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Environmental Environmental Microbiology Microbiology

Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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Page 1: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Environmental Environmental MicrobiologyMicrobiology

Page 2: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Applied & Environmental Applied & Environmental MicrobiologyMicrobiology

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

foodfood

microorganisms 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 Earth

to 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!

Page 3: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 4: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 5: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 6: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Nutrient Acquisition within an Nutrient Acquisition within an EcosystemEcosystem

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

material created material created by producersby producers

Page 7: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Nutrient Acquisition within EcosystemNutrient Acquisition within Ecosystem

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

producers and producers and consumersconsumers

detritus ( fresh or detritus ( fresh or partially decomposed partially decomposed organic matter)organic matter)

– bacteria and fungi are bacteria and fungi are key players in the key players in the process of decompositionprocess of decomposition

Page 8: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

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

polysaccharide encased polysaccharide encased community of community of microorganismsmicroorganisms

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

Page 9: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Microbial competition and antagonismMicrobial competition and antagonism

most environments are suitable to many kinds of most environments are suitable to many kinds of microorganismsmicroorganisms

only 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

Page 10: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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”

Page 11: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 12: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

environmentenvironment

additional 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)

Page 13: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 14: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

The Study of Microbial EcologyThe Study of Microbial Ecology

somewhat 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

Page 15: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Microbial HabitatMicrobial Habitat

aquaticaquatic– marine: marine:

deep waters are usually stable and consistentdeep waters are usually stable and consistent

shoreline habitat varies due to nutrient rich run-offshoreline habitat varies due to nutrient rich run-off

Page 16: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Microbial HabitatMicrobial Habitat

freshwater: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

Page 17: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Microbial HabitatMicrobial Habitat

moving watermoving water– riversrivers

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

circulationcirculation

river ostracod

Page 18: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 19: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 20: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 21: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

NitrogenNitrogen Cycle Cycle

Page 22: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Carbon cycleCarbon cycle

Page 23: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world
Page 24: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 25: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Microorganisms in Sewage TreatmentMicroorganisms in Sewage Treatment

decreasing biochemical decreasing biochemical oxygen demand (BOD) oxygen demand (BOD) decreases impact of decreases impact of sewage on the sewage on the environmentenvironment

BOD 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

Page 26: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 27: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

Microorganisms in Sewage TreatmentMicroorganisms in Sewage Treatment

sewage 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

Page 28: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 29: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 30: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

CompostCompost

microorganisms are needed to breakdown the organic material

Page 31: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 32: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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 degradation

scientists 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

Page 33: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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

Page 34: Environmental Microbiology. Applied & Environmental Microbiology applied microbiology is the interaction of the microbial world and the rest of the world

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)