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Chapter 22

Applied and Environmental Microbiology

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Lecture prepared by Mindy Miller-Kittrell North Carolina State University

Food Microbiology

Microorganisms are involved in producing many foods and beverages Fermentation produces desirable characteristics of various foods Microbial metabolism has other functions
Acts as a preservative Destroys many pathogenic microbes and toxins Can add nutritional value in form of vitamins or other nutrients

Microbes are used in food production Microbes can help control food spoilage
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Food Microbiology

The Roles of Microorganisms in Food Production


Fermentation
Any desirable change to a food or beverage that occurs as a result of microbial growth

Spoilage is unwanted change to a food due to various reasons


Undesirable metabolic reactions Growth of pathogens Presence of unwanted microorganisms in the food
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Food Microbiology

The Roles of Microorganisms in Food Production


Use starter cultures in commercial food and beverage production
Composed of known microorganisms
Consistently perform specific fermentations

Many common products result from fermentation of vegetables, meats, and dairy products

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Figure 25.1 The cheese-making process

Pasteurization kills unwanted microorganisms Addition of starter bacterial culture

Coagulation of milk proteins (curd formation)

Disposal of liquid whey as waste product

Production of unprocessed cheeses

Cutting of curds

Production of processed cheeses through pressing, addition of secondary microbial cultures, and aging (ripening)

Food Microbiology

The Roles of Microorganisms in Food Production


Products of alcoholic fermentation
Alcoholic fermentation
Microorganisms convert simple sugars into alcohol and carbon dioxide

Specific starter cultures used in commercial applications of alcohol fermentation Various alcoholic products made through fermentation

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Figure 25.2 The wine-making process

Preparation of must by stemming and crushing of grapes (or other fruit) Addition of starter culture of yeast and bacteria Fermentation of must (crushed fruit) or of juice alone into wine

Clarification of wine

Aging of wine

Bottling of wine

Figure 25.3 The beer-brewing process


Barley is moistened and germinated, producing enzymes that convert starch into sugars. Barley is then dried to halt germination, and crushed to produce malt.

Mashing malt and adjuncts with warm water allows enzymatic activity to generate more sugars. Solids are removed to produce wort.

Mashing kettle

Addition of hops for flavoring

Cooking of wort halts enzymatic activity, extracts flavor from hops, and kills the microorganisms present. Removal of hops Addition of yeast culture

Wort ferments into beer.

Aging, filtering or pasteurization, and bottling finish the process.

Food Microbiology

The Causes of Food Spoilage


Food spoilage results from intrinsic or extrinsic factors
Intrinsic factors are inherent properties of the food itself Extrinsic factors involved with processing or handling of food

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Table 25.2 Factors Affecting Food Spoilage

Food Microbiology

The Causes of Food Spoilage


Classifying foods in terms of potential for spoilage
Three categories based on likelihood of spoilage
Perishable
Nutrient rich, moist, and unprotected by coverings

Semi-perishable
Can store sealed for months without spoiling Many fermented foods are semi-perishable

Nonperishable
Dry or canned foods that can be stored indefinitely Often nutrient poor, dried, fermented, or preserved

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Food Microbiology

The Causes of Food Spoilage


The prevention of food spoilage
Food-processing methods
Industrial canning
Eliminates mesophilic bacteria and endospores

Pasteurization
Lowers microbe numbers, but some microbes survive

Lyophilization
A vacuum draws off ice crystals from frozen foods

Gamma radiation
Can achieve complete sterilization

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Figure 25.4 Industrial canning

Food Microbiology

The Causes of Food Spoilage


The prevention of food spoilage
Use of preservatives
Salt and sugar remove water from the food Garlic contains allicin, which inhibits enzyme function Benzoic acid interferes with enzymatic function Certain spices and herbs interfere with the functions of membranes of microorganisms Chemical preservatives can be purposely added to foods

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Food Microbiology

The Causes of Food Spoilage


The prevention of food spoilage
Attention to temperature during processing and storage
High temperatures desirable to prevent food spoilage
Proteins and enzymes become denatured

Low temperatures are desirable for food storage


Cold slows metabolism and retards microbial growth Listeria monocytogenes can grow in cold storage Found in certain dairy products

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Food Microbiology

Foodborne Illnesses
Consumption of spoiled foods or foods containing harmful microbes or their products Two categories of food poisoning
Food infections
Consumption of living microorganisms

Food intoxications
Consumption of microbial toxins rather than the microbe

Symptoms include nausea, vomiting, diarrhea, fever, fatigue, and muscle cramps
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Industrial Microbiology

Important field within the microbiological sciences Industrial microbiology used in various applications
Microbes in fermentation Microbes in the production of several industrial products Treatment of water and wastewaters Disposal and cleanup of biological wastes Treatment of mine drainage
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Industrial Microbiology

The Roles of Microbes in Industrial Fermentations


Industrial fermentations
Large-scale growth of particular microbes for producing beneficial compounds Examples include amino acids and vitamins

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Industrial Microbiology

The Roles of Microbes in Industrial Fermentations


Primary metabolites
Produced during active growth and metabolism Required for reproduction or are by-products of metabolism

Secondary metabolites
Produced after the culture has entered stationary growth Substances are not immediately needed for growth
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Figure 25.5 Fermentation vats

Industrial Microbiology

Industrial Products of Microorganisms


Microorganisms produce array of industrially useful chemicals Recombinant organisms add to this diversity
Produce substances not normally made by microbial cells

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Industrial Microbiology

Industrial Products of Microorganisms


Enzymes and other industrial products
Microbial products used as food additives and supplements Include vitamins, amino acids, organic acids, dyes

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

Pharmaceuticals
Includes antimicrobials, recombinant hormones, and other cell regulators
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Figure 25.6 Burning methane gas released from a landfill

Industrial Microbiology

Industrial Products of Microorganisms


Pesticides and agricultural products
Microbes used to help crop management

Biosensors and bioreporters


Use of microorganisms to solve environmental problems Biosensors
Bacteria or microbial products combined with electronic measuring devices

Bioreporters
Composed of microbes with innate signaling capabilities
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Industrial Microbiology

Water Treatment
Water pollution
Water pollution can occur three ways
Physically Chemically Biologically

Polluted waters support a greater than normal microbial load

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Industrial Microbiology

Water Treatment
Waterborne illnesses
Consuming contaminated water can cause various diseases
Diarrheal diseases occur worldwide

Waterborne diseases rare in the United States


Outbreaks are point-source infections

Water treatment removes most waterborne pathogens

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Industrial Microbiology

Water Treatment
Treatment of drinking water
Potable water is water considered safe to drink
Water is not devoid of microorganisms and chemicals
Levels are low enough that they are not a health concern

Presence of coliforms in water indicates fecal contamination


Increased likelihood that disease-causing microbes are present

Treatment of drinking water involves four stages


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Figure 25.7 The treatment of drinking water-overview

Industrial Microbiology

Water Treatment
Water quality testing
Majority of waterborne illnesses caused by fecally contaminated water 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 by simple tests

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Figure 25.8 Two water quality tests-overview

Industrial Microbiology

Water Treatment
Treatment of wastewater
Wastewater
Water that leaves homes or businesses after use

Wastewater contains a variety of contaminants Treatment intended to remove or reduce contaminants Processed to reduce the biochemical oxygen demand (BOD)
Oxygen needed by aerobic bacteria to metabolize wastes Levels reduced so unable to support microbial growth
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Figure 25.9 Traditional sewage treatment-overview

Figure 25.10 A home septic system

Sedimentation in septic tank

Filtration in leach field

House

Sludge (must be pumped out eventually)

Pipes beneath ground distribute water through leach field

Figure 25.11 Wastewater treatment in an artificial wetland

Houses and businesses of planned community release sewage

Pond 1: Aeration
Aerobic digestion of wastes in water column Anaerobic digestion of wastes in sludge Water

Marsh
Soil microbes digest organics Water

Pond 2: Still water


Algae continue digestion of organics Water

Meadow
Grasses filter out pollutants

Water release into third pond or waterway

Environmental Microbiology

Studies the microorganisms as they occur in their natural habitats Microbes flourish in every habitat on Earth Microbes are important to the cycling of chemical elements

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Environmental Microbiology

Microbial Ecology
Study of the interrelationships among microorganisms and the environment Two aspects to consider
Levels of microbial associations in the environment Role of adaptation in microbial survival

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Figure 25.12 The basic relationships among microorganisms and between microorganisms and the environment

Biosphere

Soil ecosystem

Heterogeneous microbial communities (all guilds together)

Soil habitats

Guilds of related populations (e.g., photosynthetic microorganisms at surface)

Soil particle microhabitats

Populations of microbes inhabit microhabitats (e.g., cyanobacteria, algae)

Environmental Microbiology

Microbial Ecology
Role of adaptation in microbial survival
Most microorganisms live in harsh environments
Microbes must be specially adapted to survive

Microbes must adapt to constantly varying conditions Extremophiles


Adapted to extremely harsh conditions
Can survive only in these habitats

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Environmental Microbiology

Microbial Ecology
Role of adaptation in microbial survival
Biodiversity held in balance by various checks Competition Antagonism Cooperation

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Environmental Microbiology

Bioremediation
Uses organisms to clean up toxic, hazardous, or recalcitrant compounds by degrading them to harmless compounds Most known application is use of bacteria to clean oil spills

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Industrial Microbiology

Two Types of Bioremediation


Natural bioremediation
Microbes encouraged to degrade toxic substances in soil or water Addition of nutrients stimulate microbe growth

Artificial bioremediation
Genetically modified microbes degrade specific pollutants

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Industrial Microbiology

The Problem of Acid Mine Drainage


Drainage results from exposure of certain metal ores to oxygen and microbial action Resulting compounds are carried into streams and rivers
Causes decrease in pH
Can kill fish, plants, and other organisms Acidic water unfit for human consumption

Some microbes flourish in these acidic conditions

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Figure 25.13 The effects of acid mine drainage

Figure 25.14 An acid-loving microbe

Environmental Microbiology

Role of Microorganisms in Biogeochemical Cycles


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

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Environmental Microbiology

Role of Microorganisms in Biogeochemical Cycles


Biogeochemical cycling entails three processes
Production
Inorganic compounds converted into organic compounds

Consumption
Organisms feed on producers and other consumers

Decomposition
Organic compounds in dead organisms converted into inorganic compounds

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Figure 25.15 Simplified carbon cycle

Atmospheric CO2 and CO2 dissolved in water

Decomposition

Fixation
(into organic carbon)

Respiration

Combustion

Autotrophs (plants, algae, photosynthetic bacteria, protozoa, chemoautotrophic bacteria)

Methane Fungi, bacteria

Consumption
Animals

Dead organisms

Fossil fuels

Plastics and other artificial products

Figure 25.16 Simplified nitrogen cycle

Nitrogen fixation
N2 in atmosphere

Denitrification
Organisms (proteins, nucleic acids, etc.) NO2 NH3

Ammonification
Wastes, dead cells
Deamination

Nitrification
NO3 NO2 NH4

Anammox reactions

Figure 25.17 Simplified sulfur cycle

Amino acids

Proteins from dead organisms

Animal proteins

Dissimilation
Plant, algal, and prokaryotic proteins

Reduction

SO4

Oxidation

H 2S

Oxidation

S0

Environmental Microbiology

Role of Microorganisms in Biogeochemical Cycle


Phosphorus cycle
Environmental phosphorus undergoes little change in oxidation state Phosphorus converted from insoluble to soluble forms Becomes available for uptake by organisms Conversion of phosphorus from organic to inorganic forms
Occurs by pHdependent processes
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Environmental Microbiology

Role of Microorganisms in Biogeochemical Cycle


The cycling of metals
Metal ions are important microbial nutrients Primarily involves transition from insoluble to soluble forms
Allows trace metals to be be used by organisms

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Environmental Microbiology

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

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Figure 25.18 The soil layers and the distributions of nutrients and microorganisms within them

Organics, nutrients
Topsoil

Numbers of microorganisms Decrease with depth but still present in bedrock

Decrease with depth

Subsoil

Bedrock

Environmental Microbiology

Soil Microbiology
Environmental factors affecting microbial abundance in soils
Moisture content
Moist soils support microbial growth better than dry soils

Oxygen
Moist soils are lower in oxygen than dry soils
Oxygen dissolves poorly in water

pH
Highly acidic and highly basic soils favor fungi
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Environmental Microbiology

Soil Microbiology
Environmental factors affecting microbial abundance in soils
Temperature
Most soil organisms are mesophiles

Nutrient availability
Microbial community size determined by how much organic material is available

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Environmental Microbiology

Soil Microbiology
Microbial populations in soils
Microbial populations present in the soil
Bacteria Archaea Fungi Algae and protozoa

Microbes perform a number of functions


Cycle elements and convert them to usable form Degrade dead organisms Produce compounds with potential human uses
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Table 25.7 Selected Soilborne Diseases of Humans and Plants

Environmental Microbiology

Aquatic Microbiology
Study of microbes living in freshwater and marine environments Water ecosystems support fewer microbes than soil
Due to dilution of nutrients

Types of aquatic habitats


Freshwater systems characterized by low salt content Marine systems characterized by a salt content of ~3.5% Specialized aquatic systems salt lakes, iron springs, and sulfur springs
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Environmental Microbiology

Aquatic Microbiology
Types of aquatic habitats
Freshwater systems
Characterized by low salt content

Marine systems
Characterized by a salt content of ~3.5%

Specialized aquatic systems


Salt lakes, iron springs, and sulfur springs

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Figure 25.19 Vertical zonation in deep bodies of water-overview

Biological Warfare and Bioterrorism

Microbes can be fashioned into biological weapons Bioterrorism


Uses microbes or their toxins to terrorize human populations

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

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Biological Warfare and Bioterrorism

Assessing Microorganisms as Potential Agents of Warfare or Terror


Not all organisms have potential as biological weapons Governments have criteria to assess biological threats to humans
Evaluate the potential of microorganisms to be weaponized Help focus research and defense efforts where needed

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Biological Warfare and Bioterrorism

Assessing Microorganisms as Potential Agents of Warfare or Terror


Criteria for biological threats to humans based on:
Public health impact
Ability of hospitals and clinics to handle the casualties

Delivery potential
How easily agent can be introduced into the population

Public perception
Effect of public fear on ability to control an outbreak

Public health preparedness


Existing response measures
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Biological Warfare and Bioterrorism

Assessing Microorganisms as Potential Agents of Warfare or Terror


Criteria for assessing biological threats to livestock and poultry
Criteria similar to those used to evaluate potential human threats Include agricultural impact, delivery potential, and plausible deniability

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Biological Warfare and Bioterrorism

Assessing Microorganisms as Potential Agents of Warfare or Terror


Criteria for assessing biological threats to agriculture crops
Plant diseases generally not as contagious as animal or human diseases Criteria based on several factors
Predicted extent of crop loss Delivery and dissemination potential Containment potential

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Biological Warfare and Bioterrorism

Known Microbial Threats


Various microorganisms considered threats as agents of bioterrorism Three types
Human pathogens Animal pathogens Plant pathogens

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Table 25.8 Bioterrorist Threats to Humans in Order of Concern

Biological Warfare and Bioterrorism

Known Microbial Threats


Animal pathogens
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 is most dangerous of the agents


It affects all wild and domestic cloven-hoofed animals

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Biological Warfare and Bioterrorism

Known Microbial Threats


Plant pathogens
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

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Biological Warfare and Bioterrorism

Defense Against Bioterrorism


Much can be done to limit impact of an attack Key is coupling surveillance with effective response protocols

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Figure 25.20 One aspect of the response to a bioterrorist attack

Biological Warfare and Bioterrorism

Defense Against Bioterrorism


Agroterrorism
Little security protecting nations agricultural enterprises Livestock and poultry often moved without being tested for disease Many agricultural facilities are open to the public Methods to help defend against agroterrorism
Screening of animals Restricting public access to agricultural facilities

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Biological Warfare and Bioterrorism

The Roles of Recombinant Genetic Technology in Bioterrorism


Could use to create new or modify biological threats
Traits of various agents could be combined to create novel agents
No immunity would exist in the population

Terrorists theoretically could make their own microbes

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Biological Warfare and Bioterrorism

The Roles of Recombinant Genetic Technology in Bioterrorism


Could be used to thwart bioterrorism
Scientists can identify unique genetic sequences
May aid in tracking biological agents and determining their source

Genetic techniques could help develop vaccines, treatments, and pathogen-resistant crops

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