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• Cells are composed of macromolecules like proteins, lipids, polysaccharides, lipopolysaccharides, and nucleic acids, comprising over 96% of E. coli's dry weight

Cell Nutrition

• Microbe metabolic capacities differ and require a core set of nutrients, with macronutrients needed in large amounts and micronutrients in minute amounts

Chemical Makeup

• A single Escherichia coli weighs about 10^-12 g, with 75% being water, and has a dry weight of approximately 184 x 10^-15 g (184 fg)
• Key chemical elements in living systems, accounting for around 96% of an average bacterial cell's dry weight, include carbon (C), oxygen (O), nitrogen (N), hydrogen (H), phosphorus (P), and sulfur (S)
• Additional elements, composing 3.7% of a cell's mass, are potassium (K), sodium (Na), calcium (Ca), magnesium (Mg), chlorine (CI), and iron (Fe)
• Proteins form the vast majority, whereas DNA contributes a small amount of dry weight

Carbon, Nitrogen, and Micronutrients

• Carbon and nitrogen exist in substantial quantities
• Heterotrophs require organic carbon
• Carbon can be obtained either from breaking down organic polymers or by directly absorbing their monomeric constituents
• Autotrophs can produce organic compounds from carbon dioxide (CO2)
• Bulk is found in proteins, ammonia (NH3), nitrate (NO3-), and nitrogen gas (N2)
• All microorganisms utilize NH3, while some can use organic nitrogen sources like amino acids, and a few can use N2, a process known as nitrogen fixation
• Though in smaller quantities than carbon and nitrogen, macronutrients are also required
• Phosphorus is vital for nucleic acids and phospholipids, typically assimilated as inorganic phosphate
• Sulfur, present in amino acids like cysteine and methionine, and certain vitamins, can be assimilated from inorganic forms like sulfate or sulfide, as well as from organic sulfur compounds
• Potassium required for enzymes
• Magnesium stabilizes ribosomes, membranes, and nucleic acids, and is necessary for enzyme activity
• Calcium and sodium are exclusively needed by a select few organisms

Micronutrients and Growth Factors

• Several enzymes need a metal ion or a tiny organic molecule to catalyze reactions as a cofactor
• Growth hinges on various metals, with iron (Fe) being common in cytochromes and other enzymes vital for cellular respiration or oxidation-reduction reactions
• Metals, known as trace metals, are needed in small amounts
• Enzymes with a trace metal requirement can be synthesized in the cell and if the cell lacks trace metals it will not function properly
• Growth factors, organic micronutrients, include vitamins, which are frequently required and act as coenzymes
• Microbes may biosynthesize all growth factor, or need to assimilate them from the environment
• Microorganism growth factor requirements greatly fluctuate
• Cyanobacteria are autotrophic microbes inhabiting aquatic environments and synthesizing all growth factors
• Lactic Acid get growth factors from location (animal gut of food) whereas, Cyanobacteria can synthesize all their own growth factors
• Cells must uptake both macro- and micronutrients to facilitate grow and division

Growth Media and Laboratory Culture

• Microorganism lab cultures are developed in growth media which provides nutrient solutions designed for the specific organism
• The autoclave heats medium under pressure

Culture Media Classes

• Broadly, culture includes defined and complex types
• Defined: uses specific amounts of pure inorganic/organic chemicals with exact composition that is known
• Carbon source is a major component of any culture because cells require large amounts of it to create new cell material
• The organisms dictate specific carbon sources and concentrations
• Defined media which have one carbon source are "simple"
• Complex: comprised of digests from microbial, animal, and plant based products
• Complex uses protein, beef, soybeans or yeast rich nutrients
• Media made by Pasteur are complex but uses yeast extracts
• Growth can be selective or differential, or both
• Selective medium: utilizes components that limit growth, while others remain to grow
• Selective commercially available to isolate common pathogens or those strains that cause foodborne illness via bile salts (which kill bacteria unable to grow in gut)
• Differential medium: utilizes an indicator that indicates a color change to reveal if there has been an chemical reaction that has affected growth
• Differential is useful for distinguishing bacteria + widely used in clinical diagnostics, like detecting for bacteria by testing acidification through color change

Biosynthetic Capacity and Nutritional Requirements

• Complex is used for common bacteria like E. coli and Leuconostoc mesenteroides due to their rich nutrients that are easy to prepare
• A simple defined medium is used for E.coli due to low nutrition needs, where as L. mesenteroides is a defined medium, that uses more nutrients (or uses growth promoters)
• Has individual nutrients that can be added to the medium
• Thiobacillus thioparus, uses an aerobic sulfur oxidization to use carbon dioxide from air to creates eneryg by breaking down sulfur

Laboratory Culture

• Laboratory media is offered a semi solid, or solid material
• Solidified agar is an algal polysaccharide used in studies performed by Robert Koch
• Solid media immobilize cells as they grow
• Colonies are the visible isolated masses that are produced as cells grow in a pile
• Colonies vary by shape, color, texture, size or other factors
• Colony appearance based on organism itself, the nutrient supply or how much of the culture has been distributed
• Colony morphology refers to visible unique characteristics that can be used to identify microorganisms
• Determines if it contaminated, if contaminates it should be remixed

Microbial Cell Numbers

• Plates originating from pure contamination or culture contamination will form more than one colony type
• Aseptic process requires the aseptic transfer of cultures, which can introduced contamination through the air, liquid droplets or surfaces
• Goal in is transfer the culture from liquids so it has not come in contact w/ liquid
• Also maintains surfaces and protects agar via sterilzation
• Aseptic technique must maintained
• Spreads inoculation in sterile areas

Microscopic Cell Numbers

• In order to get a microbial count numerates the cells present
• Done via slides on on liquids
• Dried slides increase contract via staining
• Liquids require a grid (known area), squares (known volumne), square and lid (fixed volume) to be counted to give an estimate
• Microscopic counting estimates microbial populations
• Microscopic counting utilizes staining, and living cells are not able to be distinguished
• Replicated will have some variability due to limited precision and small hard to see cells

Microbial Ecology

• Ecology uses counts from natural samples, through the process of staining
• Stains shows how organisms behave through phylogenetic data
• Fluorescing stains show all cells like DAPI,
• Other stains reveal dead cells by looking at cells membrances

Microbial Numbers

• Viable cells - those that are alive
• Viable counts - performed by colony counting
• Agar often required for plate counts (Plate counts)
• Counts estimates the cell numbers as a single viable cell count
• 2 options exist, a spread place where it diluted along the medium
• Pour medium is pipetted into the medium, then molten plate agar is added
• Must carefully observe and count if there are too many colonies along the counting space (leads to erronous counts), where the best test lies between 30 - 300 colonies
• Even if counting by estimates, some count bacteria in clusters of colonies due to the form of a cell (like bacterial fillaments)
• Colony Forming unites is the accurate way to measure a population within medium
• Diluting the medium may be required, by serial dilutions with water or solutions, that still allow growth for nutrients

Plate Counts

• Plate counts are used in Dairy to analyze microbial contaminants and can be as accurate as one viable sample
• Selective mediums allow for growth of one sample by removing others
• Viable counting takes complex media to allow for quantative analysis to dictate food safety

Cavetas For Microscopic Counts

• Direct miscroscopic counts are inaccurate in soils
• Can be inaccurate as the total counts are under-represented
• May be be lower due to nutrient scarcity

Turbidimeric Numbers

• Microbial cells are counted under a microscope and light scattering
• In this situation the turbidity can be used to quantify cells quickly so there are no interuptions to the sample over time
• Spectrophotometers counts measure turbidity as a light that reads cell cloudyness and gives wavelengths
• Optimal measurements at shorter wavelengths

Growth Dynamic and Cycle

• Cell growth occurs through cell division by producing cells identical to each other
• In E. coli cells have an elongated shape, and splits into two equal daughter cells with 2 indicators per cell from original process of replication
• Septum allows the division wall to function and pinch cells equally
• Several variance that exist like Bacillus subtilis and Caulobacter

Generation

• Time required for double population called generation time by copying chromosomes
• Doubling time fluctuates
• E. coli is 20 minutes, and has a less than 10 doubling time
• batch cultures contain microbes growing in a fixed volume of liquid
• Growth Curve composed of a lag, exponential as well as decline in phases

Exponential or Lag Phases

• Occurs as there is a period between inoculation to the onset of the growth through a lag that can by shor, or extended deppending on growth requirements
• A long lag occurs from a shift from rich material to poor
• In exponetial phase cell double at regular intervals, also known as stabilized growth, during the period where they can be identically metabolized
• Can be effected by environment like the choice of material

Stationary + Death Phases

• Exponential growth can not continue
• In batch culture, due to the lack of nutrients creates waste
• Static phase is were there is an even in crease that leads to even distribution of zero
• Metabolism shifts away and focuses on energy
• Death phase decreases

Growth Data

• Population duoubles at regular intervals for exponential growth
• When we plot those numbers we see a continuous increading slope
• When charted on a log, then lines are more readable making them more readable, as logorithmic charts are easier to read

Bacterila Growth (Mathematics)

• Cell numbers at gerneration can be expressed as 2^n and easily be counted and the result is doubled growth for exponentially growing samples

Expressing Growth as a Function

• If a population beguns with one cell for over 3 turns that will indicate 40 to the 7th power in numbers
• specific growth rate express an exponential increase across at an instant (measured via integration of an amount) as well as time

Implications + Limitations

• Growth has implications that increase at a extreme rate, but has limits that may occur or be circumvented via using a continuous culture device or most common chemostat

Steady State:

• enables the control of specific culture amounts. Also causes a stable and equal balance in fresh and wasted medium (balanced through volume )
• Creates a fixed volume that stays consistent at equilibrium and then reach stability

Steady Relationships + Chemostats

• Diluition does not effect grow unless substrates has grown wash
• The Chemostat aids populations by enabling exponential growth
• Expressional most desirable for physiology
• Chemostats replicate natural events and allow for study of communities in a low nutrient environment

Biofilms

• Growth in fluid like swimming cells are planks
• Whereas growth on a surface or a "Biofilm Surface" is sessile
• Colonies initiate as cells enmesh in matrix
• Can begin by surface attachment, but in water it disperser with a lot of stress

Biofilm Formation

• Can be analyzed via fluids within glass

Biofilm Analysis

• Biofilm uses Pseudomonas aeruginosa
• The bacterium helps with medical relevance + creates resistant biofilm.
• Bacteria shows more resistance + increased metabolic differentiation

Nature Biofilm Growth Form

• Biofilms are common for bacterial growth within nature, due to the woven nature that prevents chemicals from reaching through the structure preventing grazing effects
• Multilayer forms are microbial mats
• Hot Spring runof = microbial growth
• Affects human life with joint infects, heart disease, etc...
• Responsible for cavities in teeth, and causes corruption in water pipes

Alternative Growth

• Planktonic cells creates balanced growth during exp phase
• Cultures are identifiable, genetically
• uniform cultures are suitable for systems
• cells do not exhibit stable growth and are characterized by varying rates of growth

Cellular Growth + Function

• Cellular buds of mothers create cells that show differentiation that is unique to that cell
• Where there is division, and growth not linked by cell division there exists filaments known as hyphael
• Those weaves result in Arthritic spores that protect cells
• Cells tend to go in all directions along filaments (through spore growth), that happens when there in an increase in intracellular offspring being produced

Temperature

• Affects growth in opposing ways as a catalyst
• Can Denature from heat, if a temp is too cold
• Minimum limits are set based on temp
• All of these traits characterize the species that is in the colony
• Psychophils can live at 0 but optimums can be above 100
• Microbial life does exist at extreme ends from antarticas and 50°C surface soil

Environment Classification

• Cold in Antarctic's or temperate lake
• Growth can still occur inside of frozen materials and allow microbes to metabolize

Adaptation

• Adaptation in cold environemnts
• Bacteria and archaea are in permafrost, with as low as - 15°C growth limits
• Tolerant organisms do exist, some bacteria have been shown to function at - 20°C
• Organism adaptation include enzyme creation, less rigid and bonded cells

Cellular Characteristics

• Cells are mostly unsaturated, and shorter
• In short the function has reduced chain lengths to not stiffen them
• Where there exists heat, then membranes are also created that can withstand it and form proteins that are cold shock

Microbial Characteristics

• Hydrothermal vents can survive for as long as a 350°F
• Scientists study growth rates of heat- loving microbes in springs by placing a slide in the water.
• Bacteria/Archaea survive above as thermal enforcer = protein composition

Heat and Bacteria

• Thermophils can affect bacterial proteins due to their shape

Bacteria Conditions + Growth

• The condition of bacterial and growth can also be increased (but not as much)
• Some microbes use fatty acids and can form structures (at a monolayer level) as they get hot

Microbial State

• The pH state the alkalinity is very dependent for microbial growth
• The water as 7 pH when in a neutral form

Environment in Microbes

• The outside determines which microbes live
• Optimal pH is necessary, and a limited range is necessary to maintain a culture

Buffer

• The buffer system protects a culture, because it keep pH with a range depending on environment and solute.

Acidity + Solutes

• Acidity of the solvent is important

Availability

• Water is need to prevent water loss as the solute concentrations are higher in the membrane preventing it
• Concentrations increase solutes
• With a low activity it won't work
• Matric activity needs a dry area
• Some have lower levels than before due to a protective effect for the organism

Microbes + Tolerance

• All of the traits that determine microbes, are what let them thrive
• High-quality solute can alter salinity

Oxygen

• Oxygen as a nutrient as well as a inhibitor in a culture

Oyxgen Grouping + Bacteria

• Bacteria that can have varying tolerances as high oxygen, respire with full oxygen
• Anaerobes and Microaerophils can have the opposite effect when around oxygen

Anearolic Culture Methods

• Must have containers, to grow bacteria
• A reducing agent is used to clear traces of O2
• Thioglycolate broth, agar and top
• If there is oxygen they can exist at the top, top (both anaerobes) as oxygen is not needed

Enxymes

• oxygen creates toxic intermediates that need to be cleared
• The toxic by products can also reduce the amount of cells
• Enzymes can also attack this form of cells by releasing O2 and H2o from H2o
• Superodise dismutase and catalyst help with by products (that is the reason it is helpful)
• O2 and H2o are by products made to harm
• Super enzymes function to remove those compounds