Study Notes on the Diversity of Bacteria and Archaea
Diversity of Bacteria and Archaea
Prokaryotic Classification
Estimated Species: Roughly 1 million species of prokaryotes; only 6000 described and classified.
Taxonomy: The scientific study that organizes living organisms into groups, or taxa, based on shared characteristics.
Identification: Involves characterizing organisms to group them together.
Nomenclature: The system for naming organisms.
Classification: The arrangement of organisms into similar or related groups.
Strategies for Identifying Microorganisms
Microscopic Examination: Observing the organism's structure visually under a microscope to gain insights into its morphology.
Culture Characteristics: Analyzing how microorganisms grow in controlled environments such as petri dishes.
Biochemical Tests: Evaluating biochemical properties of microorganisms, such as fermentation patterns or enzyme presence.
Nucleic Acid Analysis: Using genetic information (DNA/RNA sequencing) for more precise identification.
Disease Symptoms: Relating specific microorganism presence to symptoms manifested in disease.
Phylogeny
Refers to the evolutionary relationships among organisms. Determining phylogenetic relationships is more complex in prokaryotes due to:
Asexual Reproduction: Limits the markers typically used for evolutionary relationships since genetic recombination is less frequent.
Few Differences in Cell Morphology: Many prokaryotes appear morphologically similar.
Sequencing Genes: Helps assist in classifying and identifying species based on genetic relatedness.
Remember Your Domains
Three Domains of Life:
Bacteria
Archaea
Eucarya
Subcategories of Bacteria:
Filamentous Anoxygenic Phototrophic bacteria
Gram-positive bacteria (e.g., Methanosarcina, Spirochetes)
Halobacteria, Proteobacteria, Thermococcus, etc.
Prokaryotic Diversity
Prokaryotes grouped based on distinctive characteristics include:
Lactic Acid Bacteria
Anoxygenic Phototrophs
Endospore Formers
Sulfide Reducers
Note: Groups with similar phenotypic and physiological traits may not share genetic relations.
Energy and Carbon Sources of Prokaryotes
TABLE 4.5: Energy and Carbon Sources Used by Different Groups of Prokaryotes
Types of Prokaryotes:
Photoautotroph
Energy Source: Sunlight
Carbon Source: CO₂
Photoheterotroph
Energy Source: Sunlight
Carbon Source: Organic compounds
Chemolithoautotroph
Energy Source: Inorganic chemicals (H$2$, NH$3$, NO$2$, Fe²⁺, H$2$S)
Carbon Source: CO₂
Chemoorganoheterotroph
Energy Source: Organic compounds (e.g., sugars, amino acids)
Carbon Source: Organic compounds
Evolution of Prokaryotes
Prokaryotes have existed for billions of years, gaining adaptations to various environmental conditions.
Anaerobic Chemotrophs
Early prokaryotic life existed in anoxic (no O₂) conditions for approximately 1.5 million years.
Current anaerobic environments include:
Soil
Aquatic environments
Human body (e.g., gastrointestinal tract)
Types of Organisms:
Anaerobic Chemolithotrophs
Anaerobic Chemoorganotrophs
Anaerobic Chemolithotrophs
Utilize Anaerobic Respiration:
Energy Source: Inorganic chemicals
Terminal Electron Acceptors: CO₂ and S.
Typically belong to Archaea (e.g., Methanogens):
Use H₂ gas and CO₂, releasing methane.
Habitats include sewage, swamps, marine sediments, and mammalian digestive tracts.
Highly sensitive to O₂.
Anaerobic Chemoorganotrophs
Obtain energy primarily through fermentation:
Genus Clostridium:
Characteristics: Gram-positive bacilli, produce endospores.
Noteworthy species and diseases:
C. tetani (Tetanus)
C. perfringens (Gas gangrene)
C. botulinum (Botulism)
Lactic Acid Bacteria
Classification: Typically Gram-positive, often obligate fermentors that produce lactic acid:
Genus Streptococcus:
Characteristics: Cocci that form chains, common normal microbiota.
S. pyogenes: Causes beta-hemolytic strep throat.
Genus Lactococcus: Known for use in the dairy industry.
Genus Enterococcus: Present in animal intestinal tracts.
Genus Lactobacillus: Forms chains or exists as single cells; common in normal flora, especially vaginal flora, and in food production.
Anoxygenic Phototrophs
Photosynthesis type that uses hydrogen sulfide or organic molecules as the electron source:
Unlike oxygenic phototrophs that use water and produce oxygen.
Found in aquatic habitats like bogs and upper layers of mud.
Includes purple and green sulfur bacteria.
Oxygenic Phototrophs
Photosynthetic bacteria using water as the source of electrons:
Cyanobacteria:
Earliest photosynthetic organisms, Gram-negative.
Habitat: Soil, rocks, freshwater, marine environments.
Capable of nitrogen fixation; exist as unicellular or multicellular forms.
Can cause blooms, releasing toxins.
Aerobic Chemoorganotrophs
Utilize organic compounds for energy, employing oxygen as their terminal electron acceptor.
Can be classified into:
Obligate Aerobes:
Exclusively use aerobic respiration. Example genera include:
Genus Micrococcus: Gram-positive cocci, found in soil. Produces pigmented colonies, such as M. luteus.
Genus Mycobacterium: Gram-positive, acid-fast bacilli (e.g., M. tuberculosis).
Genus Pseudomonas: Gram-negative, motile ang pigmented, often found in water (e.g., P. aeruginosa).
Facultative Anaerobes
Includes many members in the family Enterobacteriaceae (Enterics):
Gram-negative bacilli residing in the intestinal tract, many as normal microbiota.
Notable medically significant species include:
E. coli
Shigella species
Salmonella enteric strains (e.g., Salmonella typhi leading to typhoid fever).
Coliforms are common intestinal Enteric bacteria that can ferment lactose, often assessed as indicators of fecal pollution.
Survival in Terrestrial Environments
Prokaryotes such as those from Bacillus and Clostridium species can form resting stages to endure dry conditions:
Structures include endospores, cysts, fruiting bodies, and mycelium.
Endospores specifically exhibit high resistance to environmental insults compared to other resting structures.
Survival in Aquatic Environments
Prokaryotic organisms develop mechanisms for nutrient acquisition, including:
Forming chains encased in tubes to help locate favorable habitats. Notable genera include Sphaerotilus and Leptothrix.
Animals as Habitats for Bacteria
Animal bodies harbor diverse ecological niches:
Skin: Inhabited by Staphylococcus species, key components of skin flora.
Mucous Membranes: Home to genera such as Bacteroides, Bifidobacterium, Campylobacter, Helicobacter, Neisseria, and Treponema.
Intracellular parasites such as Rickettsia, Orientia, and Ehrlichia dwell within blood-sucking arthropods like ticks or lice.
Medically Important Bacteria
TABLE 11.3: Medically Important Bacteria
Gram-Negative Rods:
Includes genera such as Escherichia, Salmonella, Shigella, and Yersinia, often associated with significant diseases (e.g., E. coli causing UTIs).
Gram-Positive Rods:
Example: Bacillus anthracis (causing anthrax, used in bioterrorism).
Gram-Positive Cocci:
Includes Staphylococcus and Streptococcus genera, causing a range of infections from skin to systemic diseases.
Archaea Thriving in Extreme Conditions
Extreme Halophiles: Adapted to high-salt environments (e.g., salt lakes), requiring around 9% salt concentration. Includes Halobacterium and others.
Understanding Microbial Diversity
Microorganisms are diverse, existing in various habitats and conditions. Their metabolism must support survival, influencing their ecological roles positively.
How to Study This Material
Familiarize yourself with key terms related to microbial classification and identification.
Understand major groups discussed: Anaerobic chemotrophs, Anoxygenic phototrophs, Oxygenic phototrophs, Aerobic chemolithotrophs, and Chemoorganotrophs.
Begin familiarization with discussed microbes.
Discussion Questions
Soil Characteristics: Consider how Clostridium species' characteristics allow them to thrive in areas with drastic environmental changes.
Lake Ecosystem Changes: Discuss factors contributing to algal blooms in polluted waters, analyzing underlying water composition and remediation strategies.