Prokaryotic and Metabolic Diversity

Diversity of Prokaryotes

• Scientists are in the early stages of understanding the vast diversity of microbial life
• Only a small percentage of the over 4 million prokaryotic species has been described
• 22,919 prokaryotic species are validly named and published under the International Code of Nomenclature of Prokaryotes (ICNP)
• The majority of prokaryotic species have not been isolated
• New molecular techniques are aiding in the discovery and characterization of prokaryotes

Metabolic Diversity

• Prokaryotes exhibit a broad range of metabolic strategies

• Anaerobic Chemotrophs

  • Anaerobic Chemolithotrophs: Obtain energy from inorganic chemicals in the absence of oxygen
  • Anaerobic Chemoorganotrophs: Obtain energy from organic compounds in the absence of oxygen, using anaerobic respiration or fermentation

• Anoxygenic Phototrophs

  • Do not produce oxygen
  • Purple Bacteria
  • Green Bacteria
  • Other Anoxygenic Phototrophs

• Oxygenic Phototrophs

  • Cyanobacteria

• Aerobic Chemolithotrophs

  • Sulfur-Oxidizing Bacteria
  • Nitrifiers
  • Hydrogen-Oxidizing Bacteria

• Aerobic Chemoorganotrophs

  • Obligate Aerobes
  • Facultative Anaerobes

Anaerobic Chemotrophs

• Prokaryotes first inhabited Earth when the atmosphere was anoxic for approximately 1.5 billion years
• Early chemotrophs likely used anaerobic respiration
  • Using terminal electron acceptors like CO2 or S
• Others may have used fermentation
  • Passing electrons to an organic molecule, such as pyruvate
• Anaerobic habitats are still common today
  • Aerobes consume oxygen
  • Mud and tightly packed soil limit gas diffusion
  • Aquatic environments can become limiting
  • Human body, such as the intestinal tract, provides one such habitat
  • Anaerobic microenvironments exist in the skin and oral cavity

Anaerobic Chemolithotrophs

• Chemolithotrophs oxidize inorganic chemicals to obtain energy
• Anaerobes use alternative terminal electron acceptors
  • CO2 or S
• Relatively few have been discovered
• Most belong to the domain Archaea
  • Methanogens are one group

Methanogens

• Consist of a group of methane-producing archaea
• Oxidize H2 gas to generate ATP
• Alternative energy sources
  • Formate
  • Methanol
  • Acetate
• Use CO2 as a terminal electron acceptor: 4H2 + CO2 → CH4 + 2H2O
• Smaller energy yield than other electron acceptors
• Very sensitive to O2
• Commonly found in sewage, swamps, marine sediments, rice paddies, and digestive tracts where H2 and CO2 are available
• Cows produce approximately 10 cubic feet of CH4 gas per day

Anaerobic Chemoorganotrophs

• Chemoorganotrophs oxidize organic compounds, such as glucose, to obtain energy
• Anaerobes often use sulfur or sulfate as a terminal electron acceptor
• Sulfur and Sulfate Reducing Bacteria produce hydrogen sulfide with a rotten-egg smell
• H2S is corrosive to metals
• Important in the sulfur cycle
• At least a dozen recognized genera
  • Desulfovibrio is the most studied species; Gram-negative curved rods
• Some archaea can reduce sulfur and sulfate

Fermentation

• Numerous anaerobic bacteria ferment
• ATP is generated via substrate-level phosphorylation
• Many different organic energy sources and end products
  • Glucose → Pyruvate → Lactic acid
• Clostridium and Clostridioides are common fermenters

Clostridium and Clostridioides

• Collectively referred to as clostridia
• Gram-positive rods that can form endospores
• Common soil inhabitants that live in anaerobic microenvironments
• Endospores tolerate O2, heat, drying, chemicals, and irradiation
• Germinate and multiply when conditions become favorable
• Pathogenic Clostridium species cause tetanus (C. tetani), gas gangrene (C. perfringens), and botulism (C. botulinum)
• Clostridioides difficile causes an antibiotic-associated diarrheal disease referred to as C. difficile infection (CDI)
• Some are normal inhabitants of the intestinal tract of humans and other animals

Lactic Acid Bacteria

• Gram-positive bacteria that produce lactic acid as a product of fermentation
• Most can grow in aerobic environments but typically lack catalase, so they only ferment
• Streptococcus inhabit the oral cavity and are part of the normal microbiota
  • Some are pathogenic, for example, β-hemolytic S. pyogenes [group A] -S. thermophilus is used to make yogurt
• Lactococcus species is used to make cheese
• Enterococcus inhabit the human and animal intestinal tract
• Lactobacillus are rod-shaped and common in the mouth and vagina
  • Break down glycogen deposited in the vaginal lining
  • Resulting low pH helps prevent vaginal infections
  • Present in decomposing materials
  • Imporatnt in the production of fermented foods and beverages, such as Masato from the Amazon

The Genus Propionibacterium

• Gram-positive pleomorphic rods
• Produce propionic acid via fermentation
• Can also ferment lactic acid
• Important in the dairy industry for the production of Swiss cheese
  • Typical nutty flavor
  • CO2 creates signature holes

Anoxygenic (Anaerobic) Phototrophs

• Likely the earliest photosynthesizers
• Use hydrogen sulfide or organic compounds (not water) to make reducing power for biosynthesis
  • Do not generate O2: 6CO2 + 12H2S → C6H12O6 + 12S + 6H2O
• Modern-day phylogenetically diverse with the following characteristics
  • Live in bogs, lakes, and upper layers of mud
  • Live in places with little or no O2, but light penetrates
  • Have different photosystems than plants, algae, and cyanobacteria
  • Use unique bacteriochlorophyll that absorbs deep-penetrating wavelengths

Purple Bacteria

• Gram-negative appear red, orange, or purple
• Photosynthetic apparatus in the cytoplasmic membrane
  • Unlike other anoxygenic phototrophs, folds increase surface area
• Purple Sulfur Bacteria
  • Large cells, some motile
  • May have gas vesicles to control depth
  • Most store sulfur in intracellular granules
  • Preferentially use H2S to generate reducing power
    • Other inorganic (H2) or organic (pyruvate) compounds
  • Some can grow aerobically in the absence of light and oxidize reduced inorganic and organic compounds
• Representatives include Chromatium, Thiospirillum, and Thiodictyon

Purple Non-Sulfur Bacteria

• Found in moist soils, bogs, and paddy fields
• Preferentially use organic molecules instead of H2S as a source of electrons
• Lack gas vesicles
• May store sulfur, granules form outside the cell
• Remarkably diverse metabolism
  • Many use H₂ or H2S like purple sulfur bacteria
  • Most can grow aerobically in the absence of light using chemotrophic metabolism
• Representatives include Rhodobacter and Rhodopseudomonas

Green Bacteria

• Gram-negative typically, green or brownish
• Green Sulfur Bacteria have
  • Habitats similar to purple sulfur bacteria
  • Use H2S and form sulfur granules outside of the cell
  • Accessory pigments located in chlorosomes
  • Lack Flagella
  • May have gas vesicles
  • Strict anaerobes
  • None are chemotrophic
  • Representatives include Chlorobium and Pelodictyon

Filamentous Anoxygenic Phototrophic Bacteria

• Form multicellular arrangements
• Exhibit gliding motility
• Many have chlorosomes
  • 16S rDNA shows that they are unrelated to green sulfur bacteria
• Metabolically diverse
  • Some preferentially use organic compounds to generate reducing power, and can grow in the dark aerobically using chemotrophic metabolism
• Chloroflexus is the best studied and are especially thermophilic strains that are found in hot springs

Other Anoxygenic Phototrophs

• Other anoxygenic phototrophs exist, although green and purple bacteria are the most extensively studied
• Members include Heliobacterium
  • Gram-positive endospore-forming rods
  • Related to Clostridium

Oxygenic (Aerobic) Phototrophs

• Cyanobacteria
  • Earliest oxygenic phototrophs
  • Introduction of O2 began roughly 3 bya
  • Consumes water as the source of electrons for reducing power
  • Still play an essential role as primary producers that harvest sunlight to convert CO2 into organic compounds: 6 CO2 + 6H2O → C6H12O6 + 6O2
  • Initially thought to be algae and were called blue-green algae
  • Diverse group of Gram-negative bacteria
  • Many convert N2 to ammonia, meaning that they perform nitrogen fixation

Cyanobacteria Characteristics

• Morphologically diverse
• Unicellular forms: cocci, rods, spirals
• Multicellular forms: filamentous associations called trichomes - May be in a sheath - Motile trichomes glide as a unit
• Those that live in an aquatic environment have gas vesicles for vertical movement in water

Cyanobacteria: Blooms and Photosystems

• Can accumulate in large numbers in freshwater habitats and are called bloom
  • Sunny, hot weather can lyse cells causing a scum to form
• Photosystems are like those in chloroplasts of algae and plants, which evolved from ancestral cyanobacteria
• Have phycobiliproteins that absorb additional wavelengths that are not well absorbed by chlorophyll

Nitrogen Fixing Cyanobacteria

• Critically important ecologically, as they incorporate N2 and CO2 into organic material that used by other organisms
• Nitrogenase is destroyed by O2 and must be protected -Anabaena forms specialized heterocysts
  • Do not have photosystem II because it produces O2 -A. azolae fixes N2 in the special sac of Azolla fern -Synechococcus fixes N2 in the dark

Aerobic Chemolithotrophs

• Aerobic chemolithotrophs gain energy by oxidizing reduced inorganic chemicals
• Sulfur-oxidizing bacteria
  • Gram-negative rods, spirals -Energy from oxidation of sulfur and sulfur compounds including H2S and Na2S2O-3 -O2 is the terminal electron acceptor, producing sulfuric acid: S + O2 + H2O → H2SO4 -Important in the sulfur cycle -Unicellular forms can affect the environmental pH -Filamentous forms may interfere with wastewater treatment facilities
• Nitrifiers are a diverse group of Gram-negatives that -Oxidize inorganic nitrogen compounds for energy -They are a concern for farmers using ammonium fertilizer -Can deplete water of O2 , if wastes are high in ammonium -Two groups usually grow in close association -Ammonium oxidizers: Nitrosomonas and Nitrosococcus: NH4 + O2 → NO2 + H2O -Nitrite oxidizers: Nitrobacter and Nitrococcus: NO2 + O2 → NO3
• Aquifex and Hydrogenobacter are among the few hydrogen-oxidizing bacteria that are obligate chemolithotrophs -Thermophilic and typically live in hot springs -Aquifex have maximum growth at 95 oC -One of the earliest bacterial forms to exist on earth -O2 requirements are low and possibly available in certain niches due to photochemical processes that split water: H2 + O2 → H2O

Aerobic Chemoorganotrophs

• Oxidize organic compounds for energy
• Use O2 as the terminal electron acceptor
• Some inhabit specific environments, while others are more generalists: organic compounds + O2 → CO2 + H2O

Obligate Aerobes

• Obligate Aerobes cannot ferment
• The genus Micrococcus -Gram-positive cocci -Found in soil, dust particles, inanimate objects, and mammalian skin -Are pigmented colonies -Tolerate dry, salty conditions

Genus Mycobacterium

• Acid-fast bacteria -Mycolic acid in cell wall prevents Gram-staining and requires acid-fast staining to be used -Nocardia species are also acid-fast -Generally pleomorphic rods -Many are saprophytes, living on dead and decaying matter -Notable pathogens include: M. tuberculosis and M. leprae -More resistant to disinfectants and often resistant to antimicrobial drugs

Genus Pseudomonas

• Gram-negative rods that exhibit polar flagella and frequently produce pigments -Most are obligate aerobes and do not ferment. They are also oxidase positive -Exhibit extreme metabolic diversity which is important in degradation and some have this ability from plasmids -Widespread in soil and water -Most are harmless however some are pathogens including P. aeruginosa, a common opportunistic pathogen

Thermus and Deinococcus

• These genera are related and have unusual cell walls -Thermus are thermophilic, valuable for their heat-stable enzymes, and stain Gram-negative -Deinococcus are extraordinarily gamma radiation resistant, because they are able to use enzymes to repair damage to their shattered genome -Scientists hope to genetically engineer this for cleaning up radioactive wastes and stain Gram-positive

Facultative Anaerobes

• Use aerobically respiration but can ferment if O2 is not available
• Corynebacterium: Gram-positive pleomorphic rods that: -Are widespread -Are often club-shaped and form V shapes or palisades (also called coryne forms or diphtheroids) -Generally facultative anaerobes but can also be strict aerobes -Many are harmless and part of the normal microbiota but C. diphtheriae causes diphtheria

The Family Enterobactieriaceae

• All are enterics or enterobacteria -Gram-negative rods that exist in intestinal tracts of humans and other animals. Some live in soil -Normal intestinal microbiota including Enterobacter, Klebsiella, Proteus, and most E. coli strains -Diarrheal disease caused by Shigella and Salmonella enterica, and some E. coli strains -Life-threatening diseases: typhoid fever (Salmonella serotype Typhi) and bubonic and pneumonic plague (Yersinia pestis) -Facultative anaerobes that ferment glucose -Lactose fermenters are termed coliforms -Include E. coli which is indication of possible fecal pollution

The Genus Vibrio

• Live in marine environments and obligately require some Na+ for growth
• Gram-negative straight or slightly curved rods
• Pathogens including V. cholerae, which causes cholera
• Some are bioluminescent

Ecophysiological Diversity

• Study of the adaptations of physiological mechanisms that prokaryotes use to live in terrestrial and aquatic environments
• As a group, prokaryotes show remarkable diversity in their physiological adaptations to a wide range of habitats, including the bodies of animals

Ecophysiological Diversity Subcategories

• Thriving in Terrestrial Environments
• Thriving in Aquatic Environments
• Animals as Habitats
• Archaea That Thrive in Extreme Conditions

Thriving in Terrestrial Environments

• Microorganisms living in soil must tolerate all sorts of conditions -Wet and dry, warm and cold, abundant to sparse nutrients -Several genera can form a resting stage that allows them to survive dry periods -Endospores are the most resistant to environmental extremes

Bacteria that Form a Resting Stage

• Endospore forming -Bacillus and Clostridium are most common -Gram-positive rods -Clostridium species are obligate anaerobes -Bacillus include obligate and facultative anaerobes -Both organisms can cause disease: -C. tetani causes tetanus and B. anthracis causes anthrax
• Azotobacter -Gram-negative pleomorphic rods -Form resting called a cyst -Withstand drying and UV radiation, but not high heat -Fix nitrogen in aerobic conditions -High respiratory rate maintains low O2 in a cell and protein binds nitrogenase, protecting from O2 damage
• Streptomyces -Over 500 species of aerobic Gram- positive bacteria that resemble fungi and form a mass of branching hyphae -Chains of spores (conidia) develop at tips and are resistant to drying -Produce extracellular enzymes and medically useful antibiotics

Bacteria that Associate with Plants

• Agrobacterium-Gram-negative rods -Can genetically alter plants for their own benefit -The bacterium uses its Ti plasmid transfer its DNA through wounded areas into the tissue which has the ability to synthesize plant growth hormone resulting in a plant tumor Also encodes of synthesis of unusual amino acid derivatives that benefit the bacterium

Bacteria Living in Relationship with Legumes

• Rhizobia Gram-negative rods that can fix nitrogen and function as endosymbionts in nodules on roots of legumes
  • The host plant synthesizes leghemoglobin that binds and controls O2 levels to yield microaerobic environments, so that the bacteria can fix nitrogen

Thriving in Aquatic Environments

• Most aquatic environments lack steady nutrient supply -Therefore bacteria have evolved mechanisms for obtaining and storing nutrients
• Sheathed Bacteria form chains of cells within a tube -Sheaths protect and help bacteria attach to solid objects in a favorable habitat -They are streaming from rocks in water due to nutrient-rich effluents and may clog pipes Include Gram-negative rods -Sphaerotilus and Leptothrix -Motile swarmer cells exit open end of sheath and move to new surface

Prosthecate Bacteria

Diverse group of Gram-negatives the uses Extensions of cytoplasm and cell wall called prosthecae to increase increased surface area for nutrient absorption and some allow attachment

• Caulobacter is commonly used for cellular differentiation studies

Bacteria that the derive nutrients from other organisms

• Bioluminescent bacteria emit light -Symbiotic relationship with fish and squid to help with camouflage -Luminescence catalyzed by enzyme luciferase (lux) -Gram-negative straight or curved rods that are facultative anaerobes inmarine environments