Lecture 10: Environmental Microbiology Flashcards
Define biogeochemical cycling
The sum of microbial and chemical processes that drive the flow of elements between sediments, waters, and the atmosphere
What are the 6 key elements of environmental microbiology?
1) C
2) N
3) S
4) P
5) Fe
6) Mg
What are the 6 key factors of environmental microbiology?
1) Temperature
2) Pressure
3) Salinity
4) pH
5) Nutrient availability
6) Redox potential
Humans produce a lot of carbon dioxide through industry; thankfully bacteria can do what?
Carbon dioxide fixation and carbon monoxide oxidation
The degradation of organic matter is dependant on what 4 things?
- Redox potential of environment
- Nutrient availability
- Abiotic conditions (pH, Temp, O2)
- Microbial community
Define mineralization
The process by which complex organic matter is decomposed to release simpler, inorganic compounds
1) What influences organic carbon decomposition?
2) What do fossil fuels release into the environent?
1) Oxygen
2) Methane, carbon dioxide, carbon monoxide, other problematic chemicals
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?
1) CO2, CH4, and nitrous oxide
2) Global temperature has had more variation but is generally rising
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?
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
1) Describe the marine carbon cycle
2) What is the marine carbon cycle entirely dependent on?
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.
1) Name 4 things that can be seen in the nitrogen cycle
2) __________ species does denitrification of nitrates into nitrites (NO2-)
1) Nitrites, nitrates, ammonia, and bacteria.
2) Nitrobacter
1) Describe the abundance of nitrogen
2) Where is nitrogen often stored?
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
Name the 7 bacteria involved in the nitrogen cycle and what type of reaction they are involved in
1) Fixation: Azotobacter and Rhizobia
2) Nitrification: Nitrosomonas and Nitrobacter
3) Denitrification: Pseudomonas and Paracoccus denitrificans and thiobacillus
Define ammonification and nitrification
1) Ammonification: Release of ammonia (NH3) due to deamination (proteins into amino acids)
2) Nitrification: Ammonium ion is oxidized to produce nitrate
Define denitrification and nitrogen fixation
1) Denitrification: Nitrate ion is used as an electron acceptor in the absence of oxygen
2) Nitrogen fixation: Conversion of nitrogen gas into ammonia
1) What plays a minor part in the fixing of nitrogen?
2) Define eutrophication
3) Define leaching
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
1) Define an anammox (anoxic ammonium oxidation) reaction
2) What is an assimilatory reaction?
3) What is a dissimilatory reaction?
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
Nitrogen cycle:
1) What does microbial decomposition do?
2) What does microbial ammonification do?
3) What does nitrogen-fixation do?
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)
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?
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
Name the 5 bacteria involved in the sulfur cycle
1) Alteromonas
2) Desulfovibrio
3) Thiobacillus
4) Thiothrix
5) Thiomargarita
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?
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.
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?
1) Needed for life but only a small fraction of biomass.
2) Organisms have difficulty processing sulfur.
3) Underground.
What part of the sulfur cycle is a regulator of the global climate? How?
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.
1) List 4 things involved in the sulfur cycle
2) What does Thiobacillus do? What does it require?
1) Sulfite, sulfate, elemental sulfur, hydrogen sulfide
2) Produces sulfate from elemental sulfur; requires nitrogen
Name 2 things that contribute sulfur. Include what form they contribute sulfur in.
1) Volcanoes (SO2)
2) Deep sea vents (H2S)
Describe the roles of algae, the continental shelf, and hydrothermal vents in the sulfur cycle
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.
Lots of _______ and _________ have evolved to contribute to the sulfur cycle
bacteria and archaea
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?
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.
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?
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.
Name the bacteria that is involved in all 3 cycles (nitrogen, sulfur, phosphorus) and describe its role in the phosphorus cycle
Thiobacillus produces an acid that causes phosphate to be released
Define bioremediation, biosensors, and exposing coliforms.
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
List and describe the 4 steps of water treatment
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
Define the following:
1) Mutualism
2) Cooperation
3) Commensalism
4) Predation
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
Define the following:
1) Parasitism
2) Amensalism
3) Competition
1) Parasitism: Parasite lives in host
2) Amensalism: One hurts the other
3) Competition: One outcompetes the other or both coexist at lower levels
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?
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.
1) Give 2 examples of cooperation
2) Give an example of am
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)
List the 5 bacteria involved in the sulfur cycle and if the reactions they’re involved in are assimilatory and dissimilatory
1) Alteromonas: dissimilatory
2) Desulfovibrio: dissimilatory
3) Thiobacillus: assimilatory
4) Thiothrix: assimilatory
5) Thiomargarita: assimilatory
