Microbiology: Beneficial and Pathogenic Microbes, Techniques, and Taxonomy

How do beneficial microbes impact our lives?

Microbes benefit humans through food production (yogurt, cheese, bread), decomposition and nutrient cycling, production of antibiotics and other products, normal microbiota, biotechnology, and wastewater treatment.

How do pathogenic microbes impact our lives?

Pathogenic microbes cause infectious diseases in humans, animals, and plants by damaging tissues, producing toxins, invading cells, or triggering harmful immune responses.

How do we prevent food spoilage?

We control microbial growth using refrigeration/freezing, heating, drying, salting/sugaring, fermentation, canning, pasteurization, chemical preservatives, and aseptic handling.

What is aseptic technique?

A set of procedures used to prevent contamination by unwanted microorganisms and to protect samples, people, and the environment from microorganisms.

How is aseptic technique used in the laboratory?

It is used when transferring cultures, opening containers, sterilizing equipment, flaming/sterilizing openings, and minimizing exposure of sterile materials to the environment.

How is aseptic technique used in hospitals?

It is used during procedures such as injections, surgery, catheter placement, wound care, and handling sterile equipment to prevent infection.

What is a prokaryote?

A cell without a membrane-bound nucleus or other membrane-bound organelles; includes Bacteria and Archaea.

What is a eukaryote?

A cell with a membrane-bound nucleus and membrane-bound organelles; includes Eukarya.

Prokaryotes vs. eukaryotes: nucleus

Prokaryotes lack a membrane-bound nucleus; eukaryotes have one.

Prokaryotes vs. eukaryotes: organelles

Prokaryotes lack membrane-bound organelles; eukaryotes contain membrane-bound organelles.

Prokaryotes vs. eukaryotes: size

Prokaryotic cells are generally smaller than eukaryotic cells.

What is an acellular agent?

An infectious entity that is not made of cells, such as viruses, viroids, satellites, and prions.

Why are acellular agents different from cellular microbes?

They lack cellular structures and do not independently perform normal cellular metabolism or reproduction.

What are cyanobacteria?

Photosynthetic bacteria that use light energy and release oxygen; they are important primary producers and some can fix nitrogen.

Where are cyanobacteria found?

In aquatic environments, soil, and other environments exposed to light.

What are halophiles?

Microorganisms that require or prefer high concentrations of salt.

Where are halophiles found?

Highly saline environments such as salt lakes, salt flats, and salt evaporation ponds.

What are thermophiles?

Microorganisms that grow optimally at high temperatures.

Where are thermophiles found?

Hot environments such as hot springs, geothermal areas, and hydrothermal vents.

What are barophiles/piezophiles?

Microorganisms that grow best under high pressure.

Where are barophiles/piezophiles found?

Deep ocean environments and other high-pressure habitats.

Why is agar preferred over gelatin in microbiological media?

Agar melts at a higher temperature and remains solid at typical incubation temperatures; most microbes cannot degrade it.

What are the three domains?

Bacteria, Archaea, and Eukarya.

What are the four kingdoms of Eukarya?

Protista, Fungi, Plantae, and Animalia.

What is binomial nomenclature?

The two-part scientific naming system consisting of genus and species.

How is a scientific name written?

The genus is capitalized and the species is lowercase; both are italicized when typed or underlined separately when handwritten.

What is the first part of a scientific name?

The genus.

What is the second part of a scientific name?

The specific epithet/species designation.

Why are scientific names useful?

They provide a standardized worldwide naming system and reduce confusion caused by common names.

What is a culture collection?

A collection of microbial strains preserved for future study and research.

What are common long-term methods for preserving microbial strains?

Freezing at very low temperatures, lyophilization (freeze-drying), and cryopreservation.

What is classical taxonomy?

Classification based on observable characteristics and phenotypic traits.

What features are used in classical taxonomy?

Cell morphology, staining characteristics, metabolism, biochemical properties, growth characteristics, environmental requirements, and physiological characteristics.

What is genetic taxonomy?

Classification based on genetic or molecular characteristics.

What genes are commonly used in genetic taxonomy?

Conserved genes such as 16S rRNA genes in bacteria and archaea; other conserved genes may also be compared.

Why are conserved genes useful for genetic taxonomy?

They change relatively slowly and allow evolutionary relationships between organisms to be compared.

What are the two major genetic taxonomy methods?

DNA-DNA hybridization and nucleic acid sequencing.

What does DNA-DNA hybridization measure?

The degree to which DNA from two organisms can hybridize, indicating genetic similarity.

What are the basic steps of DNA-DNA hybridization?

Isolate DNA → separate DNA strands → mix DNA from different organisms → allow complementary strands to hybridize → measure the amount/stability of hybridization.

What is nucleic acid sequencing?

Determining the exact order of nucleotides in DNA or RNA.

What are the basic steps of sequencing for taxonomy?

Isolate/amplify the target gene → determine its nucleotide sequence → compare sequences between organisms → infer relatedness.

What is magnification?

The increase in apparent size of an object produced by a microscope.

What is resolution?

The ability to distinguish two objects as separate; higher resolution means greater ability to see fine detail.

How does wavelength affect resolution?

Shorter wavelengths generally provide better resolution.

Which type of microscopy uses visible light?

Light microscopy/optical microscopy.

Which type of microscopy uses ultraviolet light?

UV microscopy.

Which type of microscopy uses electrons?

Electron microscopy.

What does parfocal mean?

Once an object is focused with one objective lens, it remains approximately focused when switching to another objective.

What are the main lenses in a compound light microscope?

The ocular lens and objective lenses.

What are common objective lenses?

Scanning (4×), low-power (10×), high-power (40×), and oil-immersion (100×).

How do you calculate total magnification?

Ocular magnification × objective magnification.

What is the total magnification with a 10× ocular and 40× objective?

400×.

What is the total magnification with a 10× ocular and 100× objective?

1000×.

Light microscopy vs electron microscopy

Light microscopes use light and glass lenses; electron microscopes use electron beams and electromagnetic lenses and generally provide much higher resolution.

What is the electron source in electron microscopy?

An electron gun.

What type of lenses are used in electron microscopes?

Electromagnetic lenses.

What is TEM?

Transmission electron microscopy; electrons pass through a thin specimen to reveal internal structures and provide very high resolution.

What is SEM?

Scanning electron microscopy; electrons scan the surface and produce detailed three-dimensional-looking surface images.

What is STM?

Scanning tunneling microscopy; uses a probe to examine surfaces at extremely high resolution, especially conductive materials.

What is AFM?

Atomic force microscopy; uses a physical probe to measure surface features and can examine materials at very high resolution.

When would you use TEM?

To examine internal structures/ultrastructure of cells or viruses.

When would you use SEM?

To examine the external surface and three-dimensional surface features of specimens.

What is bacterial morphology?

The shape and form of bacterial cells.

Common bacterial shapes

Coccus (spherical), bacillus (rod-shaped), vibrio (comma-shaped), and spirillum/spirochete (spiral).

What is a coccus?

A spherical bacterial cell.

What is a bacillus?

A rod-shaped bacterial cell.

What is a vibrio?

A curved/comma-shaped bacterial cell.

What is a spirillum?

A rigid spiral-shaped bacterial cell.

What is a spirochete?

A flexible spiral-shaped bacterial cell.

What is an arrangement?

The way bacterial cells remain connected after cell division, such as pairs, chains, or clusters.

What is a diplo- arrangement?

Cells occurring in pairs.

What is a strepto- arrangement?

Cells occurring in chains.

What is a staphylo- arrangement?

Cells occurring in grape-like clusters.

What are the three major prokaryotic cytoskeletal proteins?

FtsZ, MreB, and crescentin.

What is FtsZ?

A tubulin-like cytoskeletal protein involved in cell division and formation of the division ring.

What is MreB?

An actin-like cytoskeletal protein associated with rod-shaped cell growth.

What is crescentin?

A cytoskeletal protein associated with the curved shape of some bacteria such as Caulobacter.

What is peptidoglycan?

A rigid polymer of sugars and peptides that provides structural strength to bacterial cell walls.

What are the two sugars in peptidoglycan?

NAG (N-acetylglucosamine) and NAM (N-acetylmuramic acid).

How are NAG and NAM arranged in peptidoglycan?

They alternate in long glycan chains: NAG-NAM-NAG-NAM.

Where are peptide cross-links found?

Peptide side chains attached to NAM are cross-linked between adjacent peptidoglycan strands.

What is the function of peptidoglycan?

It provides rigidity and prevents bacterial cells from bursting due to osmotic pressure.

What is characteristic of Gram-positive cell walls?

A thick peptidoglycan layer containing teichoic acids and no outer membrane.

What is characteristic of Gram-negative cell walls?

A thin peptidoglycan layer located in the periplasmic space plus an outer membrane.

What are teichoic acids?

Negatively charged polymers found in Gram-positive cell walls that contribute to cell wall structure and surface charge.

What is lipoteichoic acid?

A teichoic acid anchored to the cytoplasmic membrane of Gram-positive bacteria.

What is the outer membrane?

An additional membrane found in Gram-negative bacteria outside the thin peptidoglycan layer.

What are the two layers of the Gram-negative outer membrane?

An inner phospholipid layer and an outer layer containing lipopolysaccharide (LPS).

What are the three components of LPS?

Lipid A, core polysaccharide, and O antigen.

What is Lipid A?

The portion of LPS embedded in the outer membrane; it functions as endotoxin.

What is the core polysaccharide?

The central portion of LPS connecting Lipid A to the O antigen.

What is the O antigen?

The outer polysaccharide portion of LPS that varies between strains and contributes to antigenic specificity.

Why are Gram-positive and Gram-negative bacteria negatively charged?

Gram-positive cells have negatively charged teichoic acids; Gram-negative cells have negatively charged LPS and membrane components.

What is the purpose of Gram staining?

To differentiate bacteria based primarily on differences in their cell wall structure.

What is the correct order of Gram stain reagents?

Crystal violet → iodine → alcohol/acetone decolorizer → safranin.

What is the primary stain in Gram staining?

Crystal violet.

What is the mordant in Gram staining?

Iodine.

What is the decolorizer in Gram staining?

Alcohol or an alcohol/acetone mixture.

What is the counterstain in Gram staining?

Safranin.

What color are Gram-positive cells after Gram staining?

Purple.