Transcript H 2 CO 3

Exam Results: 09/27/2013
3rd Period: 81.08 % Average
4 Failures
2 Grades over 100%
5th Period: 87.65% Average
1 Failure
2 Grades over 100%
4th Period: 77.33% Average
7 Failures
2 Grades over 100%
6th Period: 83.07% Average
2 Failures
1 grade over 100%
The End of the 6-weeks is Friday: Current Failures
3rd Period: 82.89 % Average
100038256 (31)(M1)
100022936 (51)(F1,F2)
100022659 (49)(F1,MP)
100032725 (55)(F1,M2)
100023403 (67)(M1)
4th Period: 82.01% Average
100023226 (57)(F1,F2)
100023533 (57)(F1,F2)
100035267 (64)(F1,F2)
100042317 (50)(F2)
5th Period: 86.36% Average
100022705 (50)(M1)
100040640 (52)(F1,F2)
6th Period: 72.82% Average
100042216 (57)(M1)
100039069 (41)(MP,M2)
100023192 (54)(MP,F2)
100023502 (45)(MP,M2)
100042538 (5)(M1,MP,F2)
100041128 (21)(F1,MP,M2)
Bellwork: 09/28/2012
1) What is a buffer? Why are buffers important for the function of aquatic
systems?
2) If an aquatic system has a high concentration of bicarbonate, what will the pH
of that system be? Is this within the ideal range for aquatic organisms?
3) What role does limestone/other similar minerals play in the carbonate cycle?
Instructions: Classroom Samples
**In groups of THREE OR LESS!
1. Get a microscope, plastic slide, plastic pipette, and your water
sample.
2. Collect a sample from any tank within the classroom. You will need
to collect two from freshwater tanks & two from salt water tanks.
3. Place one or two drops from your water sample onto the slide & use
the lower two objectives of the microscope to find any large &
mobile organisms in the sample. Draw a detailed picture of the
organism you find & describe its movement. Mr. Young must sign
off on each sample!
4. From what you observed, which of the previously mentioned
organisms does your sample most resemble? Describe why you
think this.
5. Rinse off the slide and repeat the above steps with different.
Organisms.
Instructions: Classroom Samples – Analysis Questions
1. Diatoms are the most commonly found specimen in this classroom.
What does this tell you about the adaptability, evolution, and niche
of these organisms?
2. Concerning the organisms that were taken from the
sand/gravel/surface of rocks, etc: Which of these organisms are
benthic, nektonic, or planktonic? How do you know this?
3. Look up the approximate pH for the following: bleach, liquid
plumber, battery acid, ammonia, DEET, motor oil.
Bellwork: 10/01/2012
1) How is a salt formed?
2) Define Alkalinity:
3) Review Expectations for cumulative data
Bellwork: Drinking Water Quality
Source  Treatment  Distribution
 What do consumers care about?
 How can that be protect and provided?
 What are the most important chemical parameters?
 HOMEWORK: Bring a sample of outdoor water.
Examples: water in a horse trough, creek, ditch,
puddle in a yard. Your sample needs to be at least 4
fluid ounces.
Bellwork: 10/02/2012
1) What is the difference in species abundance &
species richness? Give an example of each.
2) When considering microbial biology, what is a guild?
3) What is the percentage of global fresh water that is in
glacial form?
4) Important dates: Friday – Extra credit is due,
Aquarium data is due.
Bellwork: 10/0/2012
1) DO NOT change your water yet!
2) Arrange the carbonate compounds from the
carbonate buffering system from most basic to most
acidic. What defines an acid? Base?
3) Which of the toxins used yesterday & today are
hydrophobic? How can you tell?
Bellwork: 10/05/2012
1. Describe the effects of the following situations on microbes within
the environment, how that can effect higher-level organism, and
how the situation could be remediated & prevented in the future:
a) A factory that produces DEET uses water from a local bay to
cool its machinery. A small amount DEET leaks into the bay
once a week when the machines are cleaned.
b) An explosion on an oil platform in the Gulf of Mexico causes
oil to spew into Gulf for two straight weeks.
c) An individual who refuses to properly dispose of his trash
chooses instead to dump his trash in the Brazos River. There
is a very high concentration of half-filled drain cleaner in his
trash that quickly moves into the water.
Extra Credit Opportunity (1/2 Exam Grade)
 Create 10 LAMINATED note cards with the following information:
 Front of Notecard:
 Large, clear, color picture of an organism in the classroom
 Common name & Scientific name
 Back of the Notecard:
 What are some unique and/or defining characteristics of the species?
 What are the differences between males & females if there are any?
Where do they live?
 What do they eat?
 Due Friday: 10/05/2012
Instructions:
1. Get a microscope, plastic slide, and plastic pipette.
2. Place one or two drops from your water sample onto the slide &
use the lower two objectives of the microscope to find any large &
mobile organisms in the sample. Draw a detailed picture of the
organism you find & describe its movement.
3. Add one of the six available toxins to your sample while your lab
partner is looking through the microscope. After several minutes,
draw & describe the resulting effect on the organism you were
observing.
4. Rinse off the slide and repeat the above steps with different
organisms until you have used all six toxins.
5. With your remaining sample(s), test the DO and Nitrate of your
sample using the probes at the front of the classroom.
Questions:
1. What were the responses the organisms had to the toxins?
2. Which toxin seemed to have the greatest effect on the
microscopic organisms? The least? Why do you think this is?
3. What are the expected effects to an ecosystem if the lower-level
organisms died off?
4. Many of the water samples contain very high levels of nitrates
(TAN) and very low DO. Why can the microbes you found survive
at these chemical levels?
5. Name some ideas of how to keep these toxins out of our water
supplies. How can these toxins be removed from a water system
once they are introduced?
6. List the toxic from most dangerous to least dangerous according
to what you thought about these toxins before doing this lab.
Questions: Review
1. What were the responses the organisms had to the toxins?
- Motor oil 
-
Transmission Fluid 
-
DEET 
-
Bleach 
-
Drain Cleaner 
-
Oxalic Acid (Stove Cleaner ) 
Questions: Review
1. What were the responses the organisms had to the toxins?
- Motor oil relatively unreactive, less dense than water
- Transmission Fluid  relatively unreactive, less dense than water
- DEET Causes cells to express caspase is apoptosis cascade
- Bleach Causes the proteins in cells to unravel
- Drain Cleaner Cell membranes lose integrity & lyse
- Oxalic Acid (Stove Cleaner) triggers apoptosis & overwhelms
biochemical reactions
Questions:
2. Which toxin seemed to have the greatest effect on the microscopic
organisms? The least? Why do you think this is?
Questions:
3. What are the expected effects to an ecosystem if the lower-level
organisms died off?
Questions:
4. Many of the water samples contain very high levels of nitrates
(TAN) and very low DO. Why can the microbes you found survive at
these chemical levels?
Questions:
5. Name some ideas of how to keep these toxins out of our water
supplies. How can these toxins be removed from a water system
once they are introduced?
Questions:
6. List the toxic from most dangerous to least dangerous according to
what you thought about these toxins before doing this lab.
Water Chemistry
Drinking Water Quality
Source  Treatment  Distribution
 What do consumers care about?
 How can that be protect and provided?
 What are the most important chemical parameters?
Chemical Compounds in Water
 Inorganic
 Salts dissolve in water and become ions
NaCl  Na+ + Cl-
H2SO4  2H+ + SO4-2
 Acids and bases dissociate depending on pH
 Organic (contain C, H, O and other elements)
 Hydrophilic compounds associate with water
 Ex. Organic acids and phenols dissociate depending on pH
CH3CO2H  H+ + CH3CO2-
Alkalinity
 Alkalinity is a measure of water’s ability to buffer
against addition of an acid, i.e., ability to resist change
of pH upon addition of an acid
 Must understand carbonate system in water to
understand alkalinity
Carbonate System
Carbonic Acid
CO2(g)
Carbonate
Bicarbonate
CO2(aq)
HCO3–
H2CO3
H+
H2O
CO32H+
Ca2+
4
6
pH
8
10
CaCO3(s)
limestone
Carbonate Chemistry
CTOT = [H2CO3] + [HCO3-] + [CO32-]
1.0
[HCO3–]
Fraction of C TOT
[H2CO3]
[CO32-]
0.5
[H2CO3]
0.0
4
6
[HCO3–]
8
[HCO3–]
-0.5
pH
[CO32-]
10
12
Alkalinity
Alkalinity = sum of equivalents of all species that can
neutralize an acid
Alk (eq/L) = (HCO3–)+(CO32-)+(OH–)-(H+)
Microbial Examples
 Diatoms:
 “Brown Algae”
 Fresh and Salt Water phytoplankton
Microbial Examples
 Euglena:
 Single-Celled Protist
 Has both plant and animal features (chloroplasts &
consumes other organisms)
Microbial Examples
 Volvox:
 Type of green algae
 Heavily flagellated
 Rolling/swimming algae cities
Microbial Examples
 Paramecium:
 Single-Celled Protist
 Covered in cilia
 Freshwater organisms that generally feed on bacteria
Microbial Examples
 Hydra:
 Simple fresh water animal
 Has a unique regenerative ability
Microbial Examples
 Daphnia:
 “Water fleas”
 Used as an indicator species
 Consumes yeast, algae, and detritus
Microbial Examples
 Amoeba:
 Single-Celled Protist
 Uses “arms” to move
 Consumers other organisms via phagocytosis
Bellwork: 10/06/2011
1) Where do humans get the majority of their fresh drinking water?
2) How much of the Planet’s water is fresh water?
3) Which organisms are responsible for nitrogen fixation? Are they
aerobic or anaerobic? What is the reaction for nitrogen fixation?
Ecological Concepts
 Microbes account for ~ 50% of all biomass on Earth
 They are ubiquitous on the surface and deep within
the earth
Ecological Concepts
 The diversity of microbial species in an ecosystem can
be expressed in two ways
 Species richness: the total number of different species
present
 Species abundance: the proportion of each species in an
ecosystem
 Microbial species richness and abundance is a function
of the kinds and amounts of nutrients available in a
given habitat
Microbial Species Diversity
High Species Richness and Low to
Moderate Abundance
Low Species Richness and High Abundance
Figure 23.1
Microbial Ecosystems
 Guilds
 Metabolically related microbial populations
 Sets of guilds form microbial communities that
interact with other larger organisms and abiotic
factors in the ecosystem
Populations, Guilds, and Communities
Environments and Microenvironments
 The growth of microbes depends on resources and growth
conditions
 Difference in the type and quantity of resources and the
physiochemical conditions of a habitat define the niche for each
microbe
 For each organism there exists at least one niche in which that
organism is most successful (prime niche)
 Microenvironment
 The immediate environmental surroundings of a microbial
cell or group of cells
Bellwork: 10/04/2012
1. Give an example of a guild.
2. How is organic different than inorganic? Give two examples of
each.
Biofilms: Microbial Growth on Surfaces
 Surfaces are important microbial habitats because
 Nutrients adsorb to surfaces
 Microbial cells can attach to surfaces
Biofilms: Microbial Growth on Surfaces
 Biofilms
 Assemblages of bacterial cells adhered to a surface
and enclosed in an adhesive matrix excreted by the
cells
 The matrix is typically a mixture of polysaccharides
 Biofilms trap nutrients for microbial growth and help
prevent detachment of cells in flowing systems
Examples of Microbial Biofilms
Biofilm on medical
catheter
Natural Biofilm on a Leaf Surface
Cross-Sectional View of
Experimental Biofilm
Biofilm of Iron-Oxidizing Prokaryotes Attached to Rocks
Biofilm Formation
Biofilms: Advantages and Control
 Bacteria form biofilms for several reasons
 Self-defense
 Biofilms resist physical forces that sweep away
unattached cells, phagocytosis by immune system cells,
and penetration of toxins (e.g., antibiotics)
 Allows cells to remain in a favorable niche
 Allows bacterial cells to live in close association with
one another
Freshwater Environments
 Biochemical Oxygen Demand (BOD)
 The microbial oxygen-consuming capacity of a body of
water
Fish Kills from pollution
resulting in increased BOD.
Result: Asphyxiation
Open Oceans
 Most of the primary productivity in the open oceans
is due to photosynthesis by prochlorophytes
 Prochlorococcus accounts for
 > 40% of the biomass of marine phototrophs
 ~50% of the net primary production
Percentage of Total Prokaryotes in the North Pacific Ocean
Figure 23.19
The Deep Sea and Barophilism
 Deep sea microbes are
 Psychrophilic (cold-loving) or psychrotolerant
 Barophilic (pressure-loving) or barotolerant
Hydrothermal vent
Black Smoker
Growth of Barotolerant and Barophilic Bacteria
Figure 23.20
Hydrothermal Vent Microbial Ecosystems
 Deep-sea hot springs
(hydrothermal vents)
support thriving animal
communities that are
fueled by
chemolithotrophic
microbes
Hydrothermal Vent Microbial Ecosystems
 Diverse invertebrate communities
develop near hydrothermal vents,
including large tube worms, clams,
mussels
 Chemolithotrophic prokaryotes that
utilize reduced inorganic materials
emitting from the vents form
endosymbiotic relationships with
vent invertebrates such as vent
tube worms
Tube Worms
Hydrothermal Vent Microbial Ecosystems
Black Smokers
 Thermal vents that
emit mineral-rich hot
water (up to
350°C) forming a
dark cloud of
precipitated material
on mixing with cold
seawater
Microbial Ecology: Biogeochemical
Cycles
The Carbon Cycle
Carbon is cycled through all of Earth’s major carbon reservoirs
(atmosphere, land, oceans, sediments, rocks, and biomass)
The Carbon Cycle
 CO2 in the atmosphere is the most rapidly transferred
carbon reservoir
 CO2 is fixed primarily by photosynthetic land plants and
marine microbes (autotrophs fix carbon dioxide)
 CO2 is returned to the atmosphere by respiration of animals
and chemoorganotrophic microbes as well as by the
activities of humans.
 Microbial decomposition is the largest source of CO2
released to the atmosphere
Nitrogen Cycle
 Nitrogen is essential for amino acids, nucleic acids, etc.
 80% of atmosphere is molecular nitrogen N2
 For plants to use nitrogen it must be fixed (combined with other
elements). Only a few species of bacteria can fix nitrogen!!
 Nitrogen fixation: nitrogen gas is converted to ammonia (requires
enzyme nitrogenase)
 Free-living nitrogen-fixing bacteria
 Symbiotic nitrogen-fixing bacteria
Nitrogen Cycle
Degradation of Chemical by Microbes
Bioremediation
 Bioremediation
 Refers to the cleanup of oil, toxic chemicals, or
other pollutants from the environment by
microorganisms
 Often a cost-effective and practical method for
pollutant cleanup
Petroleum Biodegradation
 Prokaryotes have been used in bioremediation of
several major crude oil spills
Oil Spilled into the Mediterranean Sea
Environmental Consequences of Large Oil Spills
Contaminated Beach in Alaska containing
oil from the Exxon Valdez spill of 1989
Environmental Consequences of Large Oil Spills
Center rectangular plot (arrow) was
treated with inorganic nutrients to
stimulate bioremediation
Petroleum Biodegradation

Diverse bacteria, fungi, and some
cyanobacteria and green algae can oxidize
petroleum products aerobically

Oil-oxidizing activity is best if temperature and
inorganic nutrient concentrations are optimal

Hydrocarbon-degrading bacteria attach to oil
droplets and decompose the oil and dispense
the slick
Petroleum Biodegradation
Some microbes can produce petroleum
 Particularly certain green algae
 Plastics of various types are xenobiotics that are not readily
degraded by microbes
 The recalcitrance of plastics has fueled research efforts into a
biodegradable alternative (biopolymers)
The green alga
Botryococcus braunii
shown here is
excreting oil droplets