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 conditionswet 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 Microbiologyspoilage: 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

Intrinsic Growth Factors

biological barriers: shells, rinds– protect foods from invading

microorganisms

antimicrobial chemicals:– naturally occurring in some

foodsegg whites have lysozyme which will destroy lysozyme susceptible bacteria

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 badprobably are not harmful– microorganisms that cause food spoilage compete with

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

are winningevidence 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 microorganismsymptomatic about 1 day following ingestion of contaminated foodcommon 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