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
Nutrient Acquisition within an Nutrient Acquisition within an EcosystemEcosystem
2. consumers2. consumers– heterotrophsheterotrophs– utilize organic material utilize organic material
created by producerscreated by producers
Nutrient Acquisition within an Nutrient Acquisition within an EcosystemEcosystem
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