always on

Production of: light, virulence factors, and biofilm; energy costly!

1. molecule is always inside and is diffused out.
2. once population density is high enough, QSM diffuses back inside and is represented

ex. Vibrio fischeri

environments are not constant

microbes prefer to form on surfaces

Nutritional Stress

Interaction with other organisms

Competition

predation/parasitism:  Bdellovibri

Synergism/mutualism: dental biofilms

Nutritional Stress

starvation survival

Rapid growth vs. survival

 Lab generation time vs. nature gen. time

Nutritional Stress

high affinity uptake

Siderophores (Fe)

Active transport via specific binding proteins

Nutritional Stress

habitat selection

chemotaxis

motility: actin "rockets"

organisms selected for survival (evolution)

Nutritional Stress

Alternative Metabolism

In Situ Techniques

Direct Observation

Dissapearance of food

Appearance of byproducts (acid/NO₃)

radioactive substrates: tagged sugars

Fluorescent In Situ Hybridization

specific or general probes used

Lab Techniques

Culture and Growth

Lab Techniques

Enrichment Culture Technique

Lab Techniques

Model Environment

Mimic environmental condition in Lab

Wingradsky Column (core sample) for sedimentorgansims

physical, chemical, biological properties

ecology= interactions within environment

Root-surface organisms: Rhizospheres (symbiotic)

Plant Diseases: Agrobacterium tumefaciens; induces opine production

Hydrothermal vent: worms with bacteria

Aquifer and subsurface

Nutrient Cycling

Microbes can cycle:

Carbon, Nitrogen, Phosphorous, Iron, Sulfur

Nitrogen required for:

protein synthesis

nucleic acid synthesis

other cell components

N₂ = 78% atmosphere: microbes use NO₃^- / NH₃ / R-NH₂

N₂ → NH₃

Enzyme: Nitrogenase 

highly regulated; energy extensive (16 ATP/N₂)

O₂ sensitive (no O₂ present)

NO₃^• → N₂ or NH₃

most common

Nitrate used as final electron acceptor

Carbon Cycle

 CO₂ fixation

 CO₂ → organic Carbon

 CO₂ major reservior of carbon

 CO₂ fixation done by primary producers; Autotrophs (photosynthetic and lithotrophs)

Carbon Cycle

Carbon Mineralization

(Decomposition)

Organic Carbon → CO₂

Sugar/protein/lipid decomposition

carbon trapped in complex molecules; cellulose, lignan

 Sulfur Cycle

Sulfur Oxidation

 H₂S → elemental sulfur

 Beggiatoa, Thiothri

 H₂S → SO₄^2-

 Thiobacillus

Sulfure Cycle

Sulfur Reduction

 SO₄^2- → S₂^-

SO₄^2- is used as an electron acceptor; "dissimilatory sulfate reduction"

ex: Desulfovibrio / some Clostridium sp.

SO₄^2- can also be used as a sulfur source; "assimilatory reduction"

Aquatic Microbiology

Impacting Factors

Temperature

 Ocean water range: -2° → 100° (most below 5°C)

Deep sea thermal activity

growth on ice as well

Aquatic Microbiology

Impacting Factors

Hydrostatic Pressure

Barotolerant and Barophilic

most = psychrophiles (grow in extreme conditions)

Aquatic Microbiology

Impacting Factors

Light and Turbidity

photosynthetic organism live in Photic Zone 

Turbidity impacts range of photic zone

Aquatic Microbiology

Impacting Factors

Salinity

Range: 0% (fresh) – 3.7% (sea)

Saturated = Great Salt Lake 32%

Halotolerant and Halophilic

Aquatic Microbiology

Impacting Factors
pH

different levels impact community composition

Laguna Diamante

– pH 11

– 5X salt concentration

– 20,000X arsenic

– High UV, low O2

microbes and flamingos

Water can be a pathogen reservoir;

V. cholerae, Shigella, Salmonella, some E. coli

Detection is key; pathogens at low levels

1. be present only in polluted H2O
2. be present when pathogens are present
3. # of IOs correlate with pollution level
4. Survive longer than pathogen
5. Uniform & Stable properties
6. be "harmless" to animals/humans
7. be present in greater # than pathogen
8. Relatively easy to detect

Indicator Organisms

E. coli is the most common:

Coliform: a Gram negative, lactose fermenting rod; 

normal inhabitant of the intestinal tract

 Streptococcus faecalis also used

High Coliform counts = water is not potable, lakes closed

Drinking Water Treatment

 Filtration: removes particulates

Treatment with chlorine: kills microbes

Optional:

Reverse osmosis or charcoal filtration; Remove chemical contaminants

Biochemical Oxygen Demand (BOD)

BOD= Term for O₂ consumption over 5 days

Organic matter dumped into water = problem

aerobic microbes deplete oxygen

Food and Beverage Microbiology

Bad vs. Good

Bad: food spoilage, food-borne infections

Good: fermentations (beer, cheese, etc.), occasionally microbe is eaten (yogurt)

Food/beverage= Culture media

Good: milk eggs meat

Bad: flour, sugar, cereal (dry), vinegar (low pH)

Initial # of microbes present

Processing/sterilization of food and/or equipment

Damage to containers

Storage conditions

 Metabolites produced may be harmful;

– Neurotoxin from C. botulinum

– Enterotoxin from S. aureus

Can cause infection;

– E. coli, Salmonella, L. monocytogenes

Food Spoilage Prevention

High Temps - Pasteurization

Used for: milk, eggs, crabmeat, beer, wine, cheese

Milk pathogens: M. bovis, L. monocytogenes

Check for milk coliforms (determine fecal contamination)

Microwave ovens: ineffective (uneven heating)

Food Spoilage Prevention

Low Temps

Refrigeration; bacteriostatic,

Produce: heated before freezing; inactivates oxidase enzymes that alter food quality

Food Spoilage Prevention

High osmotic pressure

High salt or sugar content is bacteriostatic; salted fish/jams

*still prone to fungal contamination

Food Spoilage Prevention

Spices

Add flavor and cover ‘off’ flavors

enhances preservation

Food Spoilage Prevention

chemical additives

Organic acids (sorbic, lactic, citric) control growth 

of molds and bacteria

Nitrates and nitrites inhibit growth, also 

contribute to “redness” of meat;

Raises concern about carcinogenic effect

Food Spoilage Prevention

Radiation

Foods exposed to UV or gamma radiation

Will either pasteurize or sterilize food; exposure dependent

Microbes can be grown in batch or continuous culture:

Conditions must be monitored closely;

– Aeration, temperature, pH

Microbes at Work

Alcoholic Beverages

Saccharomyces cerevisiae; used for bread

Developing Strains:  

Alcohol tolerance (normal 8-9%)

speed/purity of alcohol production

ability to flocculate (loosely coagulate)

growth rate

Ethanol Production by

S. cerevisia

Glucose enters glycolysis

Glucose→ G6P→F6P→→→Pyruvate

Ethanol Production by

Pyruvate→ acetyl CoA→ Krebs cycle

Pasteur Effect: cell growth, 0 EtOH production

Ethanol Production by

Pyruvate → acetyl CoA + CO₂ → Ethanol

Enzyme 1: pyruvate decarboxylase

Enzyme 2: alcohol dehydrogenase

0 cell growth, EtOH production

If O₂ is present, ethanol can be oxidized to 

acetic acid by Acetobactre spp.

Curddling of milk: 4.6 pH

Lactic acid byproduct; enhances taste and preservation

Examples: Buttermilk, yogurt, cottage cheese, cheddar cheese, cream cheese