Microbiology - Ch. 26: Applied & Environmental Microbiology

Applied Microbiology

- Commercial use of microorganisms
- 2 distinct fields: Food Microbiology & Industrial Microbiology

Food Microbiology

- Use of microbes in food production
- Prevention of food spoilage and food-related illnesses

Industrial Microbiology

Application of microbes to industrial manufacturing and solutions to environmental, health, and agriculture issues

Environmental Microbiology

How microbes affect other organisms and the environment

Fermentation: Food Microbiology

- Produces flavors, aromas, and consistencies of foods
- Any desirable change is a result of microbial growth
Ex: yeast used to leaven bread; lactic acid gives sourdough characteristic tase

Microbial Metabolism Functions

1. Acts as a preservative - wine, pickles, cheese, silage
2. Destroys many pathogenic microbes and toxins
3. Can add nutritional value in form of vitamins or other nutrients

Spoilage: Food Microbiology

- Any undesirable change that occurs in a food or beverage due to various reasons:
Undesirable metabolic reactions - chunky milk
Growth of pathogens - food poisoning
Presence of unwanted microorganisms in the food

Starter Cultures: Food Microbiology

- Used in commercial food and beverage production
- Composed of known microorganisms that consistently perform specific fermentations

Secondary Cultures: Food Microbiology

- Further modify flavor and aroma of foods from starter cultures
- Different secondary cultures give Swiss cheese and blue cheese distinct flavors

Fermented Vegetables: Food Microbiology

- People ferment many types of vegetables
- Lactic acid bacteria used to produce most of these
Ex: Kimchi, soy sauce, chocolate, pickles
- Silage used as animal feed on many farms - made by natural fermentation of various vegetables

Fermented Meat Products: Food Microbiology

- Fermentation combined with drying or smoking used to preserve meats
- Pork, beef, and fish are commonly fermented meats

Fermented Dairy Products: Food Microbiology

- Milk fermentation relies on lactic acid bacteria
- Produces characteristic textures and aroma
- Used to produce buttermilk, yogurt, cheeses

Alcoholic Fermentation: Food Microbiology

- Process by which various microorganisms convert simple sugars into ethanol & carbon dioxide (CO2)
- Specific starter cultures used in the large-scale commercial applications of alcohol fermentation

Causes of Food Spoilage: Food Microbiology

- Spoilage alters nutritional value, taste, appearance of food
- Economic loss and illness
- Results from intrinsic or extrinsic factors

Intrinsic Factors - Food Spoilage: Food Microbiology

Inherent properties of the food itself
Ex: enzymes

Extrinsic Factors - Food Spoilage: Food Microbiology

Involved with the processing or handling of food - environmental contamination

Perishable Foods - Food Spoilage: Food Microbiology

- Nutrient rich, moist, and unprotected by coverings
- Spoil quickly if not kept cold
Ex: strawberry; steaks

Semiperishable Foods - Food Spoilage: Food Microbiology

- Can store sealed for months without spoiling
Ex: mayo, Velveeta cheese

Nonperishable Foods - Food Spoilage: Food Microbiology

- Dry or canned foods that can be stored indefinitely
- Often nutrient poor, dried, fermented, or preserved
Ex: cereal

Industrial Canning - Prevention of Food Spoilage: Food Microbiology

- Eliminates mesophilic bacteria and endospores
- Hyperthermophilic microbes are not killed
- Clostridium species and coliforms are the most common contaminants of canned goods (botulism)

Pasteurization - Prevention of Food Spoilage: Food Microbiology

- Lowers microbe numbers but some microbes survive
- Foods will spoil without refrigeration

Desiccation - Prevention of Food Spoilage: Food Microbiology

- Drying
- Reduces microbes but does not kill endospores

Lyophilization - Prevention of Food Spoilage: Food Microbiology

- Freeze dry
- A vacuum dries frozen foods

Gamma Radiation - Prevention of Food Spoilage: Food Microbiology

- Irradiation
- Can achieve complete sterilization

Aseptic Packaging - Prevention of Food Spoilage: Food Microbiology

- Sterile packages
- Sterilize food containers with hot peroxide solution, UV light, or steam

Use of Preservatives - Prevention of Food Spoilage: Food Microbiology

- Salt and sugar: remove water from food
- Garlic: contains allcin which inhibits enzyme function
- Benzoic acid: interferes with enzymatic function
- Certain spices & herbs: interfere with the functions of membranes of microorganisms
- Chemical preservat

Role of Temperature - Prevention of Food Spoilage: Food Microbiology

- HIGH temps: desirable for processing - proteins and enzymes become denatured; some toxins not inactivated by heat
- LOW temps: desirable for food storage - cold slows metabolism and retards microbial growth
Ex: Listeria monocytogenes: can grow in cold s

Food-borne Illness: Food Microbiology

- Categories of Food Poisoning: Food Infections & Food Intoxications
- Symptoms: nausea, vomiting, diarrhea, fever, fatigue, muscle cramps
- Common source epidemics - 48 million annual cases

Food Infections: Prevention of Food Spoilage: Food Microbiology

Consumption of living microorganisms

Food Intoxications: Prevention of Food Spoilage: Food Microbiology

Consumption of microbial toxins rather than the microbe

Industrial Microbiology

- Microbes in fermentation
- Microbes in production of several industrial products
- Pre & Post treatment of water and waste ways
- Disposal and cleanup of biological wastes

Industrial Fermentation: Industrial Microbiology

- Large-scale growth of particular microbes for producing beneficial compounds such as amino acids and vitamins
- Often use the waste product from another process as growth medium
Ex: molasses from sugar production; leftover grain from fermentation

Primary Metabolites: Industrial Microbiology

- Produced during ACTIVE growth and metabolism
- Required for reproduction or are by-products of metabolism
Ex: Alcohol, fermentation products, vitamins

Secondary Metabolites: Industrial Microbiology

- Produced after the culture has entered stationary growth
- Substances are not immediately needed for growth
- Recombinant microorganisms used in some industrial applications
Ex: antibiotics

Continuous Fermentation: Industrial Microbiology

Continually adding new nutrients

Batch Fermentation: Industrial Microbiology

Let them go until stationary phase where most will die

Industrial Production of Microorganisms

- Microorganisms produce array of industrially useful chemicals
- Recombinant organisms: produced substances not normally manufactured by microbial cells
Ex: Eukaryotic Proteins (Insulin)

Enzymes & Other Industrial Products: Industrial Production of Microorganisms

- Enzymes among most important products made by microbes
- Microbial products used as food additives and supplements
Ex: vitamins, amino acids, organic acids, dyes

Alternative Fuels: Industrial Production of Microorganisms

- Some microbes produce carbohydrates used as fuel
- Other microbes convert biomass into renewable fuels

Pharmaceuticals: Industrial Production of Microorganisms

Includes antimicrobial drugs, recombinant hormones, and other cell regulators

Pesticides & Agricultural Products: Industrial Production of Microorganisms

- Microbes used to help crop management
- Microbial products used as insecticides and to protect plants from freeze damage

Biosensors: Industrial Production of Microorganisms

Bacteria or microbial products combined with electronic measuring devices

Bioreporters: Industrial Production of Microorganisms

Composed of microbes with innate signaling capabilities
Ex: HIV test - color change

Water Treatment - Water Pollution

1. Physically: presence of particulate matter
2. Chemically: presence of inorganic or organic compounds
3. Biologically: too many or non-native microorganisms

Waterborne Illnesses

- Consuming contaminated water results in diarrheal diseases worldwide (1.26 million deaths annually)
- Rare in the US - outbreaks are point-source infections

Treatment of Drinking Water

Potable Water: considered safe to drink; not devoid of microorganisms & chemicals - levels low enough that it is not a health concern
- Presence of coliforms in water indicates fecal contamination

Water Quality Testing

- Indicator organisms signal possible presence of pathogens
- E. coli or other coliforms used as indicator organisms
- E. coli is a good indicator organism:
Consistently found in human waste
Survives in water as long as most pathogens
Easily detected
- Mu

Treatment of Wastewater

- Processed to reduce the biochemical oxygen demand (BOD)
- Oxygen needed by aerobic bacteria to metabolize wastes in water
- Levels reduced, too low to support microbial growth

Treatment of Agriculture Waste

- Oxidation Lagoons often used to treat animal waste:
- Waste sits in lagoons for up to 3 months
- Microorganisms break down sediment that settles to the bottom
- Remaining water pumped into secondary lagoon
- Aerobic microbes break down organic chemicals

Environmental Microbiology

- Studies microorganisms as they occur in nature
- Microbes flourish in every habitat on Earth

Microbial Ecology

- Study of the interrelationships among microorganisms and the environment
1. Levels of microbial associations in the environment
- Biodiversity: # of species living within an ecosystem
- Biomass: mass of all organisms in ecosystem
2. Role of adaptation i

Adaptation: Microbial Ecology

- Most microorganisms live in harsh environment; must adapt constantly
- Extremophiles: adapted to extremely harsh conditions
- Competition: best-adapted microbes have advantageous traits
- Antagonism: 1 microbe actively inhibits the growth of another
- B

Bioremediation: Landfills

- Large pit where wastes are dumped, compacted, and buried
- Soil microbes break down biodegradable wastes
- Methanogens degrade organic molecules to methane


- Recalcitrant substances resist decay, degradation, or reclamation by natural means
- Bioremidation uses organisms to clean up toxic, hazardous, or recalcitrant compounds, degrading them to harmless compounds
- Well-known application is use of microbes t

Problem of Acid Mine Drainage

- Results from exposure of certain metal ores to oxygen and microbial action
- Upon exposure to air, iron in water leached from mine tailings is oxidized to Fe3+
- The activity of iron-sulfur bacteria reduces the pH of water to a level that is destructive

Elements Making up Macromolecules


Biogeochemical Cycles

- Processes by which organisms convert elements from one form to another
- Elements often converted between oxidized and reduced forms
- Involve the recycling of elements by organisms

Processes of Biogeochemical Cycles

Production: Inorganic to Organic
Consumption: Primary eaten by secondary (organic to organic)
Decomposition: Organic to Inorganic

Phosphorous Cycle: Role of Microorganisms in Biogeochemical Cycle

- Phosphorous converted from insoluble to soluble form (available for uptake by organism)
- Conversion of phosphorous from organic to inorganic forms (occurs by pH-dependent processes)
- Phosphate-rich runoff can result in eutrophication, which causes ove

The Cycling of Metals: Role of Microorganisms in Biogeochemical Cycle

- Metal ions are important microbial nutrients
- Primarily involves transition from insoluble to soluble forms (allows trace metals to be used by organisms)
- Biomining: Ex: Uranium Minins
- Microbes oxidize metals so the metals dissolve in water
- Extrac

Soil Microbiology

- Examines the roles played by organisms living in soil
- Nature of soils: soil arises from the weathering of rocks; soil also produced through the actions of microorganisms

Factors Affecting Microbial Abundance in Soils

- Moisture content
- Oxygen: most soils are lower in oxygen than dry soils; anaerobes predominate in waterlogged soils
- pH: highly acidic and highly basic soils favor fungi
- Temp: most soil organisms are mesophiles; temp between 3-20 ft. deep is relativ

Microbial Populations: Soil Microbiology

- Bacteria are numerous and found in all soil layers
- Archeae present but difficult to study
- Fungi are populous group of organisms
- Algae live on or near surface of soil
- Most protozoa require oxygen and remain in topsoil

Microbial Functions: Soil Microbiology

- Cycle elements and convert them to useable form
- Degrade dead organisms and their waste
- Produce compounds with potential human uses

Soilborne Disease of Humans and Plants

- Microorganisms deposited in soil in feces or urine
- Soil is a vehicle for transmitting pathogen among host
- Majority of soilborne agents are fungal or bacterial
- Infections acquired by direct contact, ingestion, inhalation

Aquatic Microbiology

- Study of microbes living in freshwater and marine environments
- Water ecosystems support fewer microbes than soil due to dilution of nutrients
- Many organisms exist in biofilms attached to surfaces which allow organisms to concentrate nutrients
- Dome

Freshwater Systems

- Groundwater, wells, springs, surface waters

Marine Systems

Characterized by a salt content of about 3.5%
- Open oceans and costal waters

Vertical Zonation in Deep Bodies of Water

Littoral Zone (highest layer, high nutrients, high microorganisms, higher temp., lower pressure)
Limnetic Zone
Profundal Zone
Benthic Zone
Abyssal Zone (deepest layer, lowest nutrients, low # of microorganisms, low temp, high pressure)

Specialized Novel Aquatic Ecosystems

Salt lakes, iron springs, sulfur springs
- Inhabited by microorganisms adapted to the conditions
- Halobacterium salinarium survives the highly saline water of Great Salt Lake


- Uses microbes or their toxins to terrorize human populations
Ex: Anthrax


- Uses microbes to terrorize human populations by destroying the food supply

Criteria for Assessing Biological Threats to Humans

1. Public Health Impact: ability of hospitals and clinics to handle the casualties
2. Delivery Potential: how easily agent can be introduced into the population
3. Public Perception: effect of public fear on ability to control an outbreak
4. Public Health

Criteria for Assessing Biological Threats to Livestock & Poultry

- Similar to those used to evaluate potential human threats
- Threats: Agricultural impact, delivery potential, plausible deniability
- Livestock in herds or flocks most susceptible to infectious agents
- Spread by contact or inhalation - easier for terro

Criteria for Assessing Biological Threats to Agriculture Crops

- Plant diseases often less contagious than animal/human threats
- Threats: predicted extent of crop loss, delivery & dissemination potential, containment potential
- Greatest threats are pathogens that cause crop loss or produce toxins: such agents exist

Known Types of Microbial Threats

1. Human pathogens
2. Animal pathogens
3. Plant pathogens

Animal Pathogens: Microbial Threats

- Divided into categories based on level of danger
- Some agents could potentially amplify an outbreak: infect wild animal populations in addition to livestock
- Foot-and-Mouth Disease: most dangerous; affects all wild and domestic cloven-hoofed animals;

Plant Pathogens: Microbial Threats

- Most potential agents are fungi
- Dissemination could easily result in contamination of soils
- All agents are naturally present: detecting difference between a natural outbreak and an intentional attack would be difficult

Defense Against Bioterrorism

- Key is coupling surveillance with effect response protocols
- Category A diseases are reportable: must be reported to state health departments when occur; active monitoring helps identify unusual outbreaks
- Forced quarantine, distribution of antimicrob

Defense Against Agroterrroism

- Little security
- Livestock and poultry often not checked for disease
- Facilities open to public
- Methods to help defend: screening of animals; restricting public access

Roles of Recombinant Genetic Technology in Bioterrorism

- Could use to create new or modify biological threats
- Could combine traits of various agents to create novel agents - no immunity would exist in population
- Terrorist could make own microbe
- Genetic sequencing: could aid in tracking and determining t