Final Exam - Mic 425

Front 1

4 factors impacting rates of biodegradation

Back 1

1. Contaminant bioavailability

2. Genetic Make up (degrading enzymes)

3. Contaminant Structure

4. Environmental Factors

Front 2

Two steps required for biodegredation

Back 2

1. Uptake and transport of contaminant into cell

2. Metabolism

Front 3

The presence of the following structures generally inhibit biodegradation

Back 3

· Unusual atoms (Halogens) R – CH2 – Cl

· Branching

· Aromatic ring systems

· High molecular weight

Front 4

4 basic biodegradation terminology

Back 4

1. Tranformation

2. Mineralization

3. Cometabolism

4. Biosynthesis

Front 5

Example of Cometabolism

Back 5

Oxidation of TCE by methane-utilizing microbes

Front 6

Bioremediation for petroleum spills

Back 6

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

Front 7

Intrinsic bioremediation(or natural attenuation

Back 7

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

Front 8

In situ treatments

Back 8

1. Bioventing

2. Air sparging

3. Permeable reactive barriers

Front 9

Ex situ treatments

Back 9

1. Biofiltration

2. Soil vapor extraction andtreatment

3. Ground water extraction andtreatment

Front 10

Be able to list threetoxic metals of concern

Back 10

Arsenic

Lead

Mercury

Front 11

The difference between bioavailable (bioaccessible) and total metal

Back 11

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

Front 12

Factors that affect metal bioavailability

Back 12

1. Metal sorption by soil

2. pH

3. Redox potential

Front 13

Be familiar with the different mechanisms of metal toxicity

Back 13

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

Front 14

Be familiar with the different metal resistance mechanisms exhibited by bacteria

Back 14

Sulfate reducing bacteria

-Hg methylation (2 steps)

-Selenium methylation (1 step)

Front 15

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

Back 15

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.

Front 16

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

Back 16

1. Actinobacteria

2. Alphaproteobacteria

Front 17

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

Back 17

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

Front 18

Infection vs Pathogen

Back 18

Infection– Invasion and growth of an organism within a hostorganism

Pathogens– Infectious organisms that harm their host

Front 19

What are the five modes of Transmission?

Back 19

1. Waterborne

2. Foodborne

3. Person-to-Person

4. Airborne

5. Vector-borne

Front 20

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

Back 20

-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

Front 21

Enteric Bacteria: Salmonella ( 3 types, serotype)

Back 21

1. Salmonellosis (Serotype & diseases)

2. Typhoid fever (Serotype & diseases)

3. Paratyphoid fever (Serotype & diseases)

Front 22

Escherichia Coli (4 Different types)

Back 22

Enteropathogenic

Enterotoxigenic

Enteroinvasive

Enterohemorrhagic

Front 23

Shigella (Causes what? 4 Different serotypes)

Back 23

-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

Front 24

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

Back 24

- Gram Negative, Oxidase Positive, Facultative aerobes

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

Front 25

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

Back 25

-Lower minimal infective dose than bacteria

-Viruses last longer in environment

-Infection is usually species-specific

Front 26

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

Back 26

Rotavirus (2 types)

Norovirus

Enteroviruses

Hepatitis A virus

Influenza Virus

Front 27

How are influenzasubtypes defined?

Back 27

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

Front 28

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

Back 28

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

Front 29

Influenza Viruses ofcurrent concern

Back 29

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

Front 30

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

Back 30

-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

Front 31

Cryptosporidium parvum (Life stages )

Back 31

-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

Front 32

Cryptosporidiosis/Coccidiosis (Life stages)

Back 32

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

Immunocompromised may not be able to clear the infection

Front 33

Emerging andre-emerging infectious disease

Back 33

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

Front 34

SARS (Causes what? Lessons learned from SARS)

Back 34

-Severe acute respiratory syndrome

-Serious form of pneumonia

Lessons:

-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

Front 35

Wastewater:Definition and Composition

Back 35

Definition: Water adversely affected by anthropogenic influence

Composition:

-Organic matter

-Suspended solids

-Nutrients: P and N

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

-Microorganisms: commensals or pathogens

Front 36

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

Back 36

-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

Front 37

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

Back 37

-Measure of carbon "burned off"

-Sample combusted, then organic carbon quantified via infrared detection

Front 38

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

Back 38

-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

Front 39

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

Back 39

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

Modern:

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

-Surface skimmer removes floating particles/sludge

-Bottom skimmer removes settled solids

Front 40

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

Back 40

Biological: Microorganisms reduce N and P

-Suspended solids decompose

-reduce BOD

-reduce odors

-reduce pathogens

-Physicochemical treatment

Conventional:

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

Modern:

1. Modified Ludack-Ettinger

2. Bardenpho

Front 41

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?)

Back 41

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

Front 42

Bardenpho

Back 42

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

Front 43

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

Back 43

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

Front 44

Regulatory Standards

Back 44

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

Front 45

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

Back 45

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

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

Front 46

Direct potable Reuse (DPR)

Back 46

· 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

Front 47

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

Back 47

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.

Front 48

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?)

Back 48

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

Front 49

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? )

Back 49

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

Front 50

What defines an indicator microorganism? Why they are used?

Back 50

-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

Front 51

What are the criteria for an ideal indicator organism?

Back 51

· 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)

Front 52

What are at least three different types of indicators?

Back 52

1. Total Coliforms

-Indicator used for all types of water

-Aerobic or facultative anaerobic

-Gas production during lactose fermentation

-Ex: Escherichia

Drawbacks:

-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

Drawbacks:

-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

-Spore-forming

-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

Drawbacks:

-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

Front 53

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

Back 53

* Indicator for Environmental Hygiene

* Most common roundworm infecting human

Ascariasis:

-Adult worms living in small intestine

-No symptoms

* Poor Sanitation and hygiene

Front 54

What are the standard detection methods used to measure indicators?

Back 54

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

-Drawbacks:

1. Variation in results

2. No standard protocol

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

Front 55

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?)

Back 55

* 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

Front 56

Vibrio Cholera Environmental reservoirs

Back 56

* 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)

Front 57

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

Back 57

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

Front 58

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?)

Back 58

* 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.