Microbial Symbiosis, Ant-Fungus Mutualism, and Microbial Defense Mechanisms

Klebsiella aerogenes

A member of the family Enterobacteriaceae, living in the intestines of warm and cold-blooded animals and passed through feces into soil and water.

Bacillus subtilis

A ubiquitous bacterium in the environment, especially soil, known for producing highly resistant endospores and secondary metabolites, including antibiotics.

Clostridium tetani

The causative agent of tetanus, which enters the body through puncture wounds and releases the tetanospasmin toxin, leading to muscle contractions.

Escherichia coli

The most common inhabitant of the human intestinal tract, aids in food digestion, and indicates fecal contamination when present in food or water.

Streptococcus pneumoniae

A normal part of the mammalian respiratory tract, known for causing pneumonia, bacteremia, and meningitis.

Gram Stain

A method of staining bacterial cells to differentiate them based on the structural differences in their cell walls, in particular it would be peptidoglycan.

Gram negative

Bacteria that stain pink in the Gram staining process, indicating a thinner peptidoglycan layer.

Gram positive 2

Bacteria that stain purple/blue in the Gram staining process, indicating a thicker peptidoglycan layer.

Spore Former (Endospores)

Bacteria that can produce spores, which are highly resistant forms that can survive extreme conditions.

Non-spore forming

Bacteria that do not produce spores and are generally more sensitive to environmental stresses.

Peritrichous flagella

Flagella that are distributed all around the bacterial cell, allowing for motility.

Non-motile

Bacteria that do not have flagella and cannot move independently.

Pathogenicity

The ability of a microorganism to cause disease.

Facultative anaerobe

An organism that can grow in both the presence and absence of oxygen.

Obligate anaerobe

An organism that cannot survive in the presence of oxygen.

Streptoccocus pneumoniae

Partial hemolysis of red blood cells on blood agar, often associated with certain bacteria.

Biofilm

A complex aggregation of microorganisms marked by the secretion of a protective and adhesive matrix.

Tetanus toxoid

A vaccine that protects against the tetanospasmin toxin produced by Clostridium tetani.

Shiga-like toxin

A toxin produced by E. coli O157:H7 that destroys intestinal cells and can cause severe hemorrhagic diarrhea.

E. Coli component

A condition characterized by hemolytic anemia, acute renal failure, and low platelet count, often following infection with E. coli O157:H7.

Capsule

A protective layer surrounding some bacteria that enhances their ability to cause disease.

Secondary metabolites

Compounds produced by bacteria that are not directly involved in normal growth, development, or reproduction, often including antibiotics.

Prokaryotic Cells

Generally less complex morphologically, do not typically have other compartmentalizations or organelles, often described as having an 'open floor plan', usually single-celled, generally smaller than Eukaryotes, examples include Bacteria and Archaea.

Eukaryotic Cells

Have a membrane-enclosed nucleus, are more complex morphologically than prokaryotic cells, possess a higher level of compartmentalization with specific functions carried out in specific organelles, often described as having a 'closed floor plan', generally larger than Bacteria and Archaea, examples include plants, animals, protists, and fungi.

Definition of Life

Life is defined by a set of characteristics:

• Metabolism (undergoing biochemical reactions to sustain life)

• Growth (increasing in biological mass)

• Reproduction (procreating oneself)

• Genetic variation/evolution (experiencing changes in the genome through natural selection over multiple generations)

• Response/adaptation to the external environment (reacting to and adapting to external stimuli)

• Homeostasis (maintaining internal organization and order, usually by expending energy)

Viruses do not meet these criteria unless they are within a host cell, and therefore are not considered alive.

Two-Group System

Developed by Aristotle around 300 B.C., classified organisms simply as Animal (if they moved) or Plant (if they had a cell wall). This system became insufficient with the advent of microscopy and the discovery of new organisms.

Five-Kingdom System

Developed by Robert Whittaker and used from the 1950s to the 2000s, classified organisms into Monera, Protista, Fungi, Animalia, and Plantae, still based primarily on phenotype (looks, microscopically). Microorganisms primarily fell into Monera and Protista. Advances in molecular techniques revealed mismatches, particularly between Bacteria and Archaea, leading to its eventual replacement.

Three-Domain System

Developed due to advances in molecular techniques, specifically by Carl Woese et al. in a 1990 paper (work started in the 1970s), based on a comparison of ribosomal RNA (rRNA), specifically the gene encoding the 16-s-rRNA, divides microorganisms (and all life) into three categories: Bacteria (true bacteria), Archaea, and Eukarya (eukaryotes). This system is currently used and is based on evolutionary relationships at the gene level.

Domain Bacteria

Usually single-celled organisms, majority have cell walls with peptidoglycan (a distinguishing feature, as Archaea lack it), most lack a membrane-bound nucleus (prokaryotic), are ubiquitous (found everywhere), and some live in extreme environments. Some cause disease, but most are beneficial.

Domain Archaea

Distinguished from Bacteria by unique rRNA sequences, lack peptidoglycan in cell walls and have unique membrane lipids, some have unusual metabolic characteristics, such as methanogens producing methane, many live in extreme environments (e.g., high temperatures, acidic or alkaline pH), their role in causing diseases is unclear and not heavily studied.

Domain Eukarya - Eukaryotes

Generally larger than Bacteria and Archaea, includes Plants, Animals, and microorganisms classified as protists (algae, protozoa, slime molds, water molds) or fungi (e.g., yeasts - unicellular, molds - multicellular). Protists and fungi are microscopic eukaryotes, fungi are primarily decomposers, and some cause disease.

Viruses

Acellular infectious agents, not considered part of any domain system because they are not cells themselves and are less complex, very simple, often consisting of only proteins and nucleic acids, require a host cell to replicate and are metabolically inert until they infect a host.

Metabolism

Undergoing biochemical reactions to sustain life.

Growth

Increasing in biological mass.

Reproduction

Procreating oneself.

Genetic variation/evolution

Experiencing changes in the genome through natural selection over multiple generations.

Response/adaptation to the external environment

Reacting to and adapting to external stimuli.

Homeostasis

Maintaining internal organization and order, usually by expending energy.

Peptidoglycan

A distinguishing feature of Bacteria, present in their cell walls.

Methanogens

A type of Archaea that produces methane as a metabolic byproduct.

Cell Wall

A structural layer surrounding some types of cells, providing protection and support.

Ribosomal RNA (rRNA)

A type of RNA that is a component of the ribosome, used in the comparison for classification in the Three-Domain System.

16-s-rRNA

The gene encoding ribosomal RNA used in the Three-Domain System for classification.

Acellular

Referring to entities that are not composed of cells.

Ubiquitous

Found everywhere.

Microscopic Eukaryotes

Eukaryotes that are small enough to be observed only with a microscope.

Diseases caused by viruses

Viruses cause a range of diseases in animals, plants, and humans, and some are associated with cancers.

Infection across domains

Viruses have the ability to infect across all three domains.

Stanley Miller

In the 1950s, conducted an experiment known as the Miller-Urey Experiment at the University of Chicago.

Miller-Urey Experiment

The experiment aimed to determine if the conditions on primordial Earth could allow for the creation of macromolecules.

Organic molecules formation

Over the course of a week, Miller successfully formed organic molecules from a primordial soup.

• He created several conditions of primordial earth with a bunsen burner creating night and day, and then with the electric box he created the storms, lastly he created the oceans.

• This simulation, with several adjustments led to the creation of the essentials for life, the four macromolecules:

  • polypeptides

  • nucleic acids

  • lipids

  • polysaccarides

Initial results of the Miller - Urey experiment

The initial results yielded pyridines and purines, which are components of nucleic acids.

Creation of amino acids

With subsequent adjustments, the experiment was able to create all 20 amino acids, as well as the pyridines, purines, and other necessary building blocks for the four major macromolecules required for life.

Initial synthesis of macromolecules via Stanley Miler

This work demonstrated how the initial synthesis of the first forms of macromolecules could have occurred in Earth's early, oxygen-poor, chemical-rich environment.

Ribozymes

RNA molecules that were discovered by Thomas Cech in 1981.

Evolutionary significance of ribozymes

Their evolutionary significance lies in their dual ability: they can form peptide bonds and catalyze reactions, and they can also replicate themselves and store genetic information.

Original molecule of early life (Ribozymes)

This supports the idea that the original molecule of early life might have been a single molecule capable of both cellular work and replication.

RNA's dual purpose

The hypothesis suggests that RNA could serve the dual purpose of genetic information storage AND catalyzing reactions.

Transition from RNA to DNA

Primitive cells eventually transitioned from using RNA to DNA for storing genetic information, indicating ribozymes' role as a precursor to the current system.

Endosymbiotic Theory

A hypothesis that explains how eukaryotes appeared

• details that primitive prokaryotic microbes ingested one another and other microbes

• ingested microbes lost ability to live independently and thrived in host prokaryote, crucial for compartmentalization & evolution of eukaryotic cells

Symbiotic relationship in eukaryotes

It proposes that primitive prokaryotic microbes ingested other microbes, leading to the establishment of a symbiotic relationship.

Symbiotics of eukaryotic cells

This relationship resulted in the ingested microbe losing its ability to live independently and thriving within the host prokaryote, contributing to the compartmentalization and evolution of eukaryotic cells.

Mitochondria evolution

Mitochondria evolved from ingested microbes that could use oxygen for a respiratory process to produce chemical energy.

Chloroplasts evolution

Chloroplasts evolved from ingested microbes that could fix carbon dioxide into organic molecules using light energy.

Evidence supporting Endosymbiotic Theory

Evidence supporting this theory includes that both mitochondria and chloroplasts possess their own circular DNA, contain ribosomes similar to prokaryotes, and have membranes similar to prokaryotes.

Binomial nomenclature

The system for naming microorganisms, which was developed by Carolus Linnaeus in 1750.

Scientific name structure

Each organism's scientific name consists of two parts: the genus and the species epithet.

Binomial nomenclature

The genus name begins with a capital letter, while the species epithet is not capitalized.

Formatting scientific names

The entire scientific name (genus and species epithet) must be italicized or underlined.

Abbreviation of genus name

After the first full use, the genus name can be abbreviated (e.g., Escherichia coli becomes E.).

Robert Hooke

Renowned for his observations in the 17th century, he examined a thin slice of cork and observed 'little boxes,' which he termed cells.

Cell Theory

States that all living things are composed of cells.

Antony van Leeuwenhoek

Considered the 'Father of the field of microscopy,' he was the first person to observe and describe microorganisms accurately using a microscope.

• refined Hooke’s work

• referred to microorg as “animacules”

Hand-help microscope has few components

• focus knob

• singular lens

• specimen holder

Animalcules

The term Leeuwenhoek used to refer to the microbes he observed, which included a notable description of 'animalcules a-moving very prettily' from his own excrement.

Microscope Magnification

Leeuwenhoek's microscopes were capable of magnifying objects 50-300 times.

Giardia lamblia

A parasitic infection believed to be observed by Leeuwenhoek in his own excrement.

Microbiology Standstill

Despite groundbreaking discoveries by Leeuwenhoek, the field of microbiology experienced a standstill for approximately 200 years due to scientists not knowing how to grow, isolate, or prevent contamination of newly discovered organisms.

Spontaneous Generation

A theory proposing that living organisms could develop from nonliving or decomposing matter.

Francesco Redi

Discredited the theory of spontaneous generation for macroscopic life through an experiment with three containers of meat.

Redi's Experiment

Involved three containers with meat: one left open, one covered with paper, and one covered with gauze, showing that maggots on decaying meat came from fly eggs.

John Needham

Performed an experiment with mutton broth in flasks, which he boiled and then sealed, resulting in cloudy broth containing microorganisms.

• proved spontaneous regen

Needham's Interpretation

Supported spontaneous generation based on his results with mutton broth.

Lazzaro Spallanzani

Conducted a similar experiment to Needham but sealed the flasks before boiling, resulting in no growth of microorganisms.

Experimental Design Difference

The crucial difference between Needham and Spallanzani's experiments was that Needham boiled before sealing, allowing airborne microbes to enter, while Spallanzani sealed before boiling.

Louis Pasteur

Settled the matter of spontaneous generation for microorganisms through his famous experiment with nutrient solution in flasks with long, curved 'swan necks'.

Pasteur's Experiment

Involved boiling solutions in specially designed flasks and leaving them exposed to air, showing no growth of microorganisms.

Biogenesis

The principle established by Pasteur that life comes from life.

Pasteurization

A process developed by Pasteur demonstrating that microorganisms carried out fermentations.

John Tyndall

Further supported Pasteur's work by demonstrating that dust carries microorganisms and that nutrient broths remained sterile in the absence of dust.

Spores

Tyndall provided evidence for the existence of exceptionally heat-resistant forms of bacteria.

Ferdinand Cohn

Identified that heat-resistant bacteria could produce endospores.

Endospores

Structures produced by certain bacteria that allow them to survive extreme conditions.

Joseph Lister

Provided indirect evidence that microorganisms were the causal agents of disease and developed a system of antiseptic surgery using phenol on dressings and heating surgical tools.

Antiseptic Surgery

A surgical practice developed by Joseph Lister that uses antiseptics to reduce postoperative infections.

• heating surgical tools

• applying phenol on dressings

John Snow

Considered the first epidemiologist who mapped affected areas during the 1854 cholera outbreak in London.

Cholera Outbreak

An epidemic in 1854 in the Soho neighborhood of London, identified by John Snow as being centered on the Broad Street well.

Broad Street Well

The location identified by John Snow as the source of the cholera outbreak due to a leaking sewer pipe.

Anecdotal Evidence

A personal story or observation that lacks scientific rigor and does not equal scientific evidence.

Correlative Evidence

Suggests that two variables happen at the same time or move in relation to each other, but one does not necessarily cause the other.

Causative Evidence

Indicates that one variable directly causes a change in another variable in a controlled setting.

• Highest scientific rigor, est. with several studies and replications, w/ potential ocnfounding causes investigated and rules out