Exploring the Microbial World

Microbiology in Motion

• The microbial world has ancient, diverse, and ever-changing life forms.
• Microorganisms are Earth's life support system.
• Microbes exist in water, food, on organisms, and in virtually any natural environment.
• Microbiology explores the microbial world, with techniques like fluorescence microscopy to map cellular structures in 3D.
• The image shows human cells infected with Listeria monocytogenes; bacterial pathogen, stained red, with stained nuclei (blue) and actin filaments (green).
• Listeria, a soil organism, infects microbes, like amoebae, and adapts to live inside cells.
• Listeria hijacks cellular systems, using actin to propel itself within the host causing infection.
• Listeria can invade host vacuoles to hide and survive, potentially prolonging infection and causing antibiotic resistance.
• Research on Listeria provides updates on bacterial biology and microbial world.

Exploring the Microbial World

• This chapter introduces microbiology, microorganisms, their functions, study methods, and historical context.
• The microbial world has microscopic organisms with unique structures, origins, and impact on the biosphere.

Microorganisms, Tiny Titans of the Earth

• Microorganisms, or microbes, are too small to see with the naked eye.
• Microscopic organisms vary and inhabit every life-sustaining environment where many are undifferentiated single-celled forms.
• Some form complex structures or exist as multicellular organisms.
• Microorganisms often live in microbial communities that interact and are regulated by each other and environment.
• Microbiology examines microorganisms, their mechanisms, and roles.
• Microorganisms lived for billions of years on land and sea before plants and animals with incredible diversity.
• Microorganisms have a major part within Earth's biomass and activities.
• Oxygen is a result of microbial activity.
• Plants and animals live in a microbial world.
• The evolution and survival are affected by microbial activities, symbioses, and pathogens.
• Microorganisms exist within human life, from infectious diseases to food production, soil fertility, and fuel.
• Microbiology studies the dominant life form on Earth and their effect on living things.
• Tools include microscopy, the foundation of microbiology, in addition to methods for visualizing microorganisms.
• Microbial culture, cells grown in a nutrient medium, with media referring to liquid or solid nutrient mixtures for microorganism-growth.
• Microbiologists use word "growth" to define the increase in cell number from cell division.
• Microbe cells grow/divide to form colonies that allow microbes to be watched and grown.
• The comprehension of microbial disease and biochemical variety depends on the ability to grow microorganisms in the lab.
• Microorganisms are grown quickly/controlled, making these easy to use for research.

Microbial Cell Structure and Activities

• All share common features and elements.
• All possess a cytoplasmic membrane that separates the cell from its environment
• Cytoplasm which contains macromolecules (proteins, lipids, nucleic acids, polysaccharides), small organic molecules, inorganic ions, and ribosomes.
• All have ribosomes for creating proteins.
• Cell walls lend structural support
• Fundamental cellular organizations include prokaryotic and eukaryotic types
• Eukaryotic organisms of eukarya include plants, algae, protozoa, and fungi.
• Eukaryotic cells have membrane-enclosed organelles like the nucleus, mitochondria, and chloroplasts
• Prokaryotic cells in Bacteria and Archaea lack a nucleus and organelles.
• Archaea and Bacteria came before eukaryotes

Genes, Genomes, Nucleus, and Nucleoid

• In addition to membranes and ribosomes, all cells possess a DNA genome, the complete set of genes in a cell.
• A gene is a DNA segment that encodes protein or RNA to blueprint life.
• Prokaryotic and eukaryotic genome structure is in the form of chromosomes.
• Eukaryotic DNA has linear molecules within a nucleus, as opposed to Bacteria and Archaea chromosomes that are closed circular.
• The chromosome in prokaryotic cells forms the nucleoid which can be seen with an electron microscope, but there is no membrane.
• A prokaryotic cell contains a chromosome and plasmids possessing nonessential but special property genes.
• Bacterial/Archaeal genomes are compact, with 500 to 10,000 genes from around 0.5 to 10 million DNA base pairs.
• Eukaryotic cells have large, less streamlined genomes with 20,000-25,000 genes.

Activities of Microbial Cells

• A microorganism must survive and reproduce.
• Cells have structure and activities regarding survival and reproduction.
• Cells show metabolism, acquiring nutrients and turning these to waste/usable product.
• Energy supports structure synthesis leading to cell division, and growth of microbial matter.
• Genes hold information used by a cell to perform metabolism by regulating cellular function.
• Enzymes have catalytic activity by supplying energy/carrying out biosynthesis.
• Sequential gene expression processes synthesize enzymes during transcription and translation.
• Transcription process encodes DNA to an RNA molecule.
• Translation process synthesizes of protein with the use of RNA.
• Microbial cell expression and enzyme coordination makes sure the cell is attuned to its surroundings as they go through genome replication and division.
• Microorganisms have the ability to respond to changes of local areas.
• Motility allows cells to move based on conditions, and differentiation leads to modified cells.

Cell Size and Morphology

• Cell morphology is defined by cell size and shape.
• Cell shape often has ecological substance while small cell size affects biology.
• Micrometers are a millionth of a meter in length.
• Unaided eye can see objects less than 100 micrometers.
• Most prokaryotic cells range from 0.5 to 10 micrometers, but smallest cells can be about 0.2 micrometers, and the biggest can go to 600 micrometers.
• Eukaryotic cells average at about 5 micrometers to 100 micrometers.
• Cell size is influenced by cell structure.
• Eukaryotic cells can move molecules with complex structure, while prokaryotic cells use diffusion.
• With fast diffusion at a small distance, the rate a prokaryotic cell diffuses increases with the square of the distance travelled.

Cell Surface-to-Volume Ratios, Growth Rates, and Evolution

• Small cells gain more area with a great surface-to-volume ratio than big ones.
• Using a basic coccus as an example, the volume is a function of the cube of radius (V = 4/3πr^3) where and surface area uses sphere radius (S = 4πr^2).
• Meaning sphere (S/V) ratio = 3/r where a smaller radius = higher S/V.
• S/V ratio of P. ubique is at 22, E. coli is at 4.5, E. fishelsoni is at .05.
• Cell V and properties affects growth rate using the rate that the cells exchange nutrients and waste.
• S/V increases as cell size goes down, and cells exchange nutrients/waste quicker.
• Small cells have better use of nutrients vs bigger, so a fixed amount of nutrients supports small cells more.

Prokaryotic/Cell Morphologies

• Spherical or ovoid morphologies are termed coccus where a cylindrical cell shape is called a rod, or bacillus
• spiral-shaped cells are termed spirillum and curved comma-shaped are known as vibrio
• Spirochetes are spiral shape with cells that are flexible as opposed to the cells of spirilla being rigid.

Introduction to Microbial Life

• Cells have been classified into three domains: Bacteria, Archaea, and Eukarya.
• Viruses are microorganisms that are non-cellular and are not classified into any of the three domains.

Bacteria

• Have prokaryotic cell structure (no nucleus).
• Many diverse forms: single cells to multicellular organisms like Magnetoglobus.
• Most bacteria are unicellular.
• Thirty phylogenetic lineages which contain various classified species.
• Most bacteria belong to four phyla: Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes
• Approx. 80 bacterial Phyla in existence.

Archaea

• Exhibit prokaryotic cell structure, much like bacteria.
• Belong to Euryarchaeota, Crenarchaeota, Thaumarchaeota, Nanoarchaeota, Korarchaeota phyla.
• Historically associated with living in difficult/extreme environments.
• Live where its hot, salty, or acidic.
• Have no known plant or animal pathogens!
• Environmental DNA proposes the existence of 12 additional phyla.

Eukarya

• Have plants, animals, and fungi that are phylogenetically very young and originated with the Cambrian explosion
• Microbial eukaryotes may have come about as early as 2 billion years ago, before animals or plants.
• At least six kingdoms.
• Vary drastically, both regarding size and physiology.

Viruses

• Excluded from consideration in tree of life.
• Lack the components to be considered truly "alive" or cells.
• Must replicate within hosts.
• Take control and then produce more viruses.
• Have genomes that may be RNA or DNA, double- or single-stranded.
• Not conserved genetically between all viruses.
• May infect cells from domains in tree of life.

Microorganisms and the Biosphere

• Microbes are the oldest life form on the Earth and have performed critical functions which sustain the biosphere

Brief History of Life on Earth

• Earth is roughly 4.6 billion years and microbial cells appeared around 3.8 and 4.3 billion years ago
• Its atmosphere remained lacking oxygen for about 2 billion years and was instead made up of CO2 and N2.
• Only anaerobic metabolism survived at the time.
• At one billion year, phototrophic microorganisms happened which use sunlight.
• Earliest phototrophs are anoxygenic, such as green and purple sulfur bacteria.
• Cyanobacteria, evolved nearly after a billion years following anoxygenic species, and began the process of oxygenating Earth
• Multicellular organisms came about in time after the oxygenation of earth
• Showing us that Earth was exclusively microbial up to 80% of the time, thus it is microbial planet.

Microbial Abundance and Activity in the Biosphere

• Present wherever life is to thrive.
• Constitue a major fraction of global biomass for major global biomass.
• Estimated 2 x 10^30 microbial cells exist on earth
• Most microbes are abundant in habitats too harsh for anything else to live in, called extremophiles, existing in accordance to what life can endure
• Most ecosystems are modified in some manner by what the metabolic activities of microorganisms introduce; this would also impact what other organisms can thrive.

Microbial Impact on Human Society

• Applications include health and function such as better health agents than human agents.

Microorganisms as Agents of Disease

• Show how the amount of work of clinicians and microbiologists put together helps win against infectious diseases
• Vaccine rates help against death from infection

Agriculture

• Agriculture profits from elements that cycle through nutrient mediums; i.e. Nitrogen.

Microbial Cultivation and Horizon of Microbiology

• The cultivation of microbes in labs has advanced many diverse and important things in the world.
• Has developed a collection of aseptic techniques from the production and maintenance of nutrients.
• Also includes the maintenance of sterile which are essential to the pure nature of bacteria.
• Has the use of enrichment culture styles and procedures to determine and separate microbes from nature while making the research of microbes with various metabolic systems much easier.

Microorganisms by Way of Asceptic Technique

• Aseptic is needed to isolate and keep away anything else when doing experiments or research or any other thing relating to medicine.

Spontaneous Generation

• The creation of spontaneous microbes or creatures was an agreed upon concept for thousands of years.
• It wasn't until the time of the scientist Pasteur that we started considering there to be a need for sterilization as described back then
• It started with his early work of identifying that any and all things come from air and must be eliminated

Important Note

• If food were to not have air or sterilization then organisms would not show up at all which helped in the start of micro biology after all.

Pasteur and Lister

• Thanks to the hard efforts of Pasteur; his student Joseph Lister would make great advances in how to implement aseptic ways and methods when doing surgeries.
• After his death due to his efforts there was greatly reduced infection due to sterilization practices.

Discovery of Diversity

• In the twentieth century the understanding of organisms had broadened through several key people

The Discovery Team

• Martinus Beijerinck and Sergei Winogradsky.
• Important member Sergei Winogradsky who wanted very much to find out what there was with the different varieties that existed.
• Most notably wanted to see nitrogen and sulfur based organisms.
• He looked to one of the best specimens known, the Beggiatoa and thought it was odd that on any and all regular nutrient based environments there to be no trace

Sergi and Winogradsky Experiment

• In the end he had an environment as that was in nature.
• He determined that all that these organisms required was inorganic matter to thrive and also were able to obtain their carbon as that of normal plants