Unit 3 Review Flashcards
Review for Quiz 2
Microorganisms in the sulfur cycle can perform 2 types of metabolism. Give and define them
- Assimilative= oxidation of sulfur compounds; create organic sulfur compounds for organism
- Dissimilative= reduction of sulfur compounds; getting energy from sulfur compounds (respiration)
The 5 groups of bacteria and Archaea that control the sulfur cycle are:
- Purple sulfur bacteria
- green sulfur bacteria
- sulfate reducers
- sulfur reducers
- sulfur oxidizers
Green sulfur bacteria and purple sulfur bacteria are ______ phototrophs, meaning
anoxygenic
they can perform photosynthesis without oxygen
Sulfate Reducers
Energy sources (2):
Produce:
Sulfate Reducers
Use H2 & organic compounds (lactate) as energy sources
Produce H2S via sulfate respiration
Which bacteria (2) and archaea (1) are sulfate reducers?
Bacteria: proteobacteria (1 group) and firmicutes
Archaea: Euryarchaeota
Sulfate reducers are ____ anaerobes, meaning they perform sulfate respiration in the absence of oxygen
obligatory
Give 2 alternative metabolisms that sulfate reducers can use
- nitrite reduction
- fermentation (products= H2, CO2, acetate)
List the 7 famous sulfate reducers (6 bacteria, 1 archaea)
Bacteria:
- Desulfomonas
- Desulfotomaculum
- Desulfobacter
- Desulfovibrio
- Thermodesulfobacterium
- Thermodesulfovibrio
Archaea:
- Archaeoglobus
Sulfur reducers use what as an energy source? (2)
these act as the electron ___
- H2
- Organic compounds
these act as the electron donor
Which bacteria (1) and archaea (1) are sulfur reducers?
3 groups of proteobacteria
and
crenarchaeota (archaea)
Sulfur reducers are typically _____ anaerobes, but can use ____aerobic strategies as an alternative metabolism
anaerobes
facultative
Sulfur oxidizers use ___ and ___ as their energy source (ie electron donor)
H2S
S
Which bacteria and archaea are sulfur oxidizers?
3 subgroups of proteobacteria
crenarchaeota
Is Acidithiobacillus ferrooxidans a sulfur oxidizer or a sulfur reducer?
oxidizer
Acidithiobacillus ferrooxidans uses ___ as its electron donor
FeS2
How can Acidithiobacillus ferrooxidans be beneficial for mining?
- it oxidizes FES2, releasing iron from sulfur
- This is bioleaching= metal extraction from ores via microorganisms
- helps humans with the mining process
How can Acidithiobacillus ferrooxidans be harmful for mining?
Bioleaching (caused by oxidation of FeS2) can cause unwanted acidification and can release toxic metals (eg cadmium, aluminum)
It’s possible for many oxidizers to use H2S and O2 together because of the evolution of ecological strategies. List these 3 potential strategies.
Why are these strategies needed?
- O2 dependent positioning
- Anaerobic vacuole
- Symbiotic association
Needed because H2S and O2 are VERY reactive together
Describe the hypothesis of O2 dependent positioning to explain how sulfur oxidizers can use both H2S and O2
- cyanobacteria produce O2 via photosynthesis in the daytime (on top of microbial mats)
- Beggiatoa (a bacteria) stays on the bottom of the mats during the day, and comes up for O2 at night
Both H2S= oxidized and O2= reduced –> produces energy
Describe the hypothesis of the anaerobic vacuole to explain how sulfur oxidizers can use both H2S and O2
- bacteria “thiomargarita” uses this
- Bacteria uses H2S and NO3- (nitrate resp) –> makes S and NH4+
- this process occurs in a vacuole, where the S and NH4+ is stored
- Bacteria uses S and O2 for energy generation instead of H2S and O2
Describe the hypothesis of symbiotic association to explain how sulfur oxidizers can use both H2S and O2
- eukaryotic host= yeti crab
- this host regulates the levels of H2S and O2 (balances)
- bacterium fixes CO2 for the host
= symbiosis
_______ is the enzyme that completes nitrogen fixation (it’s O2 sensitive)
nitrogenase
T/F
Many diazotrophs evolved the ability to protect nitrogenase from oxygen (cyanobacteria)
true
What are the 3 main groups of organisms that control the nitrogen cycle?
- diazotrophs
- nitrifiers
- denitrifiers
Bacteria have __ phyla of diazotrophs, and archaea has __
9
1
T/F
LUCA was likely a sulfur oxidizer
False
LUCA was most likely a nitrogen-fixing bacteria (Diazotroph)
The diversity of diazotrophs is through the ___ gene, NOT _____
Why?
nifH gene (nitrogenase)
NOT
16S r RNA
Inconsistent b/c of horizontal gene transfer
How many unique nifH gene sequences have been described?
more than 30,000!
List 3 famous diazotrophs
- Azotobacter (free living)
- Azospirillim (free living)
- Rhizobium (symbiont)
How do diazotrophs protect dinitrogenase? List & briefly explain the 4 main ways
- Microaerophillic lifestyle: N fixation only if O2 level is less than 2%
- Specialized protective cells: heterocysts in cyanobacteria, spatial separation of N2 fixation
- Increased respiration and conformational protection : high O2 levels triggers synthesis of Shethna proteins, which shield nitrogenase
- Alternative Nitrogenase: regular nitrogenase uses molybdenum as cofactor (or vanadium or iron) –> two genes b/c of duplication = paralogs
What are shethna proteins?
A strategy for diazotrophs to protect dinitrogenase
- high O2 level triggers the synthesis of these
“nitrifiers” generate __
nitrite/ nitrate
What are the 3 groups of nitrifiers?
- Oxidize ammonia to nitrite (NO2-)
- Ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) - Oxidize nitrite to nitrate (NO3-)
- nitrite oxidizing bacteria (NOB) - Comammox
- oxidize ammonia to nitrate completely
Nitrification=
___ –> ____–> ____
NH3 –> NO2- –> NO3-
(ammonia to nitrite to nitrate)
AOB/AOA + ___= complete nitrification
NOB
Lift 5 famous nitrifiers
- Nitrosomonas multiformis
- Nitrosomonas europea
- Nitrosomonas communis
- Nitrospira
- Nitrobacter
AOB genus name begins with “___”
NOB genus name begins with “___”
Nitroso
Nitro
T/F
Nitrifiers are anaerobes and fix nitrogen via the Calvin cycle
False
Nitrifiers= aerobics
- Fix CO2 via the Calvin cycle
Denitrifiers use ___ respiration, and produce gaseous forms of ____ when respiring
anaerobic
nitrogen
Denitrifier path:
___–>___–>___–>____
NO3- –> NO2- –> NO –> N2O (& sometimes even N2)
Nitrifier denitrification= ____ in AOB that creates __ and ___
NirK (nitrite reductase)
NO and N2O
Nitrifier denitrification produces ___ nitrogen species and may ___(inc/dec) the availability of nitrite for NOB
reactive nitrogen species (RNS)
decrease
__________ __________ does nitrifier denitrification in low and high O2 conditions
nitroaomonas europea
It’s suggested that N2 fixation was developed in the early stages of evolution. Is this likely true? Explain why or why not
Fe and molybdenum were abundant on early earth- these are components of N2 fixing enzyme nitrogenase
BUT
The gene complexity for nitrogen fixation and high energy cost of it suggests this could not be the early form of life
Give 4 types of enzymes that are abundant in early anoxic earth
- hydrogenases (nickel)
- cytochromes c proteins (iron and sulfur)
- formate dehydrogenase (molybdenum)
- nitrate reductase (molybdenum)
T/F
nitrifiers are good methanotrophs
FALSE
they are not
If an enzyme had a class B transition metal (eg copper, zinc, cadmium) in early anoxic earth, was it functional?
No
The ocean was very sulfidic: sulfides reacted with transition metals, so they were not available for enzymes
T/F
methanotrophs are good nitrifiers
true!
- oxidase ammonia and hydroxylamine
- the opposite is not true though (nitrifiers are bad methanotrophs)
MOB: Use methane monooxygenase activated by oxygen to make _____ and create ____
CH3OH and H2O
AOB: use ammonia monooxygenase activated by oxygen to make ____ and create ___
NH2OH
H2O
What is the difference between MOB and AOB in terms of NH2OH oxidation?
- AOB evolved the ability to use e- from hydroxylamine oxidation via cytochromes c552 and c554= drive energy production
- Methanotrophs cannot use e- from NH2OH oxidation because they don’t have c552 and c554
T/F
MOB and AOB have different catabolic lifestyles but connection illustrating prokaryotic diversity created by modular evolution of catabolism
true
List the 7 groups of chemotrophic organisms we covered in class
- Iron (Fe3+) reducers
- Iron (Fe2+) oxidizers
- Manganese (Mn4+) reducers
- Manganese (Mn2+) oxidizers
- Predatory bacteria
- stalked bacteria
- bioluminescent bacteria
Iron reducing bacteria evolved the ability to respire solid materials
true
For iron reducing bacteria, __ is the electron acceptor.
Metal Fe3+
- insoluble external e- acceptor
T/F
Iron respiration likely existed in LUCA
true
& then was lost in some lineages
Iron reducers contain outer membrane ______. What do these do?
cytochromes
- facilitate e- transfer to insoluble minerals (nanowires)
List 3 famous iron reducing microorganisms
- thermus
- thermotoga
- geobacter
In Manganese (Mn4+) reducing microorganisms, ___ is the electron acceptor
Metal Mn4+
Anaerobic methane oxidation is coupled to manganese reduction by members of the ____ family “____________”
ANME
Methanoperedenaceae
ANME=
archaea that reduce manganese (but they can also use iron!)
- methane oxidation coupled to manganese reduction
Microbial fuel cell=
the use of metal respiration in biotechnology (metal reducers)
What are the 2 compartments of microbial fuel cell?
Anoxic
- anode
- Fe3+ oxides
- Iron oxides build anode
Oxic
- cathode
Explain the process of microbial fuel cells
- microbes grow in anoxic compartment using organic compounds
- e- are extracted
- e- end up on anode
= reduction of iron (Fe3+ reduced to Fe2+)
In microbial fuel cells, the e- are driven through the anode to the ____ (oxic area).
- In the oxic compartment, ___ is created
- The remaining energy can be captured in the __ compartment and used (to turn on light bulbs etc!)
cathode
H2O
oxic
T/F
Iron oxidation trait evolved quite late in earth history
false
early
Iron oxidizing microorganisms use __ as the e- donor. They’re strongly affected by ___ and ____
Fe2+
pH and O2
Iron oxidizers can be divided into 4 functional groups. List and briefly describe each
- Aerobic, acidophillic iron oxidizers
- respire S, live in very low pH - Aerobic, neutrophillic iron oxidizers
- oxidation of iron creates stalk; eg Gallionella - Anaerobic chemotrophic iron oxidizers
- iron-nitrate pair; potential metabolism on mars - Anaerobic phototrophic iron oxidizers
- purple and green non-sulfer iron oxidizing bacteria (Rhodobacter ferriixidans and Chlorobium ferroxidans)
There are genes that encode for enzymes involved in iron oxidation and the creation of _________
magnetosomes
Explain what magnetosomes are and what they do
= intracellular structures that contain a lipid bilayer and have their own transporters
- function= oxygen sensing
- Magnetosomes orient themselves towards earth’s magnetic pool (=aerotaxis or magneto-aerotaxis)
Thanks to the iron oxides in magnetosomes, cells are aligning and migrate together toward specific oxygen gradient
Manganese (Mn2+) oxidizing organisms:
-Oxidize _____ (electron donor)
- Reduce _____ (electron acceptor)
manganese is oxidized, oxygen is reduced
What is the purpose of Mn oxidation?
to make their own TEA
The famous Mn oxidizer is sporulating ____
bacillus
How do Mn oxidizing organisms make their own TEA?
- Have a multicopper oxidase enzyme
- the result is Mn-oxide, which serves as a protective coat
List 3 famous predatory bacteria
Vampirococcus
Bdellovibrio
Myxococcus
Vampirococcus is a(n) _______ predator
Bdellovibrio is a(n) _______ predator
Myxococcus is a(n) _______ predator
Options: Intracellular, periplasmic, social
Vampirococcus is an intracellular predator
Bdellovibrio is a periplasmic predator
Myxococcus is a social predator
Explain how the predatory bacteria “Bdellovibrio” functions
- invades periplasmic of prey cells
= periplasmic predator
Explain how the predatory bacteria “Vampirococcus” functions
- attaches to the surface of their prey
- acquires nutrients from prey’s cytoplasm and periplasm (intracellular)
Explain how the predatory bacteria “Myxococcus” functions
- lyse prey and feed on their nutrients
= social predators
Stalked bacteria produced cytoplasmic extrusions, collectively called “__________”. Give 3 examples
prosthecae
- stalks
- hyphae
- appendages
What do prosthecae do?
- allow organisms to attach to particulate matter, plant material, or other microorganisms in aquatic habitats
- can reduce cell sinking
Give 2 examples of famous stalked bacteria
- Caulobacter
- Gallionella
Caulobacter is a ___ bacteria that’s a chemoorganotroph. It’s ____ is filled with cytoplasm
stalked
stalk
Gallionella is a famous ___ bacteria. It’s a(n) _____ oxidizer, and has a stalk composed of ___
stalked
iron
Fe3+
Give 3 famous genera of bioluminescent bacteria
- vibrio
- aliivibrio
- photobacterium
Most bioluminescent bacteria live in __ enviros and some of them colonize special light organs in ___ and ___
marine
fish and squids
T/F
Bioluminescent bacteria produce light that animals often use for signaling to avoid predators/ attract prey
true
Luciferase enzyme=
found in bioluminescent bacteria
- produces light, alcohol, and water
luminescence in bacteria requires the gene ____ for luciferase
luxCDABE
T/F
luminescence in many bioluminescent bacteria only occurs at low population density
False
the opposite is true (only at high pop)
Transcription of luciferase genes is controlled via ___ ____ molecules. How do they do that?
AHL inducer molecules
- they cross cell membranes of other cells and induce luciferase expression
