Basic Principles of Microbiology PDF

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Basic Principles of Microbiology Chapters 1 and 2 Microbiology •

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Study of microorganisms o Single-celled microscopic organisms o Independent entities that can carry out life processes independently Microbe Variations o Range from life-sustaining to health-threatening o Includes viruses Two Main Themes o Understanding basic life processes ▪ Microbes help model basic life processes of unicellular and multicellular organisms ▪ Can grow rapidly in small cultures o Applying knowledge to benefit humans ▪ Roles in agriculture, medicine, industry • Used in the food industry to ensure safety or for processing • Also used in biofuel industry (green gases produced by microorganisms) • Used to help create ethanol in factories (uses fermentation) ▪ Agents of disease ▪ Help digest and recycle major nutrients ▪ Plants have nitrogen fixing bacteria in roots • This is a symbiotic relationship (plants have their nitrogen fixed, bacteria get nutrients for survival)

Importance of Microorganisms •

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Oldest form of life (4.6 billion years ago) o At first they were only anaerobic o Cyanobacteria was later developed and first to photosynthesize (aerobic) ▪ This helped to oxygenate earth and develop eukaryotic cells Hugely diverse Largest mass of living material on Earth Carry out necessary chemical reactions important to other organisms and the environment o This means they are recycling key nutrient Able to live in places where other organisms cannot survive Have many interactions with other organisms who are dependent on microbes for survival

Microbial Cells • • •

Cell: a dynamic entity forming a fundamental unit of life Cytoplasmic Membrane (Cell Membrane): barrier separating the inside and outside of the cell Cell Wall: semipermeable membrane allowing some materials to enter and exit, giving strength

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Living Cells o Have a metabolism (catabolic and anabolic to break down or synthesize nutrients) o Ability to reproduce ▪ Genetics • DNA replication (produces exact same copy)

• DNA transcribed to RNA, translated to protein Catalytic Activity • Energy conservation combines ADP and inorganic phosphate to create ATP • Metabolism generates precursors for macromolecules • Enzymes are present as metabolic catalysts Differentiated (some cells can form a spore) Can communicate Ability to locomote Evolve through time All Cells ▪ Can reproduce, metabolize, and evolve Some Cells ▪ Can differentiate, communicate, and mobilize ▪

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Important Terms • • • • •

Population: group of cells derived from a single parental cell by successive cell divisions Microbial Communities: interacting assemblages of microbial populations in nature (harmful or beneficial) Microbial Habitat: environment microbial populations live in Ecosystem: all living organisms plus their physical and chemical environments Microbial Ecology: the study of microbes in their natural environment

Careers in Microbiology • • •

Clinical medicine Research and development Microbial monitoring in food, beverage, public health

Cell Structure •

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Cell Wall o Gives cell shape o Helps to survive in harsh environments All Cells have the following: o Cytoplasmic Membrane (separates interior and exterior) o Cytoplasm (aqueous mixture) o Ribosomes (for protein synthesis) o DNA (carries instructions for operation of cell) Eukaryotic Cells o DNA enclosed in membrane-bound nucleus o Cells are larger and more complex o Contains organelles Prokaryotic Cells o Organelles are not membrane-enclosed o Smaller than eukaryotes o Bacteria and Archaea are prokaryotic

Arrangement of DNA in Microbes •

Genome: cell’s full set of genes

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Prokaryotic cells have a single circular DNA chromosome o DNA aggregates to form nucleoid region o Also have special DNA called plasmids Eukaryotic DNA is linear and found in the nucleus o Associated with proteins which help fold DNA o Usually more than one chromosome o Two copies of each chromosome o Mitosis is the means of cell division o Genome is halved for reproduction by meiosis

Viruses • • •

Can show the properties of a living organism if they have hijacked another cells reproductive mechanisms Acellular organisms Smaller, and can infect all cells

Phylogenetic Development •

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Evolution o Process of change overtime resulting in new species and organisms through mutation o Both cells and viruses can evolve over time Phylogeny o Evolutionary relationships between organisms o Compares genetic information of different specimens o rRNA helps to determine phylogeny

The Three Domains of Life •

defined by comparative rRNA sequencing o Bacteria o Archaea o Eukarya ▪ Archaea and bacteria are not closely related ▪ Archaea are more closely related to eukarya ▪ Eukaryotic microorganisms were the ancestors for multicellular organisms o Mitochondria and chloroplasts contain their own genomes ▪ These organelles were originated in bacteria lineages ▪ They then moved to eukarya ▪ The process of this occurring is a theory called endosymbiosis

rRNA Phylogenetics •

Helps with: o Phylogenetic probes o Microbial community analysis o Ribotyping

Other Phylogenetic Indicators/Methods • •

Fatty Acid Methyl Esters o Shows the lipid content of membranes DNA-DNA Hybridization

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o Identifies base differences between DNA samples GC Ratios o Identifies whole genome DNA content ratios DNA Profiling o Fingerprinting or bar coding Multi-Locus Sequencing o Multiple conserved genes Whole Genome Analysis

Bacteria • • • • • • •

Contains many prokaryotes Any pathogenic prokaryotes are called bacteria The largest phylum of bacteria is the proteo-bacteria o Gram negative Green sulfur bacteria o Photosynthetic Green non-sulfur bacteria o Photosynthetic Deinococcus o Extremely resistant to radioactivity Chlamydia o Obligate intracellular parasites o Sexually transmitted disease

Archaea •

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Two main Phyla o Euryarchaeota ▪ Methanogens→ degrade organic matter anaerobically, can also produce the natural gas, methane ▪ Extreme Halophiles → require high salt concentrations for metabolism and reproduction ▪ Thermoacidophiles → grow in moderately high temperatures and low PH environments o Crenarchaeota ▪ Vast majority are hyperthermophiles ▪ Some live in marine, freshwater, and soil systems Archaea tend to live in more extreme, harsh environments than bacteria do

Eukarya •

Fungi o o o o o

Unicellular forms including yeast and mold Multicellular forms also exist Motility is uncommon Has cell wall Aka decomposers

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Protists o Protozoa ▪ Unicellular, free-living or parasitic, motile, no cell wall, non-phototrophic o Algae ▪ Unicellular forms, photosynthetic (phototrophic), have cell wall Slime Molds o Similar to protozoa in that they are motile with no cell wall o Have a more complex life cycle (fruiting body forms spores for reproduction)

Analyzing Microbial Communities • • •

Microbiologists believe we have cultured only a small fraction of archaea and bacteria Studies have been done using molecular microbial ecology to isolate the rRNA gene sequence from samples Phylotypes are phylogenetic groups that have been isolated o These are labelled as OP2 in phylogenetic trees o E.g. Marine group in archaea

Lichens • • •

A mutualistic relationship between fungi and cyanobacteria or fungi and algae Pigments from algae are visible (green chlorophyll or multi coloured carotenoids) Both organisms are benefited

Classification of Organisms • •

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Distinguished by characteristics such as chemical composition, nutritional requirements, energy source, and morphology Morphology o Shape diversity in bacteria consist of bacilli (rod shaped), cocci (circular), vibrio, spirillum, spirochete, etc. o Can also vary in arrangement (singular, chains, clusters) o Bacteria can be star-shaped and rectangular bacteria Metabolic Diversity o To survive they need energy and a carbon source o Metabolism is an uptake of nutrients, transformation of the nutrients, then elimination of waste o Diversity is evident through cell size and shape, physiology, motility, division processes, pathogenicity, developmental processes, adaptation to extreme environments o Chemoorganotrophs ▪ Obtain energy from the utilization of organic molecules ▪ Aerobes use oxygen to obtain energy ▪ Anaerobes obtain energy in the absence of oxygen ▪ Methanogens use substrates like CO2 and HCOO- as a carbon source to produce methane, CH4 o Chemolithotrophs ▪ Obtain energy from oxidization of inorganic molecules ▪ This is only found in prokaryotes o Phototrophs ▪ Contain pigments allowing them to use light as an energy source ▪ Oxygenic photosynthesis produces oxygen ▪ An-oxygenic photosynthesis does not produce oxygen

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▪ Archaea can be chemolitotrophs or Chemoorganotrophs but not phototrophs ▪ Green non-sulfur bacterium use iron, sulfur, and hydrogen to reduce CO2 Autotrophs ▪ Use CO2 as a carbon source ▪ Referred to as the primary producers ▪ Most chemolitotrophs and phototrophs are autotrophs Heterotroph ▪ Get carbon from organic sources Extremophiles ▪ Organisms that inhabit extreme environments ▪ Such as hot springs, glaciers, salty bodies of water, high pH environment Anaerobes ▪ Do not require oxygen for growth Aerobes ▪ Require oxygen for growth Microaerophiles ▪ Require low oxygen levels to survive (too much is toxic)

Classification • •

Kingdom, Phylum, Class, Order, Family, Genus, Species Writing scientific names: o Italicized o Genus is capitalized, species is lower case o Underline both genus and species o Can abbreviate genus to one letter...