Lecture 10: Environmental Microbiology

Question 1

Define biogeochemical cycling

Answer 1

The sum of microbial and chemical processes that drive the flow of elements between sediments, waters, and the atmosphere

Question 2

What are the 6 key elements of environmental microbiology?

Answer 2

1) C
2) N
3) S
4) P
5) Fe
6) Mg

Question 3

What are the 6 key factors of environmental microbiology?

Answer 3

1) Temperature
2) Pressure
3) Salinity
4) pH
5) Nutrient availability
6) Redox potential

Question 4

Humans produce a lot of carbon dioxide through industry; thankfully bacteria can do what?

Answer 4

Carbon dioxide fixation and carbon monoxide oxidation

Question 5

The degradation of organic matter is dependant on what 4 things?

Answer 5

1. Redox potential of environment
2. Nutrient availability
3. Abiotic conditions (pH, Temp, O2)
4. Microbial community

Question 6

Define mineralization

Answer 6

The process by which complex organic matter is decomposed to release simpler, inorganic compounds

Question 7

1) What influences organic carbon decomposition?
2) What do fossil fuels release into the environent?

Answer 7

1) Oxygen
2) Methane, carbon dioxide, carbon monoxide, other problematic chemicals

Question 8

1) Global stores of ____, _____, and ______ have exploded in recent years (1900s-2000s) due to human industry
2) As these stores have risen, what else has risen?

Answer 8

1) CO2, CH4, and nitrous oxide
2) Global temperature has had more variation but is generally rising

Question 9

1) Global industry puts combusted fossil fuels back into the atmosphere, which can affect what 3 things?
2) What happens when too much land becomes deforested?

Answer 9

1) Oceans, soils, and temperature
2) Agriculture has caused changes in land use; when there’s less trees, the soil microbes respire much faster, producing much more CO2

Question 10

1) Describe the marine carbon cycle
2) What is the marine carbon cycle entirely dependent on?

Answer 10

1) CO2 can be harnessed by phytoplankton, which leads to dissolved organic matter (carbon, nitrogen, and phosphorus), which heterotrophic bacteria use to produce CO2 and inorganic nutrients.
2) Solely depends on bacteria to cycle the carbon in the water.

Question 11

1) Name 4 things that can be seen in the nitrogen cycle
2) __________ species does denitrification of nitrates into nitrites (NO2-)

Answer 11

1) Nitrites, nitrates, ammonia, and bacteria.
2) Nitrobacter

Question 12

1) Describe the abundance of nitrogen
2) Where is nitrogen often stored?

Answer 12

1) Nitrogen is the 4th most abundant element in organisms, but can be limited in many ecosystems
2) In bedrock below topsoil, subsoil, and weathered rocks

Question 13

Name the 7 bacteria involved in the nitrogen cycle and what type of reaction they are involved in

Answer 13

1) Fixation: Azotobacter and Rhizobia
2) Nitrification: Nitrosomonas and Nitrobacter
3) Denitrification: Pseudomonas and Paracoccus denitrificans and thiobacillus

Question 14

Define ammonification and nitrification

Answer 14

1) Ammonification: Release of ammonia (NH3) due to deamination (proteins into amino acids)
2) Nitrification: Ammonium ion is oxidized to produce nitrate

Question 15

Define denitrification and nitrogen fixation

Answer 15

1) Denitrification: Nitrate ion is used as an electron acceptor in the absence of oxygen
2) Nitrogen fixation: Conversion of nitrogen gas into ammonia

Question 16

1) What plays a minor part in the fixing of nitrogen?
2) Define eutrophication
3) Define leaching

Answer 16

1) Lightening actually plays a minor part in the fixation of nitrogen; its extreme heat causes oxygen to combine with nitrogen to form oxides in the atmosphere
2) Eutrophication: Ecosystem response to addition of artificial or natural substances into an aquatic system (ex: algal blooms).
3) Leaching: The loss of water-soluble nutrients from the soil due to rain and irrigation

Question 17

1) Define an anammox (anoxic ammonium oxidation) reaction
2) What is an assimilatory reaction?
3) What is a dissimilatory reaction?

Answer 17

1) Anammox reaction: Chemolithotrophs use ammonium ion as electron donor and nitrite as terminal electron acceptor to make N2 gas
2) Building reaction
3) Breaking reaction

Question 18

Nitrogen cycle:
1) What does microbial decomposition do?
2) What does microbial ammonification do?
3) What does nitrogen-fixation do?

Answer 18

1) Break down proteins and waste products into amino acids
2) Break down amino acids (-NH2) into ammonia (NH3)
3) Turn N2 into NH3 (ammonia)

Question 19

Nitrogen cycle:
1) What does Nitrosomonas do? What type of reaction is this?
2) What does Nitrobacter do? What type of reaction is this?
3) What does Pseudomonas do? What type of reaction is this?

Answer 19

1) Convert ammonium ion (NH4+) into nitrite ion (NO2-): Nitrification
2) Convert nitrite (NO2-) into nitrate (NO3-): Nitrification
3) Convert nitrate (NO3-) into N2: Denitrification

Question 20

Name the 5 bacteria involved in the sulfur cycle

Answer 20

1) Alteromonas
2) Desulfovibrio
3) Thiobacillus
4) Thiothrix
5) Thiomargarita

Question 21

1) What is a major source of sulfate?
2) Where is sulfur found?
3) What is sulfur reduced by and what is it reused in?

Answer 21

1) The weathering of rocks is a major source of sulfate
2) In fossil fuels, vegetables, etc.
3) Reduced by plants and microbes and reused in proteins, coenzymes, bridging ligands, and amino acids.

Question 22

1) Is sulfur needed for life? Does it make up a large amount of biomass?
2) Is sulfur easy to process?
3) Where are large sulfur deposits found?

Answer 22

1) Needed for life but only a small fraction of biomass.
2) Organisms have difficulty processing sulfur.
3) Underground.

Question 23

What part of the sulfur cycle is a regulator of the global climate? How?

Answer 23

Atmospheric sulfate in the air is a regulator of the global climate; helps create cloud cover that cools cities and can help with global worming.

Question 24

1) List 4 things involved in the sulfur cycle
2) What does Thiobacillus do? What does it require?

Answer 24

1) Sulfite, sulfate, elemental sulfur, hydrogen sulfide
2) Produces sulfate from elemental sulfur; requires nitrogen

Question 25

Name 2 things that contribute sulfur. Include what form they contribute sulfur in.

Answer 25

1) Volcanoes (SO2)
2) Deep sea vents (H2S)

Question 26

Describe the roles of algae, the continental shelf, and hydrothermal vents in the sulfur cycle

Answer 26

1) Algae: metabolize sulfate which produces DMSP. Many microbes can utilize DMSP to make MESH, DMS (highly reactive and escape into atmosphere)
2) Continental shelf: H2S can be re-oxidized by Thiomargarita
3) Hydrothermal vents: sulfate precipitates out of the sea water (CaSO4); lots of H2S. Allows for ecosystems to form around the vents.

Question 27

Lots of _______ and _________ have evolved to contribute to the sulfur cycle

Answer 27

bacteria and archaea

Question 28

1) What is the phosphorus cycle required for?
2) What plays a large role in the phosphorus cycle?
3) Where is phosphorus found? Where is it used?

Answer 28

1) Required for nucleic acids, lipids, some polysaccharides.
2) pH plays a large role in the form of phosphate
3) Found in rocks and bird poop. Used in fertilizer.

Question 29

1) Does the phosphorus cycle have a gaseous component?
2) In which 3 places does phosphorus collect?
3) What does the phosphorus cycle form?
4) Organic matter is broken down into what?

Answer 29

1) No gaseous component, so it collects
2) In the sea, in the earth, in calcium phosphate deposits,
3) Forms insoluble complexes and go into water sources.
4) Organic matter is broken down into elemental phosphorus to enter the cycle.

Question 30

Name the bacteria that is involved in all 3 cycles (nitrogen, sulfur, phosphorus) and describe its role in the phosphorus cycle

Answer 30

Thiobacillus produces an acid that causes phosphate to be released

Question 31

Define bioremediation, biosensors, and exposing coliforms.

Answer 31

1) Bioremediation: The use of microbes to detoxify or degrade pollutants
2) Biosensors: Microbes can locate biologically active pollutants (by exposing the presence of a chemical). Bioluminescence can be used to detect (ex: TNT).
3) Exposing coliforms: ONPG + MUG

Question 32

List and describe the 4 steps of water treatment

Answer 32

1) Water is held in reservoir, particles settle
2) Flocculation: Removal of colloidal materials (aggregates)
Flocculant: Aggregates materials (ex: Al, Fe, C, Mg)
3) Filtration: 2-4 feet of fine sand or anthracite coal. Eliminates almost all potentially harmful bacteria.
4) Ozone treatment: Disinfecting the water using UV + electricity = O3 (highly reactive) or chlorination. Ozonation leaves no taste or odor.
5) Water is stored and used by consumers

Question 33

Define the following:
1) Mutualism
2) Cooperation
3) Commensalism
4) Predation

Answer 33

1) Mutualism: Both organisms benefit; obligatory
2) Cooperation: Both organisms benefit, not obligatory
3) Commensalism: One helps the other.
4) Predation: One benefits, one is harmed

Question 34

Define the following:
1) Parasitism
2) Amensalism
3) Competition

Answer 34

1) Parasitism: Parasite lives in host
2) Amensalism: One hurts the other
3) Competition: One outcompetes the other or both coexist at lower levels

Question 35

1) What is trichonympha and what does it do?
2) What lives inside trichonympha and what does it do?
3) What do they both produce?

Answer 35

1) A protozoan that lives inside a termite gut that breaks down cellulose from wood.
2) TG1 lives inside the protozoan that converts glutamine and ammonia into amino acids and cofactors that can be broken down.
3) Both produce CO2 and many of these terminal products can be used by the host termite.

Question 36

1) Give 2 examples of cooperation
2) Give an example of am

Answer 36

1) a) Chromatium converts light into SO4-2 and OM, which is converted by Desulfovibrio into CO2 and H2S.
b) Cellulomonas (cellulose degrader) converts NH4+ onto glucose, which is converted from N2 by azotobacter (nitrogen fixer)
2) Amensalism: Attine ant cultivates a fungal garden; the parasite on the fungal garden of an ant is kept at bay because of the relationship between the ant and Pseudonocardia (which controls the parasite)

Question 37

List the 5 bacteria involved in the sulfur cycle and if the reactions they’re involved in are assimilatory and dissimilatory

Answer 37

1) Alteromonas: dissimilatory
2) Desulfovibrio: dissimilatory
3) Thiobacillus: assimilatory
4) Thiothrix: assimilatory
5) Thiomargarita: assimilatory