Evolution of Microorganisms and Microbiology

Microorganisms and Microbiology Evolution

Learning Objectives

• Learning objectives are guideposts provided at the beginning of each chapter to help guide study for exams and quizzes.

Microorganisms Overview

• Microorganisms are too small to be seen clearly by the unaided eye.
• Typically, they are one millimeter or less in diameter.
• Some, like bread molds and algae, are visible without microscopes.
• Some macroscopic microorganisms are multicellular but lack highly differentiated tissues, unlike plants and animals.

Organisms Studied in Microbiology

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

Diversity and Abundance of Microorganisms

• There are more microbes on Earth than stars in the known universe.
• Microbes inhabit almost every environment on the planet.
  • Hydrothermal vents on the ocean floor
  • Superheated water with chemicals and radioactive waste
  • Deep underground
  • Boiling hot springs (e.g., Yellowstone)
  • The human body
  • High in the atmosphere
• Microbes can colonize environments that are lethal to more complex life forms.

Examples of Microbial Habitats

• 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 have an estimated 10^{29} cells of microbes.
• A teaspoon of soil contains billions of microbes.
• Trillions of microbial cells live within humans, particularly in the gut.

Classification of Microbes

• Early classifications were based on morphological characteristics, similar to plants and animals.
• Microbes were 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.
• Until the 1980s, the five-kingdom classification system by Robert Harden Whitaker was widely used.
  • Monera: All prokaryotic cells
  • Protista: Eukaryotic, unicellular, and multicellular organisms
  • Fungi

Carl Woese and the Three-Domain System

• In the 1970s, Carl Woese introduced a classification method based on gene sequences, specifically ribosomal RNA (rRNA).
• He focused on the small subunit rRNA (SSU rRNA), a component of ribosomes present in all cellular life.
• By comparing rRNA sequences, evolutionary relationships can be inferred.
• Analysis revealed that prokaryotes consist of two very different groups.
• This led to the three-domain system: Bacteria, Archaea, and Eukarya.

Domains

• Bacteria:
  • Single-celled microorganisms.
  • Most have cell walls with peptidoglycan.
  • Lack a membrane-bound nucleus.
  • Live in various environments, including extreme ones and the human body.
  • Can be disease-causing or non-disease-causing.
• Archaea:
  • Distinguished from bacteria by unique RNA sequences and membrane lipids.
  • Possess unusual metabolic characteristics.
  • Many live in extreme environments.
  • No known archaea directly cause diseases in humans.
• Eukarya:
  • Includes protists and fungi in microbiology.
    • Unicellular (Protists) and multicellular(Fungi) organism
    • Protists
      • Unicellular, generally larger than bacteria and archaea.
      • Include protozoans (motile via cilia, flagella, or amoeboid motion).
      • Include algae (photosynthetic).
    • Fungi
      • Can be unicellular (yeasts) or multicellular (molds and mushrooms).
      • Have cell walls made of chitin, not peptidoglycan.
      • Key decomposers in ecosystems.
      • Some cause infections (e.g., Candida), while others are beneficial (e.g., penicillin from a mold).
• Plants and animals are also in the domain Eukarya.

Acellular Agents

• Acellular agents are not considered living because they require a host to survive.
• Studied in microbiology:
  • Viruses:
    • Extremely small (smallest are 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:
    • Require co-infection with a helper virus.
    • Cause animal and plant diseases (e.g., hepatitis D).
  • Prions:
    • Cause neurological diseases (e.g., mad cow disease).

Microbial World

• Microbes form the unseen majority of life.
• Carl Woese's tree of life shows that multicellular, non-microbial life is only at the tip of the evolutionary tree.
• The diversity of microbes includes various shapes (rods, spheres, spirals), microscopic fungi (yeast and molds), algae, protozoan, and acellular forms (viruses).
• Microbes drive essential processes in ecosystems and have countless interactions with humans, both beneficial and harmful.

Origin of Life on Earth

• Earth formed approximately 4.5 to 4.6 billion years ago.
• Early Earth was hot and bombarded by asteroids.
• Oceans formed about 4.4 to 4.3 billion years ago.
• The early atmosphere consisted of nitrogen, carbon dioxide, methane, ammonia, and water vapor.
• Notable absence: oxygen.
• Life was present on Earth at least 3.5 to 3.8 billion years ago.
• Life requires orderly structure, the ability to obtain and use energy, and the ability to reproduce.

Evidence of Early Life

• Stromatolites: Fossilized microbial mats found in rocks about 3.5 billion years old.
• Molecular fossils: Chemicals found in rocks or sediment that are chemically related to known biological molecules.
  • Hopanes (from bacterial hopanoids) indicate life around 3.7 billion years ago.
  • Zircon crystals hint life may have existed as far back as 4.1 billion years ago.

Theories on the Origin of Life

• Primordial soup concept: Early oceans had the right mix of chemicals, water, gases, and minerals, and an energy source (e.g., lightning or UV) to form organic molecules.
• Life may have started in structured environments like hydrothermal vents on the ocean floor, where mineral surfaces such as iron sulfide minerals could catalyze the formation of organic molecules.

Essential Molecules for Cell Function

• Proteins, DNA, and RNA are crucial for cells to function.
  • Proteins: Catalytic enzymes and structural components.
  • DNA: Stores hereditary information and is replicated.
  • RNA: Acts as a messenger, taking information from DNA to synthesize proteins.

The RNA World Hypothesis

• Early life may have been primarily RNA-based before DNA and proteins became essential.
• RNA can store information (like DNA) and catalyze reactions (like proteins).
• Ribozymes are RNA molecules that can act as enzymes.
• Ribosomal RNA within ribosomes catalyzes the formation of peptide bonds.
• The earliest life may have been RNA molecules enclosed in a primitive membrane (liposome).
• This entity could store genetic information in its RNA and catalyze chemical reactions to support replication and metabolism.

Evidences for RNA world hypothesis

• Most cellular RNA form mordant cells exists and it's in and is associated with a ribosome to construct proteins. Current cells use RNA (ribonucleotides) to produces all proteins
• Ribosomal RNA still catalyzes the peptide bond formation and protein synthesis, which can hint us to an old function of RNA.
• We still see similar structures that indicate that RNA might be the precursor to the double standard r DNA
• There are certain viruses that still store their genetic information as RNA.
• The energy source of current cells is a ribonucleotide just like RNA and it's ATP.
  *RNA can regulate gene expression

Earliest Metabolism

• Early metabolism was likely anaerobic and chemolithoautotrophic.
• Used inorganic chemicals and CO2; did not require oxygen.
• Life may have emerged around hydrothermal vent environments with inorganic chemicals and a natural proton gradient.
• Photosynthesis evolved around 2.7 billion years ago.
• Cyanobacteria mastered oxygen-releasing photosynthesis.
• The accumulation of oxygen drastically changed Earth's atmosphere (the Great Oxidation Event).
• Aerobic respiration evolved.
• The ozone layer formed, protecting Earth from UV radiation.

From Early Evolution to Three Domains

• The Last Universal Common Ancestor (LUCA) is the most recent organism from which all three types of life arose.
• LUCA was a single-celled organism with primitive DNA replication, transcription, and translation.
• It likely lived around 3.5 billion years ago.
• From LUCA, life split into two major lineages: one leading to bacteria and the other to an ancestor that later split into archaea and eukarya.

Endosymbiotic Theory

• Mitochondria and chloroplasts were once free-living bacteria that took up residence inside another cell in a symbiotic relationship.
• A primitive eukaryotic ancestor engulfed bacteria but did not digest it.
• One such bacterium was good at using oxygen and organic compounds to produce ATP, thus becoming the mitochondria.
• Mitochondria have their own circular DNA, bacterial-type ribosomes, and divide by binary fission inside cells.
• Genetic analysis shows that mitochondrial DNA is most closely related to alphaproteobacteria.
• Another engulfed bacterium was capable of photosynthesis, likely a cyanobacterium, and became the chloroplast.
• Chloroplasts also have their own circular DNA, bacterial-type ribosomes, and divide independently inside the cell.
• Chloroplast DNA and traits link them to cyanobacteria.
• Mitochondria evolved first because all eukaryotes have mitochondria or had them in the past.
• The lineage leading to plants and algae experienced a second endosymbiotic event.

Evolution and Genetic Material

• Evolution occurred through mutation of genetic material, leading to selective traits.
• New genes and genotypes evolved, producing a mosaic of genetic information.
• Bacteria and archaea increased the gene pool by horizontal gene transfer.
• Eukaryotes increased diversity through sexual reproduction.

Microbial Phylogeny and Classification Systems

• Classification systems rely on evolutionary principles.
• Phylogenetic classification systems compare organisms based on evolutionary relationships.
• Microbial phylogeny compares cell structure, biomolecules, and nucleotide sequences to infer evolutionary relationships.
• Phylogenetic trees display evolutionary relationships between organisms.

Phylogenetic Classification

• Early classification was phonetic, based on observable characteristics.
• Modern classification is phylogenetic, based on evolutionary lineage.
• The universal phylogenetic tree is based on comparisons of small subunit rRNA.
• Sequences from diverse organisms are aligned, and differences are compared to determine relatedness.
• Relatedness, but not the time of divergence, is determined this way.
• A molecular clock or fossil history is needed to determine the time of divergence.

Types of Phylogenetic Trees

• Unrooted trees: Define phylogenetic relationships rather than a primitive relationship.
  • Do not indicate the age of an organism or which node is the common ancestor.
• Rooted trees: Include a root node representing the common ancestor of all entities in the tree.
  • Give the tree a direction from the past to the present.
  • Allow statements about which lineages diverged earlier or later.
  • Often use an outgroup: an organism known to be more distantly related than any in-group organism.
  • For the universal tree of life, rooting was tricky because there is nothing outside of life with which to compare.
  • Carl Woese used duplicate genes to root the universal tree.
  • Molecular clock is required to define the time of divergence.

History of Microbiology

Early Ideas

• Lucretius (98-55 BC) suspected the existence of invisible germs and their role in diseases.
• These ideas remained conjecture until microbes could be seen and studied.

Invention of Microscopes

• Galileo Galilei made the first microscopes.
• Francesco Stelluti made early observations of organisms using microscopes.
• Robert Hooke made detailed drawings of tiny creatures and the first drawing of a microorganism (a fungus called Muker) in his book Micrographia. He also detailed how to build a microscope.
• Antony van Leeuwenhoek created microscopes that could magnify approximately 50-275x and observed bacteria and protists. Credited with the discovery of the microbial world.
• Microbiology languished for about 200 years due to the slow advancement and lack of knowledge share from Anthony Von Levenwort

Spontaneous Generation

• The belief that life can originate from non-living matter.
• Francesco Redi showed that maggots only appeared on meat where flies could lay eggs.
• Lazzaro Spallanzani proved that hay itself didn't make microorganisms in sealed environments.
• Louis Pasteur settled the matter with swan-neck flask experiments: boiled solutions in flasks with long, curved necks that allowed air contact but prevented cells from entering.
• John Tyndall demonstrated that dust carries microorganisms and proved that exceptionally resistant heat form of bacteria exists

Discovery of Sterilization

• The early microbiologists disproved spontaneous generation theories, contributing to the rebirth of microbiology.
• Developed liquid media and methods for sterilizing to culture microbes.

Microorganisms and Diseases

• Historically, infectious diseases were believed to be due to supernatural forces or imbalances of bodily humors.
• Establishing the connection between microorganisms and diseases depended on developing techniques for studying microbes.
• Agostino Bassi showed a disease of silkworms was caused by a fungus.
• M.J. Berkeley demonstrated that the potato blight of Ireland was caused by a protozoan.
• Louis Pasteur demonstrated that microorganisms can carry out fermentation and developed pasteurization to avoid wine spoilage.
• Joseph Lister developed an antiseptic surgery system to prevent microorganisms from entering wounds.
• Robert Koch established the relationship between Bacillus anthracis and anthrax and demonstrated that Mycobacterium tuberculosis is the causative agent of TB.

Koch's Postulates

1. The microorganism must be present in every case of the disease but absent from healthy organisms.
2. The suspected microorganism must be isolated and grown in pure culture.
3. The same disease must result when the isolated microorganism is inoculated into a healthy host.
4. The same microorganism must be isolated again from the diseased host.

Limitations of Koch's Postulates

• Some organisms cannot be grown in pure culture.
• We lack an animal model.
• It is unethical to infect humans.
• Molecular and genetic evidence can be used to replace these limits.

Discovery of Vaccines

• Louis Pasteur and Roux discovered that incubating cultures of bacteria for long intervals between transfer caused these pathogens to lose their ability to cause the disease.
• Used attenuated cultures to develop vaccines for chicken cholera, anthrax, and rabies.
• The rabies vaccine was given to Joseph Meister in 1885 as a post-exposure treatment, saving his life.
• Emil von Behring and Shibasaburo Kitasato discovered antitoxins (specific antibodies in serums that could neutralize toxins).
• They injected inactivated diphtheria toxins into animals and produced an antiserum that could protect against the bacteria.
• Used this antiserum to treat diphtheria in humans.

Microorganisms in the Environment

*Sergei Winogradsky studied soil microorganisms and discovered metabolic important processes such as nitrogen fixation:
* Isolated nitrifying bacteria and sulfur bacteria.
* Showed that some bacteria could oxidize inorganic compounds to gain energy and at the same time cycling elements in the environment.
* Discovered Nitrosomonas and Nitrobacter, which are nitrifying bacteria
*He created Vinogradsky columns, which are a model ecosystem, to culture diverse microbes with different metabolic strategies and layers to discover the cycling of these nutrients that happen in the environment and the importance of them.

• Martinus Beijerinck pioneered the use of enrichment cultures and selective media.
  • Isolated nitrogen-fixing bacteria in root nodules.
  • Isolated sulfate-reducing bacteria.
  • Coined the term virus for the tobacco mosaic pathogen.
  • Enrichment culture technique: creating growth conditions that favors a microbe you want to isolate
  • Created specific substrates for very specific bacteria.
• These are known as the fathers of environmental microbiology and microbial ecology.

Second Age of Microbiology

• Molecular genomic methods led to the expansion of knowledge in a variety of microbiology fields.
• 1952 - discovery of the molecular structure of DNA by Watson and Crick. The image was created by Rosalind Franklin. Revealed the helical shape of the DNA molecule.
  Watson and Kirk realized that DNA was made of these two chains of nucleotide pairs contain all the genetic information for all living things.
• Molecular genetics, biochemistry, virology, and immunology advanced.
• Antibiotic discovery: Penicillin was mass-produced.
• Microbiology has been growing since, encompassing many sub-disciplines.
• Began with simple observation on the microscopes, and now it's a vast field that's critical to medicine, ecology, genetics, and biotechnology.