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Chapter 25. Applied and Environmental Microbiology. 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

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Chapter 25

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Applied and environmental microbiology

Chapter 25

Applied and Environmental Microbiology


Food microbiology

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

© 2012 Pearson Education Inc.


Food microbiology1

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

© 2012 Pearson Education Inc.


Food microbiology2

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

© 2012 Pearson Education Inc.


Figure 25 1 the cheese making process

Pasteurization killsunwanted microorganisms

Figure 25.1 The cheese-making process

Addition of starterbacterial culture

Coagulation of milkproteins (curd formation)

Production ofunprocessedcheeses

Disposal ofliquid whey aswaste product

Cutting of curds

Production of processedcheeses through pressing,addition of secondarymicrobial cultures, andaging (ripening)


Food microbiology3

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

© 2012 Pearson Education Inc.


Figure 25 2 the wine making process

Preparation of must by stemmingand crushing of grapes (or other fruit)

Figure 25.2 The wine-making process

Addition of starter cultureof yeast and bacteria

Fermentationof must(crushedfruit) or ofjuice aloneinto wine

Clarificationof wine

Aging of wine

Bottling of wine


Figure 25 3 the beer brewing process

Barley is moistened and germinated,producing enzymes that convertstarch into sugars. Barley is then driedto halt germination, and crushed toproduce malt.

Figure 25.3 The beer-brewing process

Mashing malt andadjuncts with warmwater allowsenzymatic activityto generate moresugars. Solids areremoved toproduce wort.

Mashing kettle

Addition of hops for flavoring

Cooking of wort halts enzymaticactivity, extracts flavor from hops,and kills the microorganisms present.

Removalof hops

Addition of yeast culture

Wort fermentsinto beer.

Aging, filteringor pasteurization,and bottlingfinish theprocess.


Food microbiology4

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

© 2012 Pearson Education Inc.


Table 25 2 factors affecting food spoilage

Table 25.2 Factors Affecting Food Spoilage


Food microbiology5

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

© 2012 Pearson Education Inc.


Food microbiology6

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

© 2012 Pearson Education Inc.


Figure 25 4 industrial canning

Figure 25.4 Industrial canning


Food microbiology7

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

© 2012 Pearson Education Inc.


Food microbiology8

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

© 2012 Pearson Education Inc.


Food microbiology9

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

© 2012 Pearson Education Inc.


Industrial microbiology

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

© 2012 Pearson Education Inc.


Industrial microbiology1

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

© 2012 Pearson Education Inc.


Industrial microbiology2

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

© 2012 Pearson Education Inc.


Figure 25 5 fermentation vats

Figure 25.5 Fermentation vats


Industrial microbiology3

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

© 2012 Pearson Education Inc.


Industrial microbiology4

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

© 2012 Pearson Education Inc.


Figure 25 6 burning methane gas released from a landfill

Figure 25.6 Burning methane gas released from a landfill


Industrial microbiology5

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

© 2012 Pearson Education Inc.


Industrial microbiology6

Industrial Microbiology

Water Treatment

Water pollution

Water pollution can occur three ways

Physically

Chemically

Biologically

Polluted waters support a greater than normal microbial load

© 2012 Pearson Education Inc.


Industrial microbiology7

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

© 2012 Pearson Education Inc.


Industrial microbiology8

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

© 2012 Pearson Education Inc.


Figure 25 7 the treatment of drinking water overview

Figure 25.7 The treatment of drinking water-overview


Industrial microbiology9

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

© 2012 Pearson Education Inc.


Figure 25 8 two water quality tests overview

Figure 25.8 Two water quality tests-overview


Industrial microbiology10

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

© 2012 Pearson Education Inc.


Figure 25 9 traditional sewage treatment overview

Figure 25.9 Traditional sewage treatment-overview


Figure 25 10 a home septic system

Figure 25.10 A home septic system

Filtration in leach field

Sedimentation in septic tank

House

Pipes beneath ground distributewater through leach field

Sludge(must be pumped out eventually)


Figure 25 11 wastewater treatment in an artificial wetland

Aerobic digestionof wastes in watercolumn

Anaerobic digestionof wastes in sludge

Soil microbes digest organics

Algae continuedigestion oforganics

Grasses filterout pollutants

Figure 25.11 Wastewater treatment in an artificial wetland

Houses and businessesof planned communityrelease sewage

Pond 1: Aeration

Marsh

Pond 2: Still water

Meadow

Water

Water

Water

Water release into thirdpond or waterway


Environmental microbiology

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

© 2012 Pearson Education Inc.


Environmental microbiology1

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

© 2012 Pearson Education Inc.


Applied and environmental microbiology

Biosphere

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

Heterogeneousmicrobial communities(all guilds together)

Soilecosystem

Guilds of relatedpopulations(e.g., photosyntheticmicroorganisms at surface)

Soilhabitats

Populations of microbesinhabit microhabitats(e.g., cyanobacteria, algae)

Soil particlemicrohabitats


Environmental microbiology2

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

© 2012 Pearson Education Inc.


Environmental microbiology3

Environmental Microbiology

Microbial Ecology

Role of adaptation in microbial survival

Biodiversity held in balance by various checks

Competition

Antagonism

Cooperation

© 2012 Pearson Education Inc.


Environmental microbiology4

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

© 2012 Pearson Education Inc.


Industrial microbiology11

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

© 2012 Pearson Education Inc.


Industrial microbiology12

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

© 2012 Pearson Education Inc.


Figure 25 13 the effects of acid mine drainage

Figure 25.13 The effects of acid mine drainage


Figure 25 14 an acid loving microbe

Figure 25.14 An acid-loving microbe


Environmental microbiology5

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

© 2012 Pearson Education Inc.


Environmental microbiology6

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

© 2012 Pearson Education Inc.


Figure 25 15 simplified carbon cycle

Atmospheric CO2 and CO2dissolved in water

Figure 25.15 Simplified carbon cycle

Combustion

Fixation(into organic carbon)

Respiration

Decomposition

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

Methane

Consumption

Animals

Fungi, bacteria

Dead organisms

Fossil fuels

Plastics andother artificialproducts


Figure 25 16 simplified nitrogen cycle

Nitrogen fixation

N2 in atmosphere

Figure 25.16 Simplified nitrogen cycle

Denitrification

Organisms(proteins, nucleicacids, etc.)

NH3

NO2

Anammox reactions

Ammonification

Wastes,dead cells

Deamination

Nitrification

NO3

NH4

NO2


Figure 25 17 simplified sulfur cycle

Proteins fromdead organisms

Aminoacids

Figure 25.17 Simplified sulfur cycle

Animalproteins

Dissimilation

Plant, algal, andprokaryotic proteins

Oxidation

Reduction

SO42

H2S

S0

Oxidation


Environmental microbiology7

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 pH–dependent processes

© 2012 Pearson Education Inc.


Environmental microbiology8

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

© 2012 Pearson Education Inc.


Environmental microbiology9

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

© 2012 Pearson Education Inc.


Figure 25 18 the soil layers and the distributions of nutrients and microorganisms within them

Organics,nutrients

Numbers ofmicroorganisms

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

Topsoil

Decreasewith depth

Decreasewith depthbut stillpresent inbedrock

Subsoil

Bedrock


Environmental microbiology10

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

© 2012 Pearson Education Inc.


Environmental microbiology11

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

© 2012 Pearson Education Inc.


Environmental microbiology12

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

© 2012 Pearson Education Inc.


Table 25 7 selected soilborne diseases of humans and plants

Table 25.7 Selected Soilborne Diseases of Humans and Plants


Environmental microbiology13

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

Marinesystems – characterized by a salt content of ~3.5%

Specialized aquatic systems – salt lakes, iron springs, and sulfur springs

© 2012 Pearson Education Inc.


Environmental microbiology14

Environmental Microbiology

Aquatic Microbiology

Types of aquatic habitats

Freshwater systems

Characterized by low salt content

Marinesystems

Characterized by a salt content of ~3.5%

Specialized aquatic systems

Salt lakes, iron springs, and sulfur springs

© 2012 Pearson Education Inc.


Figure 25 19 vertical zonation in deep bodies of water overview

Figure 25.19 Vertical zonation in deep bodies of water-overview


Biological warfare and bioterrorism

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

© 2012 Pearson Education Inc.


Biological warfare and bioterrorism1

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

© 2012 Pearson Education Inc.


Biological warfare and bioterrorism2

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

© 2012 Pearson Education Inc.


Biological warfare and bioterrorism3

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

© 2012 Pearson Education Inc.


Biological warfare and bioterrorism4

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

© 2012 Pearson Education Inc.


Biological warfare and bioterrorism5

Biological Warfare and Bioterrorism

Known Microbial Threats

Various microorganisms considered threats as agents of bioterrorism

Three types

Human pathogens

Animal pathogens

Plant pathogens

© 2012 Pearson Education Inc.


Table 25 8 bioterrorist threats to humans in order of concern

Table 25.8 Bioterrorist Threats to Humans in Order of Concern


Biological warfare and bioterrorism6

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

© 2012 Pearson Education Inc.


Biological warfare and bioterrorism7

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

© 2012 Pearson Education Inc.


Biological warfare and bioterrorism8

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

© 2012 Pearson Education Inc.


Figure 25 20 one aspect of the response to a bioterrorist attack

Figure 25.20 One aspect of the response to a bioterrorist attack


Biological warfare and bioterrorism9

Biological Warfare and Bioterrorism

Defense Against Bioterrorism

Agroterrorism

Little security protecting nation’s 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

© 2012 Pearson Education Inc.


Biological warfare and bioterrorism10

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

© 2012 Pearson Education Inc.


Biological warfare and bioterrorism11

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

© 2012 Pearson Education Inc.


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