reproduce asexually by budding, and some form multiple buds

Sheathed Proteobacteria

Form chains of cells surrounded by a tube-like sheath that provides protection and helps with nutrient absorption; found in streams, especially near sewage outlets.

They can release free-swimming cells that start new colonies.

Predatory Proteobacteria

Boring predators use a flagellum to enter a host cell, enzymes to dissolve its cell wall, and then absorb nutrients between the cell wall and plasma membrane.

Gliding predators lyse bacteria externally and may aggregate into a fruiting body that produces resistant myxospores.

Spirilla

Aerobic, spiral-shaped bacteria with polar flagella; may be free-living, symbiotic, or parasitic, and some have magnetosomes.

Examples: Campylobacter jejuni, associated with gastroenteritis, and Helicobacter pylori, associated with stomach ulcers.

Rickettsiae

Arthropod-borne intracellular parasites. Example: Rickettsia rickettsii, associated with Rocky Mountain spotted fever.

Neisseria and related Proteobacteria

nonmotile cocci usually found in pairs; some are pathogens associated with gonorrhea and meningitis.

Cyanobacteria

Photosynthetic bacteria sometimes called “blue-green algae”; may be unicellular or filamentous and can fix nitrogen gas in specialized cells called heterocysts.

Example: Prochlorococcus, noted in the lecture as an extremely abundant photosynthetic organism.

Chlorobi

Green sulfur bacteria with pigments located in sac-like structures called chlorosomes.

Chloroflexi

Green non-sulfur bacteria that can switch from photosynthesis to heterotrophy; includes filamentous thermophiles.

Deinococcus-Thermus

Thermus species are thermophiles. Thermus aquaticus is the source of Taq polymerase used in PCR. Deinococcus resists chemical mutagens due to powerful DNA-repair mechanisms. Both have slightly different peptidoglycan.

Planctomycetes

Reproduce by budding and lack peptidoglycan; some can convert ammonium and nitrate into nitrogen gas.

Chlamydiae

Very small, nonmotile, obligate parasites; associated with sexually transmitted chlamydial infection, chlamydial pneumonia, and psittacosis.

Spirochaetae

Helical, corkscrew-shaped bacteria that move using endoflagella located between the cell and outer sheath. Found in water, soil, animal intestines, mouths, and reproductive tracts.

Example: Treponema pallidum, which causes syphilis.

Bacteroidetes

very diverse group that includes free-living aquatic aerobes and obligate anaerobes in the human gut. Gut members may contribute to peritonitis if the intestines rupture.

Euryarchaeota vs. Crenarchaeota

Euryarchaeota includes the most diverse archaeal group, extreme halophiles, and methane-producing organisms; Crenarchaeota includes mostly extreme thermophiles, many of which are anaerobic and use sulfur compounds.

Actinobacteria vs. Firmicutes

Actinobacteria have high GC content and include filamentous actinomycetes and waxy-walled Mycobacterium; Firmicutes have low GC content and include endospore-forming Clostridium and Bacillus, as well as lactic acid bacteria and Streptococcus.

Enteric Proteobacteria vs. Pseudomonads

Enterics are facultative anaerobes that can ferment sugars and are identified by biochemical tests; pseudomonads use a wide range of organic compounds and include Pseudomonas aeruginosa, which can cause wound and burn infections.

Chlorobi vs. Chloroflexi

Chlorobi are green sulfur bacteria with chlorosomes; Chloroflexi are green non-sulfur bacteria that can switch between photosynthesis and heterotrophy and include filamentous thermophiles.

Chlamydiae vs. Spirochaetae

Chlamydiae are tiny, nonmotile, obligate parasites; Spirochaetae are helical bacteria that move with internal endoflagella and include Treponema pallidum.

Nitrogen-fixing vs. nitrifying bacteria

Nitrogen-fixing bacteria convert N₂ into ammonium; nitrifying bacteria obtain energy from nitrogen compounds and contribute to the nitrogen cycle.

Methanotrophs vs. methanogens

Methanotrophic bacteria use methane as an energy and carbon source; methanogenic Archaea produce methane.

Gram-positive vs. Gram-negative groups

Gram-positive phyla are Actinobacteria, Firmicutes, and Tenericutes

Gram-negative groups include Proteobacteria, Cyanobacteria, Chlorobi, Chloroflexi, Deinococcus-Thermus, Planctomycetes, Chlamydiae, Spirochaetae, and Bacteroidetes.