Chapter 1 - The microbial world

Microbial culture vs. a medium

• Culture: A collection of cells that have been grown in or on a nutrient medium.

• A medium is a liquid or solid nutrient mixture that contains all of the nutrients required for a microorganism to grow.

Specific prokaryotic organelles

• Magnetosome → a compass needle for a prokaryote, senses the magnetic field of the Earth

• Anammoxosome → A type of vacuole found in ammonium-oxidizing bacterium

• Bacterial microcompartment (BMC) → A compartment surrounded by a protein shell where certain reactions take place that often have a toxic intermediate.

Who first observed microbes?

• Antonie van Leeuwenhoek

• Made his own lenses

• First microscope.

Who first observed eukaryotic microbes?

• Robert Hooke

• First to describe cells

• Introduced the term cell

• Developed the already existing microscope

What are microbes

• Single-celled microscopic organisms

• Are essential for the well-being and functioning of other life forms and the planet.

Eukaryotes vs. Prokaryotes

Prokaryotes	Eukaryotes
Do not have a nucleus, the DNA is free in the cytoplasm → concentrated in the nucleoid	Has a nucleus
Protein synthesis all happens at similar times in the cytoplasm.	mRNA must travel through the nucleus membrane (transcription and translation are physically separated)
Exists of bacteria & archaea
One circular chromosome + plasmids (replicate independently)	Multiple chromosomes
No mitochondria, no chloroplasts, no endoplasmic reticulum	Has all of those
Bacteria Have a peptidoglycan cell wall, archaea don’t	No cell wall in animals and a simple cell wall in plants
Ribosomes is 70S → Ribosomes make amino acid chains, peptides	Ribosomes is 80S, except when the ribosomes is in a mitochondria and chloroplast.
Have no membrane-enclosed organelles	Has membrane-enclosed organelles
DNA is circular	DNA is linear

Two types of prokaryotes

• Bacteria

• Archaea → very different from bacteria but similar to eukarya

Genome

• Possessed by all cells

• The full set of genes in a cell.

Chromosomes

A condensed and organized way to store the genes.

DNA storage eukaryotes vs prokaryotes

• Eukaryotes: DNA is present as several linear molecules within the membrane-enclosed nucleus.

• Prokaryotes: Chromosomes aggregate to form the nucleoid, which is not visible in the electron microscope and is not enclosed by a membrane.

  • Most prokaryotes have only a single chromosome, but many also contain one or more small circles of DNA

  • These are known as plasmids.

  • Plasmids contain no essential genes but more additional ones.

Metabolism

• All cells do this

• Process through which nutrients are acquired from the environment and transformed into new cellular materials and waste products

Transcription

The process by which the information encoded in DNA sequences is copied into an RNA molecule

Translation

The process whereby the information in an RNA molecule is used by a ribosome to synthesize a protein.

Horizontal gene transfer

When prokaryotic cells can exchange genes with neighboring cells.

Size prokaryotic cells

Between 0.5 and 10 micrometers

• can vary, smallest can be 0.2 micrometer and largest can be more than 600 micrometers long.

size eukaryotic cells

Between 5 and 100 micrometers.

• Smallest known is 0.8 micrometers and the largest can be multiple centimeters.

What influences cell size

• Cell structure

• Eukaryotes, which are more intracellularly complex, can actively transport molecules and macromolecules within the cytoplasm.

• Prokaryotes, rely on diffusion for transport through the cytoplasm and this limits their size.

  • If prokaryotes are too big, diffusion will take much longer.

Cell size and transport

• Big cells are not fit for diffusion as it will be super slow

• Instead as cell size increases, it becomes advantageous to have cellular structures that facilitate transport and compartmentalize cellular activities.

Cells size and surface area ratio (S/V)

• As cell size increases, its S/V ratio decreases

• The larger the S/V ratio, the better

• Some cells have a larger surface area which will increase their ratio.

Importance of S/V ratio

• The S/V ratio of a cell controls many of its properties

• Including how fast it grows and shape

  • As cell size decreases, the S/V ratio of the cell increases, and this means that small cells can exchange nutrients and wastes more rapidly than can large cells.

  • As a result smaller cells are more efficient

Properties of all cells

• Structure

  • All cells have a cytoplasmic membrane, cytoplasm, a genome made of DNA and ribosomes.

• Metabolism

  • Cata and anabolism occurs in all cells.

• Growth

  • DNA is converted into proteins which can be used to grow.

• Evolution

  • Chance mutations in DNA cause new cells to have new properties, thereby promoting evolution.

Properties of some cells

• Differentiation

  • Some cells can form new cell structures such as a spore

• Communication

  • Cells interact with each other by chemical messengers

• Motility

  • Some cells are capable of self-propulsion

• Horizontal gene transfer

  • Cells can exchange genes by several mechanisms.

Name of a cell that is spherical or ovoid in morphology

Coccus (plural, cocci)

Cylindrically shaped cell

Known as a rod or a bacillus (plural, bacilli)

A spiral shaped cell

Is known as a spirillum

Cell that is slightly curved and comma-shaped

Vibrio

Spirochetes

• Looks like a spirilla due to its spiral shape.

• Is different from spirilla because its much more flexible than a spirilla.

Multiple cocci together

• In pairs: diplococci

• Long chains: streptococci

• In three-dimensional cubes: tetrads or sarcinae

• Grapelike clusters: Staphylococci

The three domains

• Bacteria

• Archaea

• Eukarya

Properties of bacteria

• Undifferentiated

• Single celled (mostly, some are multicellular)

• Between 0.5 and 10 micrometers

Properties of archaea

• Live in extreme environments, but can also be found outside of them

• Lacks any known disease-causing species.

Eukarya

• Relatively young compared to prokaryotes and archaea

• The major lineages of eukarya are traditionally called kingdoms instead of phyla.

Characteristics of viruses

• Smaller than bacteria

• Non-living because they need a host to multiply

• Lack cytoplasmic membrane, cytoplasm, and ribosomes.

• Carry out no metabolic processes, instead they take over the metabolic systems of infected cells and turn them into vessel for producing more viruses.

• Instead of having a genome composed of double stranded DNA, viruses have genomes composed of DNA or RNA that can be either double or single stranded.

  • The genome is usually very small

Evolution of microbial groups

• Initially no oxygen was present so the first microbes were anaerobic. (Between 2.8 and 4.3 billion years ago)

• After a billion years, anoxygenic phototrophic microbes, which harvest energy from sunlight appeared. (These do not produce oxygen)

• Afterwards Cyanobacteria appeared, which are differentiated versions of the anoxygenic phototrophs, these did oxygenic photosynthesis, producing oxygen.

• Then we got modern eukaryotes

Influence of microbes on the earth as it is now

• Microbes, especially bacteria/archaea are the oldest form of life on earth (3,8 billion years)

• They have created the environmental conditions as they are now.

LUCA

• The last universal common ancestor

• All cellular organisms share certain characteristics, therefore certain genes are found in all cells

• 60 genes are universally present in cells of all three domains.

Microbial abundance and activity in the biosphere

• There are an estimated 2×10³⁰ microbial cells on earth.

• The total amount of carbon present in all microbial cells is a significant fraction of Earth’s biomass.

• Additionally, the total amount of nitrogen and phosphorus within microbial cells is almost four times that in all plant and animal cells combined.

• Microbes also represent a major fraction of the total DNA, about 31%

Extremophiles

Microbes that are abundant in habitats that are much too harsh for other forms of life.

Oxygen, microbes and water

• Excess nutrients added to a habitat can cause aerobic microorganisms to grow rapidly and consume O2, rendering the habitat anoxic.

• For example due to human activities excess nutrients can enter the ocean, stimulating excessive microbial growth, causing the anoxic zones.

• The anoxic zones can cause massive mortality of fish and shellfish in coastal oceans worldwide.

Effect of microbes on disease

• At the beginning of the twentieth century, more than half of all humans died from infectious diseases caused by bacterial and viral pathogens.

• Today, infectious diseases are largely preventable due to advances in our understanding of microbiology

• Advances in:

  • Medicine: vaccination and antibiotic therapy

  • Engineering: water and wastewater treatment

  • Food safety: pasteurization

  • Better understanding of how microbes are transmitted.

Microbes, agriculture, and human nutrition

• Microbes can help in cycling of nitrogen, sulfur and carbon compounds

• E.g. legumes live in close association with bacteria that form structures called nodules on their roots.

• In the nodules these bacteria convert atmospheric nitrogen into ammonia through nitrogen fixation.

• Works as a natural fertilizer

• Rumen also have microbes in their colon to ferment cellulose.

Microbes and food

• Can cause spoilage

• Therefore microbial food safety is important.

• Microbes can also be beneficial with regards to food, to improve food safety and to preserve foods

• Some foods are made by fermentation and can improve shelf life

• Can be used for brewing too

Magnification and resolution

• Magnification; Describes the capacity of a microscope to enlarge an image

• Resolution: The ability to distinguish two adjacent objects as distinct and separate

Differential stains: the gram stain

• A method to divide bacteria into two groups

• Gram positive: appear purple violet

• Gram negative: appear pink

Louis Pasteur experiment

• Did an experiment to debunk spontaneous generation

• Heated liquid in a swan neck flask to make it sterile

• Due to the bended opening, no microbes were able to get in.

• Liquid did not get contaminated.

Beggiatoa

• Large sulfur oxidizing bacteria found in marine sediments

  • Cannot grow on richt nutrient media used by other microbiologists.

Winogradsky

• Designed a medium that chemically imitated the environment in which Beggiatoa lived.

• Showed that Beggiatoa are able to grow in the absence of organic nutrients and that their growth requires on only inorganic substances

• In this way, Winogradsky was the first to define chemolithotrophy, which is any metabolic process in which energy for growth is produced using only inorganic chemical compounds.

Chemolithotrophy

• Any metabolic process in which energy for growth is produced using only inorganic chemical compounds

• These chemolithotrophic bacteria obtain their carbon from CO₂, much like plants, though they get their energy from chemical reactions rather than from light.

How was the phylogenetic tree determined? and why was that chosen?

• By analyzing rRNA

• Because:

  1. Its present in all cells

  2. Functionally constant

  3. Highly conserved (slowly changing) in their nucleic acid sequence

  4. Adequate length to provide a deep view of evolutionary relationships

Type of rRNA used for the phylogenetic tree in prokaryotes vs. eukaryotes

• Prokaryotes: 16S rRNA

• Eukaryotes: 18S rRNA

Chemoorganotrophs

• Energy source: Organic compounds (e.g., glucose, acetate)

• Example: E. coli (uses glucose for energy)

Microbial sterilization is used to…

Kill all microbes in or on objects

Louis Pasteur accomplisments

• Determined that the alcohol-making process was mediated by microbial fermentation and thus refuted the theory of spontaneous generation

• Developed heat sterilization techniques that involved the creation of a specialized swan-necked flask

• Developed the first rabies vaccine and treated thousands of individuals

Phase contrast microscopy

• Enhances contrast in transparent specimens without the need for staining

• Best for: observing live, unstained cells and their internal structures.

Transmission electron microscopy

• Uses a beam of electrons transmitted through a thin specimen to produce high-resolution images with fine details

• Best for: examining the ultrastructure of cells, viruses and nanoparticles at a nanometer scale.

Bright field microscopy

• Simplest form of optical microscopy, where light passes through a specimen to form an image.

• Best for: Observing stained specimens such as bacteria, tissues, and fixed cells but not ideal for live, transparent cells.

  • Bright field can have living cells but staining often kills cells.

Scanning electron microscopy

• Scans a specimen with a focused beam of electrons to create a detailed 3D image of the surface

• Best for: examining surface structures of cells, materials and microorganisms at high magnifications.