Applied Microbiology

Applied Microbiology

Applied Microbiology • applied microbiology is the interaction of the microbial world and the rest of the world • genetic variances • microbial effect on soil, water, our food • microorganisms are present in most every aspect of our lives • microorganisms are critical to our survival on Earth • to be a successful ecosystem on Earth, you’d best be nice to the microorganisms!

Microbial Ecology: relationship of microorganisms with each other and their environment • ecosystem: interaction of living and non-living components • oceans, deserts, marshes, forests, tundra, lakes • microorganisms play a key role in ecosystem structure

Microbial Ecology:relationship of microorganisms with each other and their environment • microenvironment: immediately surrounds a microorganism • relevant to survival and growth of the microorganism

Nutrient Acquisition within an Ecosystem • 3 main levels exist in every ecosystem in regards to nutrient acquisition • producer • consumer • decomposer 1. primary producers: convert CO2 to organic material

Nutrient Acquisition within an Ecosystem 2. consumers • heterotrophs • utilize organic material created by producers

Nutrient Acquisition within an Ecosystem 3. decomposers • heterotrophs • digest leftovers of primary producers and consumers • detritus ( fresh or partially decomposed organic matter) • bacteria and fungi are key players in the process of decomposition

Low Nutrient Environments: common in nature • bacteria do best in biofilms if nutrition availability is low • biofilms are a polysaccharide encased community of microorganisms • microorganisms extract nutrients that are absorbed by water from air or nutrients that are adsorbed onto the biofilm

Microbial competition and antagonism • most environments are suitable to many kinds of microorganisms • only one or a few can actually occupy the environment at a given time

Competition and Antagonism: among microorganisms • competition: • fierce competition for nutrients and water • the faster a microbe reproduces the larger the population • the larger population competes better • critical, especially if the microorganisms competing utilize similar nutrients • antagonism • bacteriocins: protein produced by bacteria that destroys similar strains “WINNER TAKES ALL AND IS KING/QUEEN OF THE MICROBIAL ECOSYSTEM”

Example of Competition • stability of microbial community in human intestine is attributed to competition and antagonism amongst its members • compete nicely for nutrients • produce toxins to limit growth of new microbes

Environmental Change affect microbial population • environmental fluctuations are common and resident microorganisms may respond by • producing enzymes to help adapt to changing environment • additional or different enzymes may be necessary for survival • mutation • domination by other species (can’t compete any more)

Microbial Mat: thick, dense, organized biofilm • generally found attached to a solid substrate or at air-water interfaces Microbial mat attached to rocks Microbial mat in stream bed

The Study of Microbial Ecology • somewhat difficult to accomplish • less than 1% of environmental microorganisms can be successfully cultured in the lab

Microbial Habitat • aquatic • marine: • deep waters are usually stable and consistent • shoreline habitat varies due to nutrient rich run-off

Microbial Habitat • freshwater: • lakes • stratification allows for the mixing of the water seasonally. • Increases the presence of O2 in the deeper H2O algae paramecium

Microbial Habitat • moving water • rivers • generally aerobic due to turbulence facilitating O2 circulation river ostracod

Microbial Habitat • terrestrial • microorganisms are critical to soil habitat • composition of microbes is dependent on soil conditions • wet soil: anaerobic conditions due to water filling the pore space in the soil, soil dries and microbes go produce endospores for survival Endospores

Mutualism with Eukaryotes • mychorrhizae: fungus • assist plants in the uptake of phosphorous • mychorrizae gain nutrient from plant

Mutualism • nitrogen fixers: fix nitrogen and make it available for the use by their partner plant • most common is Rhizobium, a microorganism found in many root nodules Rhizobium in root nodules

Nitrogen Cycle

Mutualism: microorganisms and the world • microorganisms and herbivores • animal with a rumens (cow) or cecums (horse) need microorganisms to digest the plant food they ingest Bacillus in a cow rumen

Microorganisms in Sewage Treatment • decreasing biochemical oxygen demand (BOD) decreases impact of sewage on the environment • BOD is the amount of O2 needed for microbial decomposition of the organic material in a sample Grit chamber Biological filter Clarifier

Microorganisms in Sewage Treatment • if not treated the high BOD found in sewage could deplete the O2 level in the receiving water • in other words if raw sewage is deposited into a lake or stream without treatment, it would effectively suck the oxygen out of the water, leaving very little for the fish and other organisms

Microorganisms in Sewage Treatment • sewage treatment is a controlled process that strives to eliminate the excess organic material, thus diminishing the BOD • most of the removal of organic matter is done by microorganisms bacterial filaments

Microorganisms and Water Treatment and Testing • municipal water supplies are tested and treated for the removal of pathogenic microorganisms and chemicals • this is done with the use of chemicals

Microorganisms and Solid Waste Treatment • the elimination of organic waste material can be enhanced by microorganisms • increase cost to separate organic material from inorganic (glass, metal, plastic) • composting: natural decomposition of organic solid materiel results in excellent fertilizer

Compost microorganisms are needed to breakdown the organic material

Bioremediation: use of microorganisms to eliminate or make harmless pollutants in an environment • pollutants removed can include • organic solvents • toxic chemicals • hydrocarbons oil spill

Bioremediation • introduces specific organisms to the polluted area • many toxic substances are man-made/new to the environment (xenobiotics) • no time for naturally occurring microbes to have evolved biochemical pathways for their degradation • scientists are trying to develop new microbes for the degradation of environmental polluters Cleaning an oil spill

Bioremediation • scientists are also making use of organisms already found in the environment • enhance their requirements for growth, such as nutrition or water availability Bacteria in an oil spill

Why Bioremediation? • current methods of controlling some environmental polluters are incineration or storage in land fills, which result in • more pollution • health risks • bioremediation is • inexpensive • publicly accepted • non-polluting (ideally) • in situ treatment (at the site)

Food Microbiology • food is an ecosystem and microorganisms play a key role in the stability of that ecosystem • microorganisms are introduced to the food ecosystem from the soil, harvesting, handling, storage, and packaging

Food Microbiology • fermentation: good food microbiology • food that have been intentionally altered such as sour cream, cheese, beer • any desirable change a microorganism makes to food

Food Microbiology • spoilage: bad food microbiology • undesirable changes to food; sour milk, moldy bread • preservatives and refrigeration inhibit the growth of microorganisms Moldy Spam

Microorganisms in Food • factors that affect the presence of microorganisms in food include • intrinsic • extrinsic

Intrinsic growth factors: naturally present in food • water availability is measured as water activity (aw) • this is the amount available in the food • most microorganisms require an aw of 0.90 or above for growth • fungi can grow with a aw of 0.80 • fresh food have an aw 0.98

Intrinsic Growth Factors • pH • many species of bacteria are inhibited by low pH, including most pathogens Testing soil pH

biological barriers: shells, rinds protect foods from invading microorganisms antimicrobial chemicals: naturally occurring in some foods egg whites have lysozyme which will destroy lysozyme susceptible bacteria Intrinsic Growth Factors

Extrinsic Factors: environmental conditions • temperature of storage • below freezing water is unavailable for microorganisms • low temperatures (above freezing) enzyme reactions are non-existent or slow • refrigerated food microbial growth is likely psychrophiles

Extrinsic Factors • atmosphere: presence or absence of O2 • obligate aerobes (need O2)won’t grow in sealed containers • may allow growth of anaerobic microbes

Microorganisms in Food Production • using microorganisms for food production has been done for thousands of years • cheese, yeast, beer • microorganisms used in food often produce an acidic by-product as a result of metabolism • can inhibit growth of many spoilage microorganisms • can inhibit growth of many foodborne pathogens Yeast cells

Food Spoilage: undesirable changes in food • smell bad, taste bad, look bad • probably are not harmful • microorganisms that cause food spoilage compete with pathogens • in the case of food spoilage vs. pathogens, the spoilers are winning • evidence is obvious, though I wouldn’t eat anything that smelled or looked like that

Foodborne Intoxication • illness from microbial exotoxin • microorganism does not cause the illness, the toxin released by the microorganism does • common exotoxin producing microorganisms • Staphylococcus aureus • Clostridium botulinum

Foodborne Infection • requires consumption of microorganism • symptomatic about 1 day following ingestion of contaminated food • common foodborne infecting microorganisms • Salmonella and Campylobacter • poultry product infections • Escherichia coli 0157:H7 • undercooked hamburger Campylobacter Salmonella

Food Preservation: preventing growth and metabolic activities of microorganisms • spices, salting, drying are methods that have been around for years • most common methods of current food preservation are • high temperature treatment • low-temperature storage • antimicrobial chemicals • irradiation

Applied Microbiology