BIOL 1262 Living Organisms I Microbiology: Origin of Life and Introduction to Prokaryotes

Microbiology: Definition and Scope

• Microbiology is the study of microbes — living organisms that are too small to be observed by the naked eye; microscopes are required for observation and study.

Bacteria: Origin of Earth and Global Role

• Origin of Earth: approximately $4.6 \times 10^{9}$ years ago (BYA).
• Microbes have been on earth for almost $4 \times 10^{9}$ years and helped create conditions for the evolution of higher organisms.
• They are ancestors of all higher life forms and have a profound impact on the environment and higher life forms.
• Microbial diversity and numbers are extremely high on Earth.
• Mass and abundance figures:
  • A single bacterium may weigh about $1\times 10^{-11}$ g, yet collectively microbes constitute about $60\%$ of Earth\'s biomass.
  • Estimated total bacterial cells on Earth is of the order of magnitude $5\times 10^{30}$ (often cited as a figure around 5.3 × 10^{30} in some sources).
  • The human body contains roughly $3.0\times 10^{13}$ cells, and there are roughly $3.8\times 10^{13}$ bacterial cells associated with the human body.
• Microbes play a critical role in health; rhizosphere (the soil zone around plant roots) may contain >$10^{10}$ bacteria per gram of soil.
• Microbiological processes in the rhizosphere, phyllosphere, and within plants critically impact plant health and productivity.

Origin of Life: Timeline and Theories (3.5–3.9 BYA)

• Several major ideas about origin of life:
  • Creation and spontaneous generation (Aristotle, 384–322 BC).
  • Panspermia: life traveling between planets as seeds. Concept proposed by Anaxagoras (500–428 BC) with seeds of life present everywhere in the universe; modern variants by Berzelius (1830s).
  • Directed panspermia: deliberate transport of microbes by intelligent beings.
  • Primordial Soup Theory: chemical evolution, independently proposed by Oparin (Russian) and Haldane (English) in the 1920s.
• The timeline emphasizes that life arose very early on Earth and set the stage for later biological complexity.

Origin of Life Timeline and Primordial Chemistry

• Primordial soup theory:
  • Early atmosphere proposed to contain key gases for amino-acid synthesis: $\text{NH}<em>3, \text{H}</em>2, \text{CH}<em>4, \text{H}</em>2\text{O}$
  • Amino acids could be synthesized chemically under conditions of high energy (UV radiation, heat, lightning).
• Demonstrations and models showed plausible routes for chemical synthesis of amino acids under primitive conditions (schematic demonstrations include methane, ammonia, water, hydrogen, UV/lightning energy inputs in a primitive ocean/atmosphere system).
• Central question: can complex biomolecules assemble into a functional cell by chance in a suitable chemical environment? The theory faces challenges in explaining the emergence of a self-replicating, functional unit.

Complexity of a Cell and Early Cellular Architecture

• A schematic view of a bacterial cell illustrates key components:
  • Outer membrane and peptidoglycan (cell wall) layers; gram-positive vs gram-negative architectures.
  • Cytoplasmic membrane, cytoplasmic contents, ribosomes, chromosomes.
  • Surface structures: pili, capsule, inclusion bodies, flagellum, periplasmic space, porins.
  • Gram-positive bacteria: thick peptidoglycan layer; absence of outer membrane.
  • Gram-negative bacteria: outer membrane plus a thinner peptidoglycan layer; periplasmic space between membranes.
• The complexity of cell structure raises questions about the likelihood of spontaneous emergence of a fully functional cell.

Weaknesses of the Primordial Soup Theory

• Key criticisms:
  • It is unclear whether the right sequence and folding of amino acids could occur by chance to yield a functional, self-replicating cell.
  • There is evidence that the ancient atmosphere may have lacked sufficient gases such as ammonia and methane in the required concentrations.
  • Concentrations of organic compounds in the primordial environment may have been too dilute to generate significant amounts of organic matter.

Could Cells Have Originated from Viruses?

• Viruses are not considered living organisms because they cannot replicate independently and do not meet all criteria for life.
• Virus structure (virion) components:
  • Nucleic acid (RNA or DNA), capsid (protein coat) composed of capsomeres, and sometimes a membranous envelope.
  • Nucleocapsid formed by nucleic acid + capsid; envelope present in some viruses.
• Key virion examples:
  • Tobacco mosaic virus: rod-shaped, helical.
  • Adenoviruses: icosahedral with 20 triangular faces.
  • Influenza virus: enveloped virus.
• Typical virus dimensions (illustrative examples):
  • Bacteriophage T4 attacking bacteria: ~
  • Tobacco mosaic virus: ~ 18 × 250 nm.
  • Adenoviruses: ~ 70–90 nm in diameter.
  • Influenza viruses: ~ 80–200 nm in diameter with envelope.
• The virion is the infectious agent, but the origin of life is separate from the origin of viruses; viruses require host cells for replication.

History of Microorganisms on Earth: Early Life and Energetics

• The earliest microorganisms include extremophiles and chemoautotrophs that use inorganic compounds as carbon and energy sources.
• Methane and other inorganic compounds could serve as energy substrates for early life.
• Early life included anaerobes, as oxygen was not yet present in the atmosphere.
• Chemoautotrophs and chemoheterotrophs dominated early life before widespread photosynthesis.

Photosynthesis and Oxygenation: From Anoxygenic to Oxygenic

• Early photosynthesis was anoxygenic and used inorganic donors such as H_2S as electron donors.
• Oxygenic photosynthesis evolved later (roughly around $2.4 \times 10^{9}$) years ago, using water as the electron donor, leading to the release of molecular oxygen into the atmosphere.
• Purple bacteria performed anoxygenic photosynthesis with sulfur as the electron donor.
• Cyanobacteria evolved oxygenic photosynthesis and contributed to oxygen accumulation in the atmosphere.

Major Timeline in the History of Life

• Earth formation: approximately $4.6\times 10^{9}\text{ years ago}$.
• First microbes: perhaps as early as $\sim 4.1-3.8\times 10^{9}\text{ years ago}$.
• Photosynthesis evolved in bacteria (initially anoxygenic) around $3.5\times 10^{9}\text{ years ago}$.
• First eukaryotes appeared around $2.7\times 10^{9}\text{ years ago}$.
• Oxygen-producing photosynthesis by cyanobacteria evolved around $2.8\times 10^{9}\text{ years ago}$; atmospheric oxygen began to accumulate slowly.
• Multicellular organisms emerged around $6.0\times 10^{8}\text{ years ago}$.
• First land flora about $4.7\times 10^{8}\text{ years ago}$.
• Mammals, flowering plants, and social insects appeared in the last $2.5\times 10^{8}\text{ years}$ or so.
• Reference for atmospheric oxygen changes and fossil evidence is shown in schematic figures.

Stromatolites: Oldest Fossils

• Stromatolites are layered rocks primarily composed of cyanobacteria and other microbes dating back to about $3.5\times 10^{9}\text{ years ago}$.
• Modern stromatolites form in salty lagoons or bays in places such as Australia, Brazil, Mexico, and the Bahamas.

Cyanobacteria: Oxygenation of the Atmosphere

• Cyanobacteria contributed to the accumulation of atmospheric oxygen via oxygenic photosynthesis.

Classification of Life: Domains and Major Groups

• Three domains of life:
  • Eukarya: includes animals, plants, fungi, slime molds, and many protists.
  • Bacteria: diverse prokaryotes including Gram-positive and Gram-negative groups.
  • Archaea: includes extremophiles and diverse metabolic groups.
• Representative groups listed within the slide:
  • Eukarya: animals, plants, fungi, slime molds, ciliates, flagellates, microsporidia, Entamoebae, etc.
  • Bacteria (examples): green and purple bacteria, Gram- positives, cyanobacteria, Flavobacteria, Thermotogales, non-sulfur bacteria.
  • Archaea (examples): methanogens, halophiles, hyperthermophiles.

Bacteria: General Definition and Notable Exceptions

• Bacteria are generally single-celled prokaryotes within the domains Eubacteria and Archaebacteria (prokaryotes).
• Notable exceptional bacteria that are unusually large:
  • Epulopiscium fishelsoni: bacillus-shaped, typically around $80\ \mu\text{m}$ in diameter and $200-600\ \mu\text{m}$ long.
  • Thiomargarita namibiensis: spherical bacterium between $100-750\ \mu\text{m}$ in diameter.
  • Giant bacteria from Guadeloupe: Thiomargarita magnifica, average length about $1\ \text{cm}$ with some specimens up to $2\ \text{cm}$.

Reproduction and Gram-Positive/Gram-Negative Distinctions

• Most bacteria reproduce by binary fission.
• Two major groups based on Gram staining:
  • Gram-positive: thick peptidoglycan layer; retains crystal violet stain.
  • Gram-negative: have an outer membrane and a thinner peptidoglycan layer; different staining and periplasmic space.

Bacterial Morphology and Variability

• Common shapes:
  • Coccus (spherical)
  • Bacillus (rod-shaped)
  • Spirillium (spiral-shaped)
  • Coccobacillus (short rod)
  • Vibrio (comma-shaped)
  • Spirochete (corkscrew-shaped)
  • Pleomorphic (variable shapes, often due to cell wall absence)
• Additional observed forms: star-shaped and square bacteria (as seen in some electron microscopy images).
• After division, bacteria may adopt various cellular arrangements:
  • Diplococci: in pairs
  • Streptococci: chains
  • Tetrads: groups of four (two planes)
  • Sarcinae: groups of eight (three planes)
  • Staphylococci: clusters (random planes)
  • Some bacteria form filamentous structures.

Bacterial Filamentous and Large-Scale Forms

• Filamentous bacteria exist as long filaments rather than discrete cocci/bacilli.

Bacterial Phyla (Eubacteria)

• Proteobacteria (Gram-negative): a large and diverse phylum with several classes:
  • Alpha-proteobacteria: includes Rhizobia (nitrogen-fixing in legumes).
  • Beta-proteobacteria: examples include Neisseria gonorrhoeae and Neisseria meningitidis.
  • Gamma-proteobacteria: includes Enterobacteriaceae (e.g., Escherichia coli, Salmonella) and Pseudomonads.
• Firmicutes (Gram-positive):
  • Clostridia (e.g., Clostridium botulinum).
  • Bacilli (e.g., Bacillus, Staphylococcus).
• Actinobacteria: filamentous bacteria including:
  • Streptomyces (antibiotic producers).
  • Mycobacterium tuberculosis, Corynebacterium diphtheriae, Mycobacterium leprae, Propionibacterium acnes.
• Cyanobacteria: photosynthetic bacteria known for oxygenic photosynthesis.
• Note on Cyanobacteria: feature photosynthetic apparatus with thylakoid membranes and carboxysomes.
• There is some mention of cyanobacteria with explicit cell envelope features (outer membrane, cell wall, etc.).

Archaea: Distinct Domain with Unique Metabolisms

• Archaea include organisms such as methanogens, halophiles, and thermoacidophiles.
• They occupy unique ecological niches and have distinct biochemistry from bacteria.

Archaebacterial and Bacterial Phyla (Summary)

• Bacteria phyla include Proteobacteria, Firmicutes, Actinobacteria, and Cyanobacteria.
• Archaea phyla include methanogens, halophiles, and thermoacidophiles.
• Cyanobacteria are notable for oxygenic photosynthesis and for their role in atmospheric oxygenation.

Size, Shape, and Structural Details of Key Bacterial Features

• Bacteria exhibit vast diversity in size and shape, ranging from nanometers to micrometers in scale, with giant bacteria occasionally reaching hundreds of micrometers or even centimeters in length.
• The Gram stain concept helps distinguish cell wall structure and associated phenotypes, influencing staining, permeability, and antibiotic susceptibility.

References to Notable Figures and Laboratories (Conceptual)

• Morphological diagrams illustrate bacterial shapes and arrangements, including diplococci, streptococci, tetrads, sarcinae, staphylococci, diplobacilli, streptobacilli, and filamentous forms.
• Electron microscopy captures unusual shapes such as star-shaped and square bacteria, indicating broad morphological diversity.

Virus Concepts and Structures (Recap)

• Versus cellular life, viruses possess:
  • Nucleic acid (DNA or RNA)
  • Capsid made of capsomeres
  • In some cases, a membranous envelope around the capsid
• Viral examples and scales:
  • Tobacco mosaic virus: rod-shaped, helical; ~18 × 250 nm
  • Adenoviruses: icosahedral with ~70–90 nm diameter
  • Influenza viruses: enveloped; ~80–200 nm diameter
• Bacteriophages like T4 attack bacteria; virions vary in structure and genome organization.

Key Takeaways and Connections

• Life on Earth emerged very early, and microbes remain the foundational organisms shaping biosphere evolution.
• The primordial soup concept provided a plausible chemical basis for the origin of biomolecules, yet it faces conceptual and evidential challenges.
• Viruses are not freely living but represent a distinct class of biological entities with diverse structures and life cycles.
• Bacteria display extraordinary diversity in forms, metabolic strategies, and ecological roles, including extremophiles and giant bacteria that challenge intuitive size limits.
• The evolution of photosynthesis, especially oxygenic photosynthesis by cyanobacteria, transformed Earth\'s atmosphere and enabled aerobic life.
• Modern classification recognizes three domains (Eukarya, Bacteria, Archaea) with broad diversity within each domain and within major bacterial phyla such as Proteobacteria, Firmicutes, Actinobacteria, and Cyanobacteria.
• Understanding morphology, reproductive strategies, cell wall architecture, and ecological roles is essential for grasping microbial life and its impact on health, agriculture, and the environment.