Chapter 1: The Evolution of Microorganisms and Microbiology

Microorganisms and Microbiology: An Overview

• Microorganisms are too small to be seen clearly by the unaided eye, generally less than 1 mm in diameter.
• Some microorganisms, like bread molds and algae, are visible without microscopes.
• Macroscopic microorganisms are multicellular but lack highly differentiated tissues.

Diversity of Microorganisms

• Microbiology studies cellular and acellular organisms.
• Cellular organisms include:
  • Bacteria
  • Archaea
  • Protists (eukaryotes with membrane-bound nucleus and organelles)
  • Fungi (eukaryotes with membrane-bound nucleus and organelles)
• Acellular organisms include:
  • Viruses
  • Viroids
  • Satellites
  • Prions

Astonishing Diversity and Abundance of Microorganisms on Earth

• There are more microbes on Earth than stars in the known universe (an almost unimaginable number).
• Microbes inhabit virtually every environment on the planet:
  • Hydrothermal vents on the ocean floor, thriving in superheated water laden with chemicals and radioactive waste.
  • Deep underground.
  • Boiling hot springs (e.g., Yellowstone).
  • The human body (e.g., the gut).
  • High in the atmosphere.
• Microbes can adapt and colonize environments lethal to complex life forms.
• Examples:
  • Soil and ocean waters contain astronomical numbers of bacteria and archaea.
  • The biomass of life on Earth is largely microbial and hidden from plain sight.
  • Oceans are estimated to have 10^{29} cells of microbes.
  • Billions of microbes exist in a teaspoon of soil.
  • Trillions of microbial cells live in humans, especially in the gut.

Classification of Microorganisms

• Early classification of microbes was based on morphological characteristics, similar to plants and animals.
• Microbes were initially divided into prokaryotes and eukaryotes.
  • Prokaryotic cells lack a membrane-bound nucleus or organelles.
  • Eukaryotic cells have a membrane-enclosed nucleus and are larger and more morphologically complex.
• Five-Kingdom Classification System (Robert Whittaker):
  • Widely used until the 1980s.
  • Life divided into five kingdoms: Monera, Protista, Fungi, Plantae, Animalia.
  • Most microorganisms (excluding viruses and acellular organisms) were placed in Monera, Protista, and Fungi.
    • Monera: All prokaryotic cells.
    • Protista: Eukaryotic unicellular and multicellular organisms.
    • Fungi
• The five-kingdom system made it difficult to classify microorganisms into species, genera, etc.

Carl Woese and the Three-Domain System

• In the 1970s, Carl Woese introduced a revolutionary way to classify life by comparing sequences of ribosomal RNA (rRNA) genes.
• He focused on the small subunit ribosomal RNA (SSU rRNA), a component of ribosomes present in all cellular life.
• The idea was that all cellular life has a shared evolutionary history, and genes can be used as molecular fingerprints to infer evolutionary relationships.
• Analysis led to the discovery that prokaryotes consisted of two very different groups.
• Life's family tree had three main branches instead of two (prokaryotes versus eukaryotes).
• Resulted in the three-domain system of classification: Bacteria, Archaea, and Eukarya.

The Three Domains of Life

• Domain Bacteria:
  • Single-celled microorganisms.
  • Most have cell walls with peptidoglycan.
  • Lack a membrane-bound nucleus.
  • Live in diverse environments, including the human body.
  • Some cause diseases, while others do not.
• Domain Archaea:
  • Distinguished from bacteria by unique RNA sequences.
  • Unique membrane lipids.
  • Unusual metabolic characteristics.
  • Many live in extreme environments.
  • No known archaea directly cause diseases in humans.
• Domain Eukarya:
  • Contains all eukaryotes including protists and fungi.
  • Protists:
    • Unicellular (generally larger than bacteria and archaea).
    • Include protozoans that are often motile (cilia, flagella, or amoeboid motion) and animal-like (eat other organisms).
    • Include algae, which are photosynthetic protists that use sunlight to make energy.
    • Protists are diverse. Some cause diseases, while algae are crucial in ecosystems, producing oxygen and forming the base of aquatic food webs.
  • Fungi:
    • Unicellular or multicellular.
    • Yeasts are unicellular fungi used for baking and brewing.
    • Molds and mushrooms are multicellular fungi.
    • Fungi have cell walls made of chitin (not peptidoglycan).
    • Heterotrophic and key decomposers in ecosystems.
    • Some cause infections (e.g., Candida yeast infections, athlete's foot), while others are beneficial (e.g., penicillin from mold).
  • Plants and animals are also from the domain Eukarya but are beyond the scope of microbiology.

Acellular Agents

• Acellular agents are not organized as living forms because they need a host to survive:
  • Viruses: Extremely small (smallest is 10,000 times smaller than a typical bacterium). Cause many animal and plant diseases (e.g., COVID-19, rabies, influenza, AIDS, common cold).
  • Viroids: Cause numerous plant diseases.
  • Satellites: Must co-infect the cell with a helper virus and can cause animal and plant diseases (e.g., hepatitis D).
  • Prions: Responsible for neurological diseases, such as mad cow disease.

The Microbial World

• Microbes form the unseen majority of life and their diversity underlies their importance.
• Microbes drive essential processes in ecosystems and have countless interactions with humans (both good and bad).
• Microbial life likely originated before multicellular life.

Origin of Life on Earth

• Earth formed approximately 4.5 to 4.6 billion years ago.
• Early Earth was hot and constantly bombarded by asteroids.
• The planet eventually cooled enough for liquid water to appear.
• Oceans formed about 4.4 to 4.3 billion years ago.
• Geological activity released gases, forming Earth's early atmosphere (nitrogen, carbon dioxide, methane, ammonia, and water vapor).
• Notable absence: Oxygen.
• Conditions were more conducive to the origin of life.

What is Life?

• Scientists define life by these characteristics:
  • Orderly structure.
  • Ability to obtain and use energy.
  • Ability to reproduce.
• Life was present on Earth by at least 3.5 to 3.8 billion years ago, supported by evidence:
  • Stromatolites: Fossilized microbial mats found in rocks, some about 3.5 billion years old.
  • Molecular fossils: Chemicals found in rocks or sediment chemically related to known biological molecules.
  • Hopanes: Molecules fromBacterial hopanoids indicating life around 3.7 billion years ago.
  • Zircon crystals: Hints in some carbon inclusions suggest life might have existed as far back as 4.1 billion years ago.

How Did Life Begin?

• Primordial Soup Concept:
  • Early oceans or ponds had the right mix of chemicals (water, gases, and minerals) and an energy source (lightning or UV) to form organic molecules.
• Hydrothermal Vents:
  • Life may have started in structured environments like hydrothermal vents on the ocean floor, where mineral surfaces (e.g., iron sulfide minerals) could catalyze the formation of organic molecules.
• Essential Molecules:
  • Proteins: Catalytic enzymes and structural elements but require RNA and other proteins to be made.
  • DNA: Stores hereditary information, replicated and passed to the next generation, but cannot do cellular work.
  • RNA: Acts as a messenger, taking information from DNA to synthesize proteins, but requires both DNA as a template and protein as catalysts.

The RNA World Hypothesis

• Hypothesis: Early life might have been primarily RNA-based before DNA and proteins became essential.
• Why RNA?
  • It can store information like DNA.
  • Some RNAs can fold into shapes that catalyze reactions like proteins (ribozymes).
  • Ribozymes can cut and rejoin RNA strands.
  • Ribosomal RNA catalyzes the formation of peptide bonds within the ribosome.
• Earliest life: RNA molecule or set of RNA molecules enclosed in a primitive membrane (liposome).

Evidence Supporting the RNA World Hypothesis

• Most cellular RNA in modern cells is associated with the ribosome, which constructs proteins (rRNA, tRNA, mRNA).
• rRNA still catalyzes peptide bond formation and protein synthesis.
• Similar structures suggest RNA might be the precursor to double-stranded DNA.
• Viruses store genetic information as RNA.
• Energy source of current cells is a ribonucleotide (ATP).
• RNA can regulate gene expression.
• Modern cells have various RNA-based systems.

Early Metabolism and Energy Sources

• Early Earth was hot, and oxygen was absent.
• Earliest metabolism was likely anaerobic and chemolithoautotrophic (used inorganic chemicals and CO2, did not require oxygen).
• Life may have emerged around hydrothermal vent environments with a rich supply of inorganic chemicals and a natural proton gradient.
• Photosynthesis evolved around 2.7 billion years ago with cyanobacteria mastering oxygen-releasing photosynthesis.
• The release of oxygen accumulated and drastically changed Earth's atmosphere (the Great Oxidation Event).
• Aerobic respiration evolved, and an ozone layer formed.
• Oxygen was poisonous to many anaerobic microbes, causing a microbial mass extinction event.

Evolution of Life Forms: The Last Universal Common Ancestor (LUCA)

• LUCA is defined as the most recent organism from which all three domains of life arose.
• This common ancestor existed 3.5 billion years ago.
• Luca possessed a primitive form of transcription, translation, DNA replication
• There is another ancestor where the split archaea and eukarya happened (eukaryotes share a more recent common ancestor with archaea than with bacteria).
• Eukaryotes share more similarities regarding DNA replication, enzymes, and histones.

Theory of Endosymbiosis

• Theory by Lynn Margulis (1960s). Mitochondria and chloroplasts were once free-living bacteria that took up residence inside another cell in a symbiotic relationship.
  • A primitive eukaryotic/archeal host cell engulfed bacteria but did not digest it. This Bacteria that engulfed was good using oxygen and organic components to produce ATP, and thus became the mitochondria.
  • Another engulfed bacterium capable of photosynthesis, likely a cyanobacterium, provided the host cell with food via photosynthesis, this symbiote became the chloroplast.
• Mitochondria:
  • Resemble bacteria in many ways.
  • Have their own circular DNA, bacterial-type ribosomes, and divide by binary fission.
  • Genetic analysis suggests mitochondrial DNA is closely related to alphaproteobacteria.
• Chloroplasts:
  • Have their own circular DNA, bacterial-type ribosomes, and divide independently inside the cell.
  • DNA and traits link them to cyanobacteria.
  • All eukaryotes have mitochondria or had them in the past.
    • The lineage that led to plants and algae shows that the endosymbiotic evennt happen a second time.

Classification Systems

*Phylogenetic Classification:

*Classifies organisms on the basis of their evolutionary descent.

• Classify organisms, especially microbes through phylogeneric classification (evolutionary relationships

• Early was phonetic based on characteristics, modern on evolutionary linage.

• Relise on Cell structure, sequences, to inter evolutionary relationships.

• More differences bigger the evolutionary distance. Relatedness but not time is measured.

*Universal phylogenetic tree

• Based on comparison of small subunit of rRNA of Carl Woese.

• Compare gene that all organism have align them determine divergance.
  *Not time of divergance, so use of fossil history is important to calibrate.

• Phylogenetic Trees:

• Unrooted trees: define phylogetic relationships rather than primitiverelationships

• Rooted Trees Include a root node that represents the common ancestor of all entities in the tree give direction.

• Need a molecular clock or other reference for the to calibrate a tree in time.

• Using an outgroup organisms to know, its most distant

History of Microbiology

• Early ideas about invisible germs and their role in diseases from Lucretius (98-55 BC).
• Microbes were actually observed and studied with the invention of microscopes.
• Galileo Galilei created the first microscopes.
• Francesco Stelluti made early observations of organisms using microscopes; looks at bees and weevils.
• Robert Hooke made detailed drawings of tiny creatures and was first to draw a microorganism. Looked at Fungus with a drawing and descriptions of how to make a microscope. (Book Micrographia)
• Antony van Leeuwenhoek created microscopes that could magnify 50 to 275x.
• He looked at his own semen, seeing spermatozoids, bacteria, and protists in pond water.
• Leeuwenhoek credited with the discovery of the microbial world, and what exists from his work is in letters to the Royal Society of London
• Microbiology languished for about 200 years due to:
  • Few people pursuing it.
  • Leeuwenhoek not sharing his knowledge, and a belief if spontaneous generation
• Spontaneous generation: The belief that life can originate from non-living matter.
• Francesco Redi:
  • Covered meat with gauze and showed that maggots only appeared where flies could lay their eggs.
  • Disproved the theory of spontaneous generation for larger animals (flies), but people still believed in microbes.
• Lazaro Spallanzani:
  Proved hay didn't make microorganisms in a sealed environment
  *Used gravy (broth) boiled gravy, sealed left open showing the differences.

Louis Pasteur and the End of Spontaneous Generation

• Settled the matter of spontaneous generation with the swan neck flask experiments.
• Boiled solutions in flasks with long, curved necks exposed to air.
• Broth remained sterile unless the neck was broken, allowing cells to contact the solution.
• Other scientists, like John Tyndall, demonstrated that dust carries microorganisms.
• Provided evidence for exceptionally heat-resistant forms of bacteria.
• Ferdinand Cohn discovered these heat-resistant bacteria could produce endospores.
• Early microbiologists disproved spontaneous generation theories, developing liquid media and methods for sterilizing.

Microorganisms and Diseases

*Historically, the role in microorganisms and diseases wasn’t immediately obvious.

• Establishing the connection between microorganisms and diseases depended on the development of the techniques for studying their biology
  Infectious diseases were believed to be due to supernatural forces or imbalances of the four bodily fluid humors. Examples choler spreading cloud of bad air.
• Early evidence of the relationship between diseases and microorganisms:
  *Had relation that augustino base saw disease of cell forms was caused by a fungus
• 1800s: Augustino Bassi showed a disease of silkworms was caused by a fungus.
  *Demonstrated the potato blight of Ireland was caused by a protozoa
• M.J. Berkeley demonstrated that the potato blight of Ireland was caused by a protozoa.
  *Demonstrates microorganism can carry out fermentation.
• Louis pasteur demonstrated that microorganisms can carry out fermentation a started helping wineries in France to develop Pasteurization. A technique uses is today.
  *The father of modern medicine
  *Antiseptic surgery system prevents microorganisms from entering wounds, patients showed fewer post operative infections
• First indirect evidence that microorganisms were the causal agents of diseases came from Joseph Lister. Sterelization of materials was an important step.
• Later, the final relationships proven for the relationship between microorganisms and diseases came from the Robert Cock.
  *Demonstrate series of experiments related to bacillus is and traces and anthrax in a lot of organisms.
• Established the relationship between Bacillus anthracis and anthrax and demonstrated that Mycobacterium tuberculosis is the causative agent of TB.
  *Developed coxs postules the series of series of experiments that demonstrated with relationship between diseases and microorganisms.

Koch's Postulates

• Microorganism must be present in every case of the disease but absent from healthy organisms.
  *Had to develop the technique to seeing microbacterial tuberculosis staining tissue, then he would stain. Suspicious would be isolates grown.

*Must be isolated and grown in pure culture.
Could grow, tubercular bacterial blood serum. (developed pure culture) Use pure bacteria, will inoculate. Then into must result when you are inoculated. and then the same microorganism must resolve from the inoculated organism!

• Same disease must result when isolated microorganism is inoculated into a healthy host.

*Limitations

• Some organisms cannot be grown in pure culture.
• Lack an animal model or unethical to infect infect human
• Ways to overcome limits using molecular genetic evidence to replace its elements.

Vaccine Development

• Louis Pasteur and Roux: Incubating cultures of bacteria and for a long while between transfers calls the pathogen to lose the same outcome
  *The way they discover this discovered by having. forgot bacterial cultures, the start using is to old ones for infection and then not going well and the use to develop it for vaccine for chicken , cholera, anthrax and rabies.

• First time a post shot given was, in 1885 Joseph Maester Rabies shot,

• Emil von Bering and Kitasato Shibasaburo discovered antitoxins (specific antibodies and serums that could neutralize toxins).
  They discovered the antibodies ,used is it, they injected the inactive the and then they produce the body would attack the, the real sickness. So if you want to make the baby would attack disease it and what they got

• Élie Metchnikoff discovered phagocytosis (white blood cells engulfing bacteria and particles).

Environmental Microbiology and Microbial Ecology

• Sergei Winogradsky:
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• Sergei Winogradsky: Studied soil microorganisms and discovered metabolic important processes For example discovery of nitrogen fixation.
• isolating bacteria also discovered some bacteria could oxidize inorganic compounds to gain energy and cycle elements in the environment.

Pioneers of Microbiology

• Marinus Beijerinck (Dutch microbiologist), contemporary with Winogradsky.
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• Pioneer the use of enrichment cultures and selective media.

• Pioneering environmental Microbiologist discovered that the soil with soil or the organic. What the organic and very with

Second age of Microbiology : The molecular, and the Genomic methods

• Molecular biology made the discovery of dna:
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*Developed sub disciplins from those that were studied such as *virology, molcecular

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The Microscopic World

• Began with simple observation on the microscopes, and now its vast, critical to medicine, ecology, genetics, and biotechnology.
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