Microorganism characteristics

Introduction to Microorganisms

• Pathogens are microbes causing disease.
• Microorganisms are grown in microbial cultures in a nutrient medium, a liquid or solid mixture providing essential growth nutrients.
• Growth of a microorganism involves cell division, leading to an increase in cell number.
• A colony represents millions to billions of microbial cells.

Cellular Structure

• The cytoplasmic membrane is selectively permeable, separating the cell's cytoplasm from the external environment.
• Cytoplasm consists of macromolecules, small organic ions, and various inorganic ions.
• Ribosomes facilitate protein synthesis.
• The cell wall, stronger than the cytoplasmic membrane, is found in plant cells and most microorganisms outside the cytoplasmic membrane
• Prokaryotes have few internal structures and lack a nucleus and organelles; bacteria and archaea are prokaryotes.
• Eukaryotes contain membrane-enclosed organelles like the nucleus, mitochondria, and chloroplasts(plants, animals and microbial eukaryotes)
• The genome is a full set of genes, a DNA segment encoding a protein or RNA molecule.
• Chromosomes, structures formed by the genome, are linear molecules in eukaryotes housed inside the nucleus or a singular circular molecule in prokaryotes.
• A nucleoid is an aggregated chromosome region, without a membrane, in prokaryotic cells.
• Plasmids, small DNA circles in prokaryotes, confer unique properties like unusual metabolism or antibiotic resistance.
• Plasmids are often nonessential to the cell.

Cellular Processes

• Metabolism involves nutrient acquisition, transformation into cellular materials, and waste elimination.
• Enzymes are proteins with catalytic activity that enable reactions to supply energy and perform biosynthesis.
• Transcription converts DNA to RNA.
• Translation converts RNA to proteins.
• Ribosomes enable translation
• DNA replication duplicates the genome.
• Motility enables cells to move in response to the environment.
• Differentiation forms specialized cells for growth, dispersal, or survival.
• Intercellular communication occurs between microbial cells of the same and different species.
• Horizontal gene transfer involves gene exchange between neighboring cells, common in prokaryotes.
• Evolution is descent via modification.

Cell Size and Morphology

• Morphology refers to the cell's size and shape.
• Prokaryotic cells range from 0.2 μm to 600 μm long.
• Prokaryotic cells are small to allow efficient diffusion, as they cannot actively transport molecules within the cytoplasm
• Diffusion being faster at smaller sizes, it accelerates the metabolic rate in small prokaryotic cells.
• A small cell size is subject to amount of space needed to house the essential biochemical components.
• A high surface-to-volume ratio (S/V ratio) controls growth rate and shape.
• Bacteria exist as cocci, bacilli, filaments, or spirals.
• Cocci can form diplococci (pairs), streptococci (chains), tetrads/sarcinae (3D cubes), or staphylococci (grapelike clusters).
• Filamentous bacteria divide terminally to form long, thin filaments.

Microbial Life Domains

• Bacteria and Archaea are prokaryotes, while Eukarya includes plants, animals, fungi, and microbial eukaryotes.
• There is confirmed existence of at least 80 bacterial phyla while Archaea compromises five described phyla; Euryarchaeota, Crenarchaeota, Thaumarchaeota, Nanoarchaeota, and Korarchaeota.
• At least a dozen phyla likely exist for Archaea which often thrive in extreme environments.
• Eukarya's major lineages are kingdoms.
• Viruses are non-cellular obligate parasites with DNA or RNA genomes.
• Bacteriophages are viruses infecting bacteria.
• LUCA, the Last Universal Common Ancestor, existed 3.8 billion years ago before the divergence of bacteria and archaea.

Microorganisms and the Biosphere

• The early Earth's atmosphere lacked oxygen.
• Only anaerobic microorganisms survived in the anoxic atmosphere.
• Anoxygenic phototrophs, including purple and green sulfur bacteria, harvest sunlight without producing oxygen.
• Oxygenic phototrophs like cyanobacteria evolved later, producing oxygen.
• All organisms universally possess approximately 60 genes.
• Extremophiles thrive in harsh conditions, defined by physiochemical limits.

Impact on Human Society

• Bacterial and viral pathogens cause disease.
• Nutrient cycling by microorganisms aids agriculture.
• Microorganisms in the rumen of ruminants digest cellulose.
• The gut microbiome breaks down carbohydrates, synthesizes vitamins, and inhabits the human GI tract with 10¹¹ cells per gram of colonic contents.
• Flavor, taste, and spoilage prevention in foods involve microbial fermentation.
• Wastewater treatment relies on microbes.
• Bioremediation converts pollutants to nontoxic forms.
• Biofilms grow on submerged surfaces.

Improving Microscopy Contrast

• Microscopy contrast requires dyes to stain cells for light distinction
• Basic dyes have a positive charge and include methylene blue, crystal violet, and safranin, which strongly bind to nucleic acids and cell surfaces.
• Simple stains are basic dyes to stain most bacteria cells
• Gram staining is a differential stain to divide bacteria according to different wall structures either positive or negative
• Positive walls have colour of purple violet
• Negative walls have colour of pink
• Phase-contrast and dark-field microscopy improve alive and unstained contrast
• Phase-contrast microscopy involves refractive index cell difference and use light to create contrast images
• Dark-field microscopy involves specimen and lens scatter light to create dark background image
• Fluorescence microscopy uses fluorescent cells and either natural substance or stain to make cells appear in black background

Woese and Tree of Life

• Early evolution history was derived primarily from palaeontology and comparative biology yet couldn't describe microorganisms
• rRna contained genes act as a prime candidate for phylogenetic analysis and its genes are located in ribosome. Useful as present in cells, are functionally constant, change slowly and are long
• Tree of life displays phylogeny
• Cultivation occurs on the use of rRna gene isolated and extracted directly from microorganisms.
• Metagenomics is a study conducted by recovering genomic information.

Cytoplasmic Structure

• The Cytoplasmic membrane separates and surrounds from external environment. Consisting both weak and permeable layers they help transport the membrane.
• They bacteria and eukarya have phospholipid bilayer structures . . These bilayers are 8-10 Nm wide
• Phospholipids have both hydrophillic (fatty avcid tail) and hydrophobic components
• Aracheal cytoplasmic membranes instead of phospholipids contain phospholipid bylayers and mono-layers
• Isoprenoid is the hydrophobic part
• Glycerol is hydrofilic part connected to a phosphor molecule

Cytoplasmic Membrane functions

• The main role is permeability of the solutres in and out of cells
• They catalyse certain cell functions
• Both conserve and consume energy(bacteria and archea) .
• Cytoplamic membranes impereable to polar and charge thus the transport protein comes in

Transport proteins

• Solutes are accumulated againist and ensure concentation is sufficient
• Requires great energy, sensitivity and specificity to one kind of molecule.
• Some are low-affinity with high external concentration and vice cersa