Applied Microbiology

Applied MicrobiologyApplied Microbiology

Applied MicrobiologyApplied Microbiology

applied microbiology is the interaction of applied microbiology is the interaction of the microbial world and the rest of the the microbial world and the rest of the worldworld– genetic variancesgenetic variances– microbial effect on soil, water, our microbial effect on soil, water, our

foodfoodmicroorganisms are present in most microorganisms are present in most every aspect of our livesevery aspect of our lives– microorganisms are critical to our microorganisms are critical to our

survival on Earthsurvival on Earthto be a successful ecosystem on Earth, to be a successful ecosystem on Earth, you’d best be nice to the you’d best be nice to the microorganisms!microorganisms!

Microbial EcologyMicrobial Ecology:: relationship of microorganisms with each relationship of microorganisms with each

other and their environmentother and their environment

ecosystem: interaction of living ecosystem: interaction of living and non-living componentsand non-living components– oceans, deserts, marshes, oceans, deserts, marshes,

forests, tundra, lakesforests, tundra, lakes– microorganisms play a key microorganisms play a key

role in ecosystem structurerole in ecosystem structure

Microbial Ecology:Microbial Ecology: relationship of microorganisms with each other and relationship of microorganisms with each other and

their environmenttheir environment

microenvironment: immediately microenvironment: immediately surrounds a microorganismsurrounds a microorganism

– relevant to survival and growth relevant to survival and growth of the microorganismof the microorganism

Nutrient Acquisition within an Nutrient Acquisition within an EcosystemEcosystem

3 main levels exist in every ecosystem in regards to 3 main levels exist in every ecosystem in regards to nutrient acquisitionnutrient acquisition– producerproducer– consumerconsumer– decomposerdecomposer

1. primary producers: 1. primary producers: convert COconvert CO22 to to

organic materialorganic material


2. consumers2. consumers– heterotrophsheterotrophs– utilize organic material utilize organic material

created by producerscreated by producers


3. decomposers3. decomposers– heterotrophsheterotrophs– digest leftovers of primary digest leftovers of primary

producers and consumersproducers and consumersdetritus ( fresh or partially detritus ( fresh or partially decomposed organic decomposed organic matter)matter)

– bacteria and fungi are key bacteria and fungi are key players in the process of players in the process of decompositiondecomposition

Low Nutrient Environments: Low Nutrient Environments: common in naturecommon in nature

bacteria do best in biofilms if nutrition bacteria do best in biofilms if nutrition availability is lowavailability is low– biofilms are a polysaccharide biofilms are a polysaccharide

encased community of encased community of microorganismsmicroorganisms

– microorganisms extract nutrients microorganisms extract nutrients that are absorbed by water from air that are absorbed by water from air or nutrients that are adsorbed onto or nutrients that are adsorbed onto the biofilmthe biofilm

Microbial competition and antagonismMicrobial competition and antagonism

most environments are suitable to many kinds of most environments are suitable to many kinds of microorganismsmicroorganismsonly one or a few can actually occupy the environment only one or a few can actually occupy the environment at a given timeat a given time

Competition and Antagonism: Competition and Antagonism: among microorganismsamong microorganisms

competition:competition:– fierce competition for nutrients and waterfierce competition for nutrients and water– the faster a microbe reproduces the larger the the faster a microbe reproduces the larger the

populationpopulation– the larger population competes betterthe larger population competes better

critical, especially if the microorganisms critical, especially if the microorganisms competing utilize similar nutrientscompeting utilize similar nutrients

antagonismantagonism– bacteriocins: protein produced by bacteria that bacteriocins: protein produced by bacteria that

destroys similar strainsdestroys similar strains

““WINNER TAKES ALL AND IS KING/QUEEN OF THE WINNER TAKES ALL AND IS KING/QUEEN OF THE MICROBIAL ECOSYSTEM”MICROBIAL ECOSYSTEM”

Example of CompetitionExample of Competition

stability of microbial community in human intestine is stability of microbial community in human intestine is attributed to competition and antagonism amongst its attributed to competition and antagonism amongst its membersmembers– compete nicely for nutrientscompete nicely for nutrients– produce toxins to limit growth of new microbesproduce toxins to limit growth of new microbes

Environmental Change affect microbial Environmental Change affect microbial populationpopulation

environmental fluctuations are common and resident environmental fluctuations are common and resident microorganisms may respond bymicroorganisms may respond by– producing enzymes to help adapt to changing producing enzymes to help adapt to changing

environmentenvironmentadditional or different enzymes may be necessary additional or different enzymes may be necessary for survival for survival

– mutationmutation– domination by other species (can’t compete any domination by other species (can’t compete any

more)more)

Microbial Mat:Microbial Mat: thick, dense, organized biofilm thick, dense, organized biofilm

generally found attached to a solid substrate or at air-generally found attached to a solid substrate or at air-water interfaceswater interfaces

Microbial mat attached to rocks

Microbial mat in stream bed

The Study of Microbial EcologyThe Study of Microbial Ecologysomewhat difficult to accomplishsomewhat difficult to accomplish– less than 1% of less than 1% of

environmental environmental microorganisms can be microorganisms can be successfully cultured in the successfully cultured in the lablab

Microbial HabitatMicrobial Habitataquaticaquatic– marine: marine:

deep waters are usually stable and consistentdeep waters are usually stable and consistentshoreline habitat varies due to nutrient rich run-offshoreline habitat varies due to nutrient rich run-off

Microbial HabitatMicrobial Habitatfreshwater:freshwater:– lakeslakes

stratification allows for the mixing of the water stratification allows for the mixing of the water seasonally. seasonally. Increases the presence of OIncreases the presence of O22 in the deeper H in the deeper H22OO

algae

paramecium

Microbial HabitatMicrobial Habitat

moving watermoving water– riversrivers

generally aerobic due to generally aerobic due to turbulence facilitating Oturbulence facilitating O22 circulationcirculation

river ostracod

Microbial HabitatMicrobial Habitat

terrestrialterrestrial– microorganisms are critical to soil habitatmicroorganisms are critical to soil habitat

composition of microbes is dependent on soil composition of microbes is dependent on soil conditionsconditionswet soil: anaerobic conditions due to water filling wet soil: anaerobic conditions due to water filling the pore space in the soil, soil dries and microbes the pore space in the soil, soil dries and microbes go produce endospores for survivalgo produce endospores for survival

Endospores

Mutualism with EukaryotesMutualism with Eukaryotes

mychorrhizae: fungusmychorrhizae: fungus– assist plants in the uptake of assist plants in the uptake of

phosphorousphosphorous– mychorrizae gain nutrient from plantmychorrizae gain nutrient from plant

MutualismMutualism

nitrogen fixers: fix nitrogen nitrogen fixers: fix nitrogen and make it available for and make it available for the use by their partner the use by their partner plantplant– most common is most common is

RhizobiumRhizobium, a , a microorganism found in microorganism found in many root nodulesmany root nodules

Rhizobium in root nodules

Nitrogen CycleNitrogen Cycle

Mutualism: microorganisms and the Mutualism: microorganisms and the worldworld

microorganisms and herbivoresmicroorganisms and herbivores– animal with a rumens (cow) or cecums animal with a rumens (cow) or cecums

(horse) need microorganisms to digest the (horse) need microorganisms to digest the plant food they ingestplant food they ingest

Bacillus in a cow rumen

Microorganisms in Sewage TreatmentMicroorganisms in Sewage Treatmentdecreasing biochemical decreasing biochemical oxygen demand (BOD) oxygen demand (BOD) decreases impact of decreases impact of sewage on the sewage on the environmentenvironmentBOD is the amount of OBOD is the amount of O22 needed for microbial needed for microbial decomposition of the decomposition of the organic material in a organic material in a samplesample

Grit chamber

Biological filter

Clarifier

Microorganisms in Sewage Microorganisms in Sewage TreatmentTreatment

if if not treated the high BOD found in sewage could not treated the high BOD found in sewage could deplete the Odeplete the O22 level in the receiving water level in the receiving water

in other words if raw sewage is deposited into a lake or in other words if raw sewage is deposited into a lake or stream without treatment, it would effectively suck the stream without treatment, it would effectively suck the oxygen out of the water, leaving very little for the fish and oxygen out of the water, leaving very little for the fish and other organismsother organisms

Microorganisms in Sewage TreatmentMicroorganisms in Sewage Treatmentsewage treatment is a controlled process that sewage treatment is a controlled process that strives to eliminate the excess organic material, strives to eliminate the excess organic material, thus diminishing the BODthus diminishing the BOD– most of the removal of organic matter is done most of the removal of organic matter is done

by microorganismsby microorganisms

bacterial filaments

Microorganisms and Water Treatment Microorganisms and Water Treatment and Testingand Testing

municipal water supplies municipal water supplies are tested and treated for are tested and treated for the removal of pathogenic the removal of pathogenic microorganisms and microorganisms and chemicalschemicals– this is done with the this is done with the

use of chemicalsuse of chemicals

Microorganisms and Solid Waste Microorganisms and Solid Waste TreatmentTreatment

the elimination of organic waste the elimination of organic waste material can be enhanced by material can be enhanced by microorganismsmicroorganisms– increase cost to separate organic increase cost to separate organic

material from inorganic (glass, material from inorganic (glass, metal, plastic)metal, plastic)

– composting: natural decomposition composting: natural decomposition of organic solid materiel results in of organic solid materiel results in excellent fertilizerexcellent fertilizer

CompostCompost

microorganisms are needed to breakdown the organic material

Bioremediation: Bioremediation: use of microorganisms to eliminate or make use of microorganisms to eliminate or make

harmless pollutants in an environmentharmless pollutants in an environment

pollutants removed pollutants removed can includecan include– organic solventsorganic solvents– toxic chemicalstoxic chemicals– hydrocarbonshydrocarbons

oil spill

BioremediationBioremediation

introduces specific organisms to the polluted areaintroduces specific organisms to the polluted area– many toxic substances are man-made/new to the many toxic substances are man-made/new to the

environment (xenobiotics)environment (xenobiotics)– no time for naturally occurring microbes to have no time for naturally occurring microbes to have

evolved biochemical pathways for their degradationevolved biochemical pathways for their degradationscientists are trying to develop new microbes for the scientists are trying to develop new microbes for the degradation of environmental pollutersdegradation of environmental polluters

Cleaning an oil spill

BioremediationBioremediation

scientists are also making use of organisms already scientists are also making use of organisms already found in the environment found in the environment – enhance their requirements for growth, such as enhance their requirements for growth, such as

nutrition or water availabilitynutrition or water availability

Bacteria in an oil spill

Why Bioremediation?Why Bioremediation?

current methods of controlling some current methods of controlling some environmental polluters are incineration or environmental polluters are incineration or storage in land fills, which result instorage in land fills, which result in– more pollutionmore pollution– health riskshealth risks

bioremediation isbioremediation is– inexpensiveinexpensive– publicly acceptedpublicly accepted– non-polluting (ideally)non-polluting (ideally)– in situ treatment (at the site)in situ treatment (at the site)

Food MicrobiologyFood Microbiology

food is an ecosystem and food is an ecosystem and microorganisms play a key role in microorganisms play a key role in the stability of that ecosystemthe stability of that ecosystemmicroorganisms are introduced to microorganisms are introduced to the food ecosystem from the soil, the food ecosystem from the soil, harvesting, handling, storage, and harvesting, handling, storage, and packagingpackaging

Food MicrobiologyFood Microbiology

fermentation: good food fermentation: good food microbiologymicrobiology– food that have been food that have been

intentionally altered such as intentionally altered such as sour cream, cheese, beersour cream, cheese, beer

– any desirable change a any desirable change a microorganism makes to foodmicroorganism makes to food

Food MicrobiologyFood Microbiologyspoilage: bad food microbiologyspoilage: bad food microbiology– undesirable changes to food; undesirable changes to food;

sour milk, moldy breadsour milk, moldy bread– preservatives and refrigeration preservatives and refrigeration

inhibit the growth of inhibit the growth of microorganismsmicroorganisms

Moldy Spam

Microorganisms in FoodMicroorganisms in Food

factors that affect the presence of microorganisms in factors that affect the presence of microorganisms in food includefood include– intrinsicintrinsic– extrinsicextrinsic

Intrinsic growth factors: Intrinsic growth factors: naturally present in foodnaturally present in food

water availabilitywater availability is measured as water activity (a is measured as water activity (aww))

this is the amount available in the foodthis is the amount available in the foodmost microorganisms require an amost microorganisms require an aw w of 0.90 or of 0.90 or above for growthabove for growthfungi can grow with a afungi can grow with a aww of 0.80 of 0.80

fresh food have an afresh food have an aw w 0.980.98

Intrinsic Growth FactorsIntrinsic Growth Factors

pHpH– many species of bacteria are inhibited by low pH, many species of bacteria are inhibited by low pH,

including most pathogensincluding most pathogens

Testing soil pH

Intrinsic Growth FactorsIntrinsic Growth Factors

biological barriers:biological barriers: shells, shells, rindsrinds– protect foods from invading protect foods from invading

microorganismsmicroorganisms

antimicrobial chemicals:antimicrobial chemicals:– naturally occurring in some naturally occurring in some

foodsfoodsegg whites have lysozyme egg whites have lysozyme which will destroy which will destroy lysozyme susceptible lysozyme susceptible bacteriabacteria

Extrinsic Factors: Extrinsic Factors: environmental conditionsenvironmental conditions

temperature of storagetemperature of storage– below freezing water is unavailable for below freezing water is unavailable for

microorganismsmicroorganisms– low temperatures (above freezing) enzyme reactions low temperatures (above freezing) enzyme reactions

are non-existent or sloware non-existent or slow– refrigerated food microbial growth is likely refrigerated food microbial growth is likely

psychrophilespsychrophiles

Extrinsic FactorsExtrinsic Factors

atmosphere: presence or absence of Oatmosphere: presence or absence of O22

– obligate aerobes (need Oobligate aerobes (need O22)) won’t grow in sealed won’t grow in sealed containerscontainers

may allow growth of anaerobic microbesmay allow growth of anaerobic microbes

Microorganisms in Food ProductionMicroorganisms in Food Production

using microorganisms for food using microorganisms for food production has been done for production has been done for thousands of yearsthousands of years– cheese, yeast, beercheese, yeast, beer

microorganisms used in food often microorganisms used in food often produce an acidic by-product as a produce an acidic by-product as a result of metabolismresult of metabolism– can inhibit growth of many can inhibit growth of many

spoilage microorganismsspoilage microorganisms– can inhibit growth of many can inhibit growth of many

foodborne pathogensfoodborne pathogens

Yeast cells

Food Spoilage: Food Spoilage: undesirable changes in foodundesirable changes in food

smell bad, taste bad, look badsmell bad, taste bad, look badprobably are not harmfulprobably are not harmful– microorganisms that cause food spoilage compete with microorganisms that cause food spoilage compete with

pathogenspathogens– in the case of food spoilage vs. pathogens, the spoilers in the case of food spoilage vs. pathogens, the spoilers

are winningare winningevidence is obvious, though I wouldn’t eat anything evidence is obvious, though I wouldn’t eat anything that smelled or looked like thatthat smelled or looked like that

Foodborne IntoxicationFoodborne Intoxication

illness from microbial exotoxinillness from microbial exotoxin– microorganism does not cause the illness, the toxin microorganism does not cause the illness, the toxin

released by the microorganism doesreleased by the microorganism doescommon exotoxin producing microorganismscommon exotoxin producing microorganisms

– Staphylococcus aureusStaphylococcus aureus

– Clostridium botulinumClostridium botulinum

Foodborne InfectionFoodborne Infection

requires consumption of microorganismrequires consumption of microorganismsymptomatic about 1 day following ingestion of symptomatic about 1 day following ingestion of contaminated foodcontaminated foodcommon foodborne infecting microorganismscommon foodborne infecting microorganisms– SalmonellaSalmonella and and CampylobacterCampylobacter

poultry product infectionspoultry product infections– Escherichia coliEscherichia coli 0157:H7 0157:H7

undercooked hamburgerundercooked hamburger

Campylobacter Salmonella

Food Preservation:Food Preservation: preventing growth and metabolic preventing growth and metabolic

activities of microorganismsactivities of microorganismsspices, salting, drying are methods that have been spices, salting, drying are methods that have been around for yearsaround for yearsmost common methods of current food preservation aremost common methods of current food preservation are– high temperature treatmenthigh temperature treatment– low-temperature storagelow-temperature storage– antimicrobial chemicalsantimicrobial chemicals– irradiationirradiation

Documents

Applied Microbiology