Microbiology Fundamentals

Microbiology in Perspective

• Microbiology focuses on living things too small too see without magnification.

Dr. Juan Rivera-Correa

• Possesses a PhD in Immunology and infectious disease from NYU and did a Postdoc from Weill Cornell
• Research focuses on B-cells and antibodies during malaria and other infections using mouse models, veterinary and human patients in NYU, Costa Rica and Colombia.
• Office hours are A-302-E Tuesday 12-2pm
• Contact is [email protected]
• Plasmodium causes malaria and has P. falciparum, P. vivax, P. malariar, R. ovale, P. knowlesi strains
• Plasmodium's life cycle has an asymptomatic liver stage
• Malaria's blood stage is symptomatic (cerebral malaria, severe anemia).

Participation and Groups

• Students will form groups of 3-4
• Participation is mandatory with questions assigned across lectures/labs.
• Groups discuss questions and choose a representative to answer in 2-3 minutes.
• Each group will be assigned a vocabulary word that must be defined by the end of each lecture/lab.

Daily Questions

• The 8 types of microbes should be named
• At least 3 benefits of microbes to the world should be mentioned
• One key scientist in microbiology should be named
• List the 4 macromolecules and their monomers
• The classification for organisms is needed
• The Woese-Fox System classifies microbes by a main parameter

Microorganisms

• The Biology of microorganisms can be found at https://youtu.be/YSitT0oOoyс

Without Microbes

• The question is asked whether life is possible without microbes

Learning Outcomes

• Microorganisms colonize humans in various ways
• Microbes impact the earth in definable ways
• Evolution is called a theory
• Humans manipulate organisms for specific uses
• Microbes can cause human disease
• There is a difference among bacteria, archaea, and eukaryotic microorganisms
• Acellular infectious agents are studied in microbiology.
• Microbes can be compared in respect to their relative sizes

Essential Concepts

• Characteristics of life include; cellular organization, reproduction, metabolism, homeostasis, heredity, response to stimuli, growth and development, and adaptation through evolution.
• 12 Levels of Organization of life include atoms, molecules, organelles, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, and the biosphere
• The basic unit of life is the cell
• Microbes include Bacteria, Archaea, Protozoa, Algae, and Fungi, and some are parasites or helminths

Metric System

• Relative sizes on a logarithmic scale go from atoms to adult humans
• Visible using electron microscopes are proteins, lipids
• Viruses sit on the 1-100nm on the scale
• Bacteria, Plant and Animal cells sit above on the 1-10 micrometer size
• Light Microscopes generally see down to 1um
• The Naked eye generally sees down to 1mm

Mighty Microbes

• Microbiology focuses on living things too small too see without magnification.
• Microoganisms include bacteria, archaea, protozoa, fungi, helminths, algae, viruses, prions
• Prokaryotes do not have a nucleus, but they have nucleoids.
• Eukaryotes use a membrane-bound nucleus.
• Acellular entities are not alive per se.

Types of Microorganisms

• Acellular microorganisms include prions, and viruses
• Cellular microorganisms include bacterium/archaeon, and eukaryote
• Prions, made of protein, are 10nm
• Viruses are around 100nm.
• Bacterium/archaeon are normally 1000nm or 1 micrometer
• Eukaryotes are around 10,000nm or 10 micrometers and include fungi, protozoa, and helminths

Nature of Microorganisms

• Microbes are very easy and very difficult to study
• Microbes reproduce rapidly
• Microbes can be grown quickly in large populations in the laboratory
• Microbes cannot be seen directly
• Microbes are analyzed through indirect means
• Microbes and viewed through microscopes

Concept Check

• Plants are not considered microbes

Microbes and Planets

• Single-celled appeared on this planet about 3.8 billion years
• Cell types arose from a single extinct common ancestor
• Eukaryotes have a true nucleus
• Bacteria are single-celled and have no true nucleus
• Archaea are single-celled with no true nucleus, and are distinct from bacteria
• Prokaryotes are bacteria and archaea that are pre-nucleus
• Akaryotes have no nucleus as an alternate name for prokaryotes

Relatedness of Organisms

• Organisms are have 3 Domains.
• The Domains Bacteria, Archaea and Eukarya have a last common ancestor

Bacteria, Archaea, and Eukaryotes

• Bacteria and archaea are predominantly single-celled
• Eukaryotes are of many cell types, but some are single-celled
• Eukaryotes developed into highly complex multicellular organisms
• Eukaryotes are of larger size
• Eukaryotes make up a small minority compared to bacteria and archaea

Organization of Cells

• There are prokaryotes versus eukaryotes
• Eukaryotes have organelles which are small, double-membrane-bound structures performing specific functions.
• Eukaryote examples include nucleus, mitochondria, and chloroplasts
• Some eukaryotes are microorganisms while some are macroscopic
• Bacteria and Archaea are prokaryotes.
• Prokaryotes are ~10 times smaller than eukaryotes
• Prokaryotes lack organelles
• Prokaryotes are all microorganisms

Fundamental Characteristics of Cells

• Bacteria and protozoa are single cells
• Animals and plants are trillions of cells
• Cells' characteristics include a spherical, polygonal, cuboidal, or cylindrica structure
• Contain a protoplasm encased in a cell membrane
• Cells also have chromosomes containing DNA
• Cells have Ribosomes for protein synthesis
• Cells are exceedingly complex in function

Eukaryotic and Prokaryotic Cells

• Eukaryotic cells include animals, plants, fungi, and protozoa
• Eukaryotic cells have organelles encased by membranes with specific functions
• Bacteria and Archaea are prokaryotic
• Bacteria and Archaea have no nucleus or otherwise defined organelles
• Bacteria and Archaea have a complex structure
• Bacteria and Archaea can engage in same activities as eukaryotic cells

Acellular Entities

• Viruses and prions are acellular
• Viruses are not independently living cellular organisms
• Viruses exist at a level of complexity between large molecules and cells
• Viruses contain DNA/RNA hereditary material or a protein coat
• Prions are simpler than viruses
• Prions have no nucleic acid, only protein, and are infectious

Eight Types of Microorganisms

• The 8 Types of Microorganisms are: Bacteria, Archaea, Protozoa, Fungi, Helminths, Algae, Viruses, and Prions

Smallest to Largest

• Microorganisms smallest to largest include: Prion, Virus, Bacterium, Protozoan, and Helminth

Timeline

• An evolutionary timeline can be created

Microbes are Everywhere

• Microbes are ubiquitous and are found in the earth's crust, and polar ice caps and oceans.
• Microbes live inside the bodies of plants and animals and in the earth's landscape.
• Microbes are essential to life

Evolution and Science

• The theory of evolution is the accumulation of changes to organisms as they adapt to their environments.
• Evolution is documented daily all over the planet
• The theory is testable by science
• Theories in science have been tested for years and have not been disproved.
• Evolution remains a well-studied and well-established natural phenomenon
• Evolution is not just a random guess

Scientific Method

• The steps of scientific method go through hypothesis prediction, experiment, and observation
• A Law is a summary while a Theory is an explanation theories are based on hypotheses, used to make predictions, and can be revised
• Laws summarize observations about natural phenomena

Photosynthesis

• Photosynthesis involves the light-fueled conversion of carbon dioxide to organic material
• Oxygen forms during the chemical reaction
• Anoxygenic photosynthesis occurred in bacteria before plants evolved without producing oxygen but was more efficient in extracting energy from sunlight.
• Oxygenic photosynthesis evolved from anoxygenic photosynthesis
• Photosynthetic microorganisms account for 70% of the earth's photosynthesis

Shaping our Planet

• Microbes' main driving force behind the structure and content of the soil, water, and the atmosphere
• Microbes produce CO2, NO, and CH3 that insulate earth's atmosphere
• Bacteria are the most abundant cellular organisms in the oceans
• Viruses the most abundant in the oceans
• Bacteria and fungi associate with plants in obtaining nutrients, water, and disease protection

In the Earth's Crust

• Microbes are ubiquitous and are found everywhere on the planet, including the deeper layers of the earth's crust

Microbes and Us

• Historical uses of microbes by humans include bread, alcohol, cheese, treatment of wounds, mining metals, and cleaning contamination.

Human Microbiome

• The Human Microbiome Project (HMP) detailed the types of microbes on different people
• Trillions of microorganisms outnumber human cells by 10 to 1
• Overall, sets of metabolic capabilities possessed by human microbiomes are remarkably similar.

Benefits

• Most microbes (>99%) serve for benefits or commensalism.
• About ~1,400 known species of human pathogens
• Human pathogens make up less than 1% of species on earth
• Trillions of microorganisms outnumber human cells by 10 to 1
• Because of size, microorganisms make up only 1 to 3 percent of the body's mass.

Biotechnology

• Biotechnology includes genetics:
• Manipulating genetics creates new products & GMOs
• Recombinant (DNA) technology:
• DNA creates material to transfer between organisms & deliberately alters DNA
• Bioremediation:
• Clean up toxic pollutants by restoring material or adding intentionally

Harmless Microbes

• The majority of microorganisms associated with humans are harmless or beneficial (>99%)
• Pathogens (<1%) cause disease
• In most cases 2,000 microbes contribute to disease
• Ten billion infections occur across the world every year
• Diseases are important common causes of death worldwide

Infectious Killers

• COVID-19 changed all of this in from 2020-2021.
• COVID-19 became the Number One Cause of Death in the U.S. in Early 2021
• The top killer infections in the world include: tuberculosis, COVID-19, HIV/AIDS, and malaria.
• Malaria data comes from 2021.
• Tuberculosis* came back up to the top killer in 2024.

Disease

• Diseases caused by Microbes include:
• AIDS, Hepatitis C, Zika, West Nile, Tuberculosis and Malaria
• Associations between noninfectious diseases and microbes include:
• Gastric ulcers caused by Helicobacter pylori, Multiple Sclerosis, OCD, Coronary artery disease, and obesity linked to chronic infections

Explore challenges in microbiology, microbe identification, and the origins of single-celled life. Key differences between Bacteria/Archaea and Eukaryotes are discussed. Also explore the evolutionary significance of microorganisms.