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58 Cards in this Set

  • Front
  • Back

4 factors impacting rates of biodegradation

1. Contaminant bioavailability

2. Genetic Make up (degrading enzymes)

3. Contaminant Structure

4. Environmental Factors

Two steps required for biodegredation

1. Uptake and transport of contaminant into cell

2. Metabolism

The presence of the following structures generally inhibit biodegradation

· Unusual atoms (Halogens) R – CH2 – Cl

· Branching

· Aromatic ring systems

· High molecular weight

4 basic biodegradation terminology

1. Tranformation

2. Mineralization

3. Cometabolism

4. Biosynthesis

Example of Cometabolism

Oxidation of TCE by methane-utilizing microbes

Bioremediation for petroleum spills

There are normally degrading microbes present so the issues become bioavailability and environmental conditions. In ocean spills, access to the oil is limited to the surface area at the oil-water interface. In general,oxygen is not limiting but nitrogen and phosphorus are limiting

Intrinsic bioremediation(or natural attenuation

When natural activities are fast enough to control thecontaminant plume. This approach is desirable because it require only themonitoring of the contaminant plume

In situ treatments

1. Bioventing

2. Air sparging

3. Permeable reactive barriers

Ex situ treatments

1. Biofiltration

2. Soil vapor extraction andtreatment

3. Ground water extraction andtreatment

Be able to list threetoxic metals of concern




The difference between bioavailable (bioaccessible) and total metal

A very small fraction of the total metal is actually bioavailable (Defined here as soluble in water). The majority of the metal isabsorbed/adsorbed or precipitates

Factors that affect metal bioavailability

1. Metal sorption by soil

2. pH

3. Redox potential

Be familiar with the different mechanisms of metal toxicity

DNA (Transcription) --> mRNA (Translation) --> Protein synthesis

Be familiar with the different metal resistance mechanisms exhibited by bacteria

Sulfate reducing bacteria

-Hg methylation (2 steps)

-Selenium methylation (1 step)

Be able to discuss the role of microbes in the bioremediation of zinc and sulfate in the Budelcosmelter example discussed in class

Mining produces zinc metal wastes that remain in the mine long after operations cease. This environmental problem can be fixed by harnessing the metabolism of sulfate reducing bacteria, whose ability to reduce sulfate produces carbonate which neutralizes acids and sulfide, which chemically stabilizes toxic metal ions as solid metal sulfides.

Be able to discussthe different microbes and their roles in 1) making mine tailings inhospitablefor plant growth, and 2) aiding plant growth

1. Actinobacteria

2. Alphaproteobacteria

What is thedifference between a frank pathogen and an opportunistic pathogen? Give oneexample of each.

Opportunistic pathogens – Pathogens that takeadvantage of a host with a weakened immune system or an altered microbiota. Ex:Pseudomonas aeruginosa

Frank pathogen – Pathogen that is capable of causingdisease in healthy people and/or immunocompromised people. Ex: Vibrio,Salmonella

Infection vs Pathogen

Infection– Invasion and growth of an organism within a hostorganism

Pathogens– Infectious organisms that harm their host

What are the five modes of Transmission?

1. Waterborne

2. Foodborne

3. Person-to-Person

4. Airborne

5. Vector-borne

Bacteria Pathogens (Infective dose? Infectious in environment for how long? Prevented how?)

-Infective dose: 10^4 to 10^9

-Less than 24 hr 1/2 life

-Proper sanitation and chlorination of drinking water, proper food handling and preparation

Enteric Bacteria: Salmonella ( 3 types, serotype)

1. Salmonellosis (Serotype & diseases)

2. Typhoid fever (Serotype & diseases)

3. Paratyphoid fever (Serotype & diseases)

Escherichia Coli (4 Different types)





Shigella (Causes what? 4 Different serotypes)

-Shigellosis: Cramps, fever, diarrhea, malaise

o S. sonnei § Most common in US

o S. flexneri

o S. boydii

o S. dysenteriae§ Most severe

-Second most common cause of waterborne disease outbreaks in US

Vibrio Cholerae (Gram and oxidase what? Causes what disease?)

- Gram Negative, Oxidase Positive, Facultative aerobes

-Causes Cholera: Profuse watery diarrhea, vomiting, leg cramps, shock

Viral Pathogens (Infective dose? Infectious in environment for how long?)

-Lower minimal infective dose than bacteria

-Viruses last longer in environment

-Infection is usually species-specific

Viruses that cause Gastroenteritis (How do they infect their host)

Rotavirus (2 types)



Hepatitis A virus

Influenza Virus

How are influenzasubtypes defined?

HA protein – involved in virus attachment and membranefusion in the infected cell

NA (neuraminidase) protein – digests sialic acid (neuraminicacid) which most cells have on their surface as a part of virus receptor. Thisallows virus to be internalized

Both pathogens undergo antigen drift

Seasonal vs Pandemicinfluenza (Occurs how often? Immunity? Vaccines? Death poll? Impact on economy?)

Seasonal: Outbreaks follow predictable patterns and immunitybuilt up from previous seasons, vaccine available, death poll predictable,manageable impact on economy Pandemic: Occurs rarely (few times per century), littlepre-existing immunity, healthy people infected, health systems overwhelmed, novaccine available, death poll high, major impact on society, potential forsevere impact on economy

Influenza Viruses ofcurrent concern

1. H1N1 Swine Flu 2009

·Most likely come from pigs

·Pandemic over in 2010 but continues to circulatearound the globe along with seasonal flu

·H1N1 vaccine found

2. H5N1 Avian Flu

·Bird virus seems to be able to infect humanswithout having to undergo a recombination event in some other animal· · Fatality rate 60% in humans

· Concern it might mutate, or undergo reassortmentwith a human influenza virus, and acquire the ability to spread rapidly formhuman to human while still being as virulent

Waterborne protozoan parasites: Giardia Lamblia (3 Life stages) (Signal to encyst? minimal infective dose?)

-Very primitive

-Causes Giardiasis: Infection in small intestine

- Minimal Infective dose of 10 cysts

-The signal to encyst is cholesterol starvation

1. Cysts ingested with contaminated water or food

2. Cyst "encyst", and trophozoites colonize small intestine

3. Cysts passed in feces

Cryptosporidium parvum (Life stages )

-Highly resistant to chlorination

-Minimal Infective dose: 15-100 oocysts

1. Oocyst is the most hardy, resistant life stage: Passed from host in feces

2. Sporozoites bind to intestinal epithelial cells and reside between cytoplasm and cell membrane (Sporozoite matures into trophozoite and then into a type 1 meront)

3. Asexual reproduction results in eight merozoites in the Type 1 meront

-Meronts bursts and generations can either reinfect or form second generation meront (type ll meront)

-Type ll meronts invade epithelial cells, and undergo gametogony

-Flagellated microgametes leave host cell, find macrogametocytes and fertilize them to form zygote

4. Zygote undergoes meiosis and encysts to form a new oocyst

Cryptosporidiosis/Coccidiosis (Life stages)

Autoinfective: Thin-walled cysts can excyst within and reinfect original host

Immunocompromised may not be able to clear the infection

Emerging andre-emerging infectious disease

Emerginginfectious disease: Newly identified/previously unknown agents

Re-emerging infectious disease: Known infectiousagents that had fallen to such low levels that they were no longer consideredpublic health problems and are now showing upward trends in prevalence

SARS (Causes what? Lessons learned from SARS)

-Severe acute respiratory syndrome

-Serious form of pneumonia


-Important role of air travel in international spread

-Infectious disease in 1 country is a threat to all

-Negative effect on trade, travel, tourism

-WHO can play critical role

-Rapid sharing of data enhances preparedness and response

Wastewater:Definition and Composition

Definition: Water adversely affected by anthropogenic influence


-Organic matter

-Suspended solids

-Nutrients: P and N

-Priority pollutants: Metals, metalloids, benzene compounds, chlorinated compounds

-Microorganisms: commensals or pathogens

Biologicaloxygen demand (BOD): What is it? It measures what in wasterwater samples? Discharge must be what?

-Amount of oxygen used by microbes for biochemical oxidation of organic and inorganic compounds

-Measure oxygen amount consumed by mixed heterotrophic bacteria population in wastewater sample

-Discharge BOD must be less than or equal to 20 mg/L

Total Organic Carbon (TOC): Measure of what? How does it work?

-Measure of carbon "burned off"

-Sample combusted, then organic carbon quantified via infrared detection

Chemical Oxygen Demand (COD): (What is it? Oxidant?)

-O2 amount required to chemicallyoxidize ALL organic matter to CO2 and H2

-Digestion at high Temp

-Oxidant: Chromic acid or sulfuric acid/potassiumdichromate

-Chromate reacts with COD producing color

-Measure color via colomiter

Primary Treatment (Biological, Physical, chemical or Physicochemical? Examples)

Physical: separate coarse sediments/solids

1. Grit Chamber --> sand and gravel settle out

(long narrow tanks designed to slow down the flow so solids will settle out of the water)

2. Settling tank (clarifier) --> half suspended organic solids settle out to bottom as sludge


1. Dissolved air flotation --> microscopic air bubbles attach to flocculated particles causing flotation

-Surface skimmer removes floating particles/sludge

-Bottom skimmer removes settled solids

Secondary treatment (Biological, Physical, chemical or Physicochemical? Examples)

Biological: Microorganisms reduce N and P

-Suspended solids decompose

-reduce BOD

-reduce odors

-reduce pathogens

-Physicochemical treatment


1. Aeration basin (activated sludge)

-Primary effluent + Bacteria-rich slurry + oxygen

-Promote bacteria growth to decompose organics

-Return activated sludge (RAS) – sludge fromsecondary clarifier recycled into basin as bacteria rich slurry


1. Modified Ludack-Ettinger

2. Bardenpho

Modified Ludack-Ettinger (How many basins and what are they? Similar to what other treatment? What does it target specifically? What is the source of oxygen for facultative bacteria promoting breakdown?)

1. 3 basins: Aerobic, anaerobic, anoxic

2. Modification of conventional Activated sludge: recycled from secondary clarifier

3. Targeted to remove/reduce nitrogen via nitrification/denitrification

4. Nitrite (NO3) is oxygen source for facultativebacteria promoting breakdown


1. 5 basins: Anaerobic, Anoxic, Aerobic, Anoxic,Aerobic

2. Activated sludge: recycled from secondaryclarifier

3. Targeted to remove/reduce nitrogen vianitrification/denitrification

4. Nitrite (NO3) is oxygen source for facultativebacteria promoting breakdown

5. Decrease Total Phosphorus – anaerobic microbesrelease soluble inorganic phosphorus as a result of polyphosphate hydrolysis,then aerobic microbes uptake phosphorus in excess of microbial need

Tertiary treatment (Biological, Physical, chemical or Physicochemical? Examples)

a. Chemical: Disinfection inactivates remaining pathogens

1. Chlorination --> sodium hypochlorite oxidizes cellular material

2. Chloramination--> Chlorine and ammonia added at same time

-Reaction creates long time disinfectant

-Prevents other Cl compounds from being created

b. Physicochemical: further reduce organics, turbidity, nutrients, metals, and pathogens

1. Coagulation --> chemicals added to increase adsorption to solids

2. Filtration --> medium used to remove material based on size

Regulatory Standards

1. Class A+: Open access (uncontrolled)

-Fecal coliforms not detected

-Total nitrogen <10

-Turbidity never exceeds 5

2. Class A: Open access (controlled)

-Fecal coliforms not detectable

3. Class B+: Restricted Access (uncontrolled)

-Fecal coliforms <200

-Total nitrogen <10

4. Class B: Restricted Access (controlled)

-Fecal coliforms <200

5. Class C: Little human contact: irrigation in farms etc

-Fecal coliforms <1000

Purple piping (What are pipping systems for? Examples?)

·Piping systems supply WWTP final effluent topublic/private water reclamation sites

Ex: Irrigation, Golf courses, parks,universities, agriculture, wetlands, pond, lakes, etc. 2

Direct potable Reuse (DPR)

· Wastewater treated at WWTP

· WWTP final effluent pumped to DPR TreatmentFacility and treated further

· DPR effluent pumped directly to Drinking WaterTreatment Facility

· Water supplied for potable consumption

Why is it important to reduce the amount of biodegradable organic matter and nutrients (BOD) during wastewater treatment?

It is important because the runoff of sewage into natural bodies of water could result in anaerobic conditions killing fish and organisms that are dependent on oxygen in the water.

In terms of water quality, what does the presence of total coliforms indicate? (What is this test a starting point to? why is it considered an indicator? What does it mean when total coliforms are not present?)

The total coliform test is the starting point for determining the biological quality of drinking water. It is considered an indicator, since the presence of bacteria in this group indicates the possibility that disease organisms may also be present in the water. When total coliforms are not present, it is very unlikely that a disease organism is present in the water

In terms of water quality, what does the presence of heterotrophic plate counts indicate?

(What does this bacteria do? What do sudden increases in HPC levels indicate? )

The presence of heterotrophic plate counts indicates general quality of water (particularly levels of organic matter in water). Enumerates all culturable aerobic and facultative anaerobic chemoheterotrophs in water. Sudden increases in HPC levels may indicate a change in the quality of water or, that bacterial regrowth has occurred in the distribution system

What defines an indicator microorganism? Why they are used?

-A non pathogenic microorganism whose presence suggests the presence of enteric pathogens

-Indicator organisms are used because pathogens themselves are frequently difficult to detect in drinking water, wastewater & biosolids, due to:

· Low numbers

· Difficult, time consuming, or expensive to culture

· Potentially hazardous to grow

What are the criteria for an ideal indicator organism?

· Present whenever enteric pathogens are present, and absent when pathogens are absent (presence/absence proxy)

· Useful for all types of water (drinking water, wastewater, recreational water, sea water) (universal)

· Survive longer in the environment than the toughest enteric pathogen (conservative proxy)

· Do not grow in water (stable)

· Detection protocols easy and inexpensive

· Density of indicator microorganisms should correlate with the degree of fecal pollution (quantitative proxy)

What are at least three different types of indicators?

1. Total Coliforms

-Indicator used for all types of water

-Aerobic or facultative anaerobic

-Gas production during lactose fermentation

-Ex: Escherichia


-May grow in aquatic environments

-Coliforms may form biofilms (making disease organisms more resistant)

-Do not necessarily indicate fecal contamination

2. Fecal coliforms
-Able to ferment lactose and produce both acid and gas

-Ex: Escherichia


-Many of the same drawbacks as total coliforms

-Indicates fecal contamination for sure, but cannot distinguish between human and animal feces

-Can survive and grow for extended periods of time in tropical waters

3. Fecal Streptococci

-More resistant, lasts longer in environment

-Used for enteric viruses and gastroenteritis for swimmers

-Ferment sugars to lactic acid

-Ex: Enterococci

4. Anaerobic bacteria


-Spores are heat-resistant, resist disinfection, can remain viable in environment for long

-Can be used as indicator for resistant pathogens, or tracing fecal contamination in marine environment


-Common in soil, may not necessarily indicate fecal contamination

-Pathogenic (causes gas gangrene if it infects wounds, produced enterotoxin in small intestine causing gastronenteritis)

-Anaerobic culture is difficult

Ascaris lumbricoides (Indicator for what? What is it? What is Ascariasis? Symptoms? Causes?)

* Indicator for Environmental Hygiene

* Most common roundworm infecting human


-Adult worms living in small intestine

-No symptoms

* Poor Sanitation and hygiene

What are the standard detection methods used to measure indicators?

1. Most Probable Number (MPN) test

-Drawback: Heterotrophs can out compete coliforms and fecal coliforms for nutrients in the environment and mask their detection by this method

2. Membrane Filter tests

3. Presence/Absence tests e.g Colilert

-Used to detect total coliforms and E. coli

-Qualitative not quantitative

4. Plaque Assays

-Used to detect bacteriophage

5. Heterotrophic plate count

-Indicates general quality of water (particularly levels of organic matter inwater)

-Enumerates all CULTURABLE aerobic and facultative anaerobicchemoheterotrophs in water

6. Microscopic classification and counts for eukaryotic parasites

-Ex: asciaris


1. Variation in results

2. No standard protocol

3. Non-larval eggs assumed non viable after 30 days

Potential impacts of global climate change on microbial systems: Vibrio Cholera (Associated with blooms of what? Blooms vary with changing what? Why is cholera expanding? What is the complex relationship between cholera and climate?)

* Associated with some phytoplankton blooms in nutrient-rich coastal waters

* Blooms vary with changing precipitation regimes and El nino

* Cholera has been expanding as climate warms

* Complex relationship between cholera and climate:

* Changes in climate affect physical parameters (precipitation and water temperature) that result in cascading effects that can increase abundance of cholera-causing bacteria and the incidence of disease

Vibrio Cholera Environmental reservoirs

* Highly motile V. Cholerae can be ingested by new human host after shredding,or can associate with abiotic surfaces (forming biofilms), copepods, algae andChironomid eggs sacs in the environment. And then Reinfect (by detaching or bybeing ingested with reservoir)

Ecosystem-scale microbial responses to climate change (Indirect vs Direct effects)

Indirect effects:

o Result from climate-driven changes in plant productivity and vegetation structure which alter soil physicochemical conditions, the supply of carbon to soil and the structure and activity of microbial communities involved in the decomposition processes and carbonrelease form soil

Direct effects:

o Influence on soil microbes and greenhouse gas production of temperature, changingprecipitation and extreme climatic events

Thawing permafrost and Climate change (How does climate change affect permafrost? By end of century how much permafrost will be thawed? How is the thawing of permafrost related to microbes and global warming? How do microbes mediate wetland methane cyclying?)

* Heating drives permafrost collapse

* By end of century, half of all of permafrost is predicted to have thawed

* Thawing of permafrost provides a feast for microbes and is likely to be a major positive feedback to warming

o Microbial feast --> Loss of carbon to atmosphere

o Permafrost thaw --> wetlands (significant source of CH4) --> CH4 --> positive feedback to warming

o CH4 has 25 times the global

warming potential of CO2

Microbes mediate wetland methane cycling under anaerobic conditions and oxidizing it back to CO2 aerobically.