Carbon Cycle/Photosynthesis Flashcards
1
Q
Where did carbon come from originally?
A
likely from star nucleosynthesis
this idea was established in 1957
2
Q
Who was Messier?
A
an 18th century astronomer who listed over 100 objects in the sky that weren’t comets
2
Q
what is the crab nebula M1? what does the M stand for?
A
it was most likely a star that exploded by a supernova ~900 years ago
M = Messier
2
Q
why is the crab nebula M1 called a ‘visiting star’?
A
in 1024 AD when it likely exploded, there was a a very bright star visible during the day for 23 days and for 3 years in the night sky = the supernova
3
Q
what is star/stellar nucleosynthesis?
A
the creation of chemical elements from the explosion of stars
4
Q
What is the Bethe-Weizsacker cycle?
A
aka the CNO cycle - also a type of stellar nucleosynthesis
one of 2 fusion reactions that stars use to convert hydrogen to helium
caused the production of natural isotopes of C, N and O (both radioactive and stable)
5
Q
What are examples of radioactive C and N isotopes?
A
C14, N13
6
Q
Examples of stable C and N isotopes?
A
C13
N15
7
Q
Where is the largest pool of carbon on earth?
A
coal, oil, etc. and sediments
8
Q
Which phyla of bacteria are photosynthetic?
A
filamentous green bacteria (Chloroflexi)
Green sulfur bacteria (Chlorobi)
Firmicutes
Cyanobacteria
Proteobacteria
9
Q
What is the most ancient known ancestor of photosynthetic bacteria?
A
Thermotoga
10
Q
Which photosynthetic bacteria evolved first?
A
Chloroflexi (filamentous green bacteria)
11
Q
Where in BC would you expect to find green sulfur bacteria (Chlorobi)?
A
in Lake Mahoney, where there’s high sulfur concentration
12
Q
what is an example of Chlorobi (green sulfur bacteria) you’d expect to find in Lake Mahoney, BC?
A
Chlorobium (green)
13
Q
What type of ecosystems do Firmicutes live in?
A
rice paddies
14
Q
What is the only species of Firmicutes?
A
Heliobacterium
15
Q
What type of bacteria are Firmicutes?
A
gram positive
16
Q
Of the photosynthetic bacteria, which are oxygenic? anoxygenic?
A
oxygenic: Cyanobacteria
anoxygenic: Chloroflexi, Chlorobi, Firmicutes, Proteobacteria
17
Q
Which bacteria phylum was the origin of chloroplasts?
A
cyanobacteria
18
Q
Where in BC would you expect to find proteobacteria?
A
Mt Doug
19
Q
Are proteobacteria green or purple?
A
purple
20
Q
What are Firmicutes sometimes called? why?
A
Heliobacterium because they’re only one species
21
Q
What are proteobacteria sometimes called?
A
purple bacteria
22
Q
What light harvesting pigments do purple bacteria (proteobacteria), green bacteria, and heliobacterium have?
A
(Bchl) Bacteriochlorophyll
and
aliphatic, monocyclic carotenoids
23
What are the main electron carriers in proteobacteria, green bacteria, and heliobacterium photosynthesis?
bacterial ferredoxins
24
what are ferredoxins?
small proteins with iron and sulfur atoms
electron carriers
25
What light harvesting pigments do cyanobacteria (and rhodophytan chloroplasts) have?
chlorophyll a
phycobilliproteins
26
What are the main electron carriers in cyanobacteria (and rhodophytan chloroplasts) photosynthesis?
plant ferredoxins
plastoquinones
plastocyanin
cytochrome f
27
What light harvesting pigments do prochlorophytes and chlorphytan chloroplasts have?
chlorophyll a and b
Beta-carotene and derivatives
28
What are the main electron carriers in prochlorophytes and chlorphytan chloroplasts
photosynthesis?
plant ferredoxins
plastoquinones
plastocyanin
cytochrome f
29
Which bacteria have photosynthetic elements more similar to plants?
cyanobacteria
30
describe the general structure of a photosynthetic apparatus
pigment antenna detects light and surrounds and sends signals to the reaction center chlorophyll
the reaction center is 2-3 chlorophyll bound to proteins
the RCC sends signals to the + and - end of the ET system which exchanges ADP for ATP
31
Where is the pigment antenna located in a cell?
its in the membrane
32
What is the function of the pigment antenna?
to expand the range of photons that can be captured
33
What is the RCC made of?
2-3 chlorophyll bound to proteins
34
What is the ET system?
the electron transport chain
35
What is another term for reaction center?
photosystem
36
Describe the photosynthetic apparatus for purple (proteo) and green bacteria (Chlorobi, chloroflexi)
pigment antenna: carotenoids capture short visible light, bacteriochlorophyll(s) capture red and infrared light
RC: Bacteriochlorophyll receives signal from pigment antenna and transfers electrons to the ETC to produce energy
37
What is ferris?
Fe2+, grey coloured (reduced)
38
What is ferric?
Fe3+, red (more oxidized)
39
What type of light do the carotenoids in the pigment antenna of green and purple bacteria absorb?
visible light (short)
40
What type of light do the bacteriochlorophyll in the pigment antenna of green and purple bacteria absorb?
red and infrared
41
What components are in the pigment antenna of purple and green bacteria?
carotenoids
bacteriochlorophyll
the light harvesting pigments
42
What components are in the pigment antenna of cyanobacteria and chloroplasts?
phycobilliproteins
chlorophyll a
43
What type of light do the light harvesting pigments of cyanobacteria and chloroplasts absorb?
phycobiliproteins absorb 550-660 nm
chlorophyll a absorbs > 660 nm
44
Describe the photosynthetic apparatus for cyanobacteria and chloroplasts
pigment antenna:
phycobilliproteins and chlorophyll a absorb light (550-660nm, > 660 nm)
phycobiliproteins send information to RC II and can do RC I
chlorophyll a only sends to RC I
RC II splits H2O into 1/2 O2
RC I uses NADPH and NADP
electrons sent to the ET to convert ADP to ATP
45
Which is the reduced version: NADPH or NADP?
NADPH is reduced
NADP+ is oxidized
MORE H+ = MORE REDUCED
46
What are the 2 reaction centers for cyanobacteria and chloroplasts? what do they do?
RC I:
- uses photons sent from chlorophyll a
- uses NADP/NADPH
- sends e- to NADPH/NADP
RC II:
- uses photons from phycobiliproteins
- splits H2O
- sends e- to ETC
47
Which of the photosynthetic bacteria conduct oxygenic photosynthesis?
only cyanobacteria
48
What is the primary product of energy conversion for anoxic photosynthesis by green bacteria?
ATP
49
What is the primary product of energy conversion for anoxic photosynthesis by green sulfur bacteria?
ATP + NADH
50
What is the primary product of energy conversion for anoxic photosynthesis by purple and non-sulfur bacteria?
ATP
51
What is the primary product of energy conversion for anoxic photosynthesis by heliobacteria?
ATP + NADH
52
What is the primary product of energy conversion for oxygenic photosynthesis by cyanobacteria?
ATP + NADH
53
Which bacteria produce only ATP from energy conversion during photosynthesis?
non sulfur green and sulfur purple bacteria
54
Which bacteria produce both ATP + NADH as primary product of energy conversion during photosynthesis?
green sulfur bacteria
heliobacteria
cyanobacteria
55
What electron donors do green bacteria use?
organic
sulfur
thiosulfate (S2O3-)
56
What electron donors do green sulfur bacteria use?
H2
S2
So
thiosulfate (S2O3-)
57
What electron donors do purple and non-sulfur bacteria use?
H2
S2
So
thiosulfate
58
Describe the chemical structure of chlorophyll a
4 nitrogen atoms surrounding a magnesium at the center (tetrapyrrole ring)
cyclopentanone ring
phytol (long carbon chain)
reduced = more H bound
59
What is phytol?
a long carbon chain that anchors chlorophyll a and Bchl to cell membranes
60
What does the similarity of the tetrapyrrole ring in chlorophyll a to other cofactors (ex. heme b, heme d1, cobalamin, coenzyme F430)?
with 16s rRNA it can help understand the evolution of chl pigments
61
What is chlorophyll a?
a cofactor that is essential to oxygenic photosynthesis
62
What are cofactors? give examples
non-protein, inorganic chemical compounds that bind to enzymes or other proteins
these can be metals
ex. Mg, Cu, Fe, Zn, selenium
63
What are coenzymes? give examples
non-protein, organic molecules that carry chemicals BETWEEN enzymes
NAD
FAD
coenzyme A
64
What is heme?
a metal-binding compound that is incorporated into enzymes (ex. cytochromes) or other proteins (ex. hemoglobin)
65
What type of molecules contain heme?
enzymes and non-enzyme proteins
66
What are the 2 major reactions in oxygenic photosynthesis?
light reaction (absorption of photons, production and transport of e- to produce energy as ATP and NADPH)
dark reaction (Calvin cycle) (assimilation of CO2)
67
What is the model organism used to study anoxygenic photosynthesis?
Rhodobacter capsulatus
a purple non-S bacteria
68
What are the 6 major proteins involved in anoxygenic photosynthesis (Rhodobacter capsulatus)?
Light harvesting I
light harvesting II
reaction center
cytochrome bc1
cytochrome c
proton ATPase
69
Describe the protein structure of LHI for anoxygenic photosynthesis
composed of 2 small Bch-binding polypeptides (heterodimers with alpha and beta subunit)
each heterodimer binds to 2 bchl
70
Describe the protein structure of LHII for anoxygenic photosynthesis
composed of 2 small Bch-binding polypeptides (heterodimer with alpha and beta subunit)
each heterodimer binds to 3 bchl and 2 carotenoids
71
What are carotenoids? what do they do?
they are photosynthetic pigments in the antennae of reaction centers that expand the range of light absorption
72
Describe the protein structure of the RC for anoxygenic photosynthesis
large and complex protein
composed of 3 peptide subunits: L, M, H
transmembrane proteins
bind 4 bchl, 2 bacteriophaeophytin (bchl without Mg), 2 quinones, Fe, and 1 carotenoid
73
What is the RC in Rhodobacter capsulatus similar to?
the P680 (RC II) in cyanobacteria
74
Describe the protein structure of cytochrome bc1 for anoxygenic photosynthesis
composed of 2 hemes, 1 Fe-S center, and 2 quinones
2x b cytochrome bind a heme each (non-covalent)
1x c cytochrome bind a heme (covalent)
75
T or F: cytochrome bc1 is only found in purple non-sulfur bacteria
false, it's found in many bacteria and mitochondria
76
What is the function of cytochrome bc1?
it acts as a proton pump to shuttle H+ across the membranes and uses electrons from bchl (ie., creates the proton gradient between the periplasmic space and cytoplasm necessary for proton ATPase)
77
Describe the protein structure of cytochrome c for anoxygenic photosynthesis
a small, water soluble protein with one heme
78
What is the function of cytochrome c in anoxygenic photosynthesis?
it's a mobile e- carrier between the oxidizing side of the RC and the reducing side of the proton pump
it recycles e- back to the RC and maintains the cycle
79
Describe the protein structure of a proton ATPase for anoxygenic photosynthesis
2 subunits: F1 and F0
F1 subunit is very large and complex with 3 alpha, 3 beta, a gamma, a delta, and an epsilon
- in the cytoplasm
F0 is transmembrane
80
T or F: proton ATPase are only found in some bacteria
false,
they are HIGHLY conserved and are a defining characteristic of bacteria
81
What else shares the commonality of proton ATPases with bacteria?
chloroplasts and mitochondria
82
Describe the function of a proton ATPase
F0 subunit in the membrane accepts a single H+ ion from the cytoplasm per (10?) little unit, each time rotating in a circle and releasing an H+ into the periplasmic space
83
Which photosynthetic bacteria have cyclic flow in their light reactions?
all anoxygenic photosynthesis: cytochrome c recycles the e- from the ETC back to the PS (RC) to continue
cyanobacteria can have cyclic flow if the ferredoxin carries the e- to the cytochrome bf
84
Which photosynthetic bacteria have linear flow of electrons in their light reactions?
only oxygenic have the option for linear flow = cyanobacteria
but cyanobacteria can also have cyclic
85
T or F: oxygenic photosynthesis only has linear flow of e-
false, it can have cyclic too at ferredoxin in RS I sending e- to cytochrome bcf in RS II
86
What is quinone?
highly abundant e- carriers in the ETC of both oxygenic and anoxygenic photosynthesis
87
T or F: Q is only an e- carrier in oxygenic photosynthesis
false, it's present in both oxygenic and anoxygenic
88
What splits H2O to release H+ in the ETC of oxygenic photosynthesis?
cytochrome bf
89
How many H+ ions are moved from the cytoplasm into the periplasmic space by cytochrome bc1 during anoxygenic photosynthesis?
2 H+
90
How many H+ ions are pumped back from the periplasmic space into the cytoplasm by ATPase?
for every rotation of ATPase, 3 H+ ions are moved
91
What is the overall reaction for photosynthesis?
6 CO2 + hv + 6 H2O --> C6H12O6 + 6 O2
92
Describe the oxygenic dark reaction steps
6 CO2 (1 C) molecules react with 6 H2O molecules (with RuBP) = 12 PGA (3C)
12 ATP = 12 ADP + Pi
12 NADH oxidized to 12 NAD+
12 PGA converted to 12 G3P (3 C)
2 G3P will leave and enter gluconeogenesis
another 12 ATP = ADP + Pi
10 G3P used to make 6 RuBP (5 C)
RuBP combines with 6 more CO2 and cycle continues
93
What is RuBP? what does it stand for?
Ribulose 1,5-bisphosphate
an organic molecule that accepts CO2 during oxygenic photosynthesis
it is used to accept CO2 and then regenerated during the dark reaction (Calvin cycle)
94
What are the products of the oxygenic light reactions?
18 ATP + 12 NADPH (reduced)
ENERGY to power the dark reactions
95
What are the inputs for the dark reactions of oxygenic photosynthesis?
products of the light rxns
18 ATP + 12 NADPH (energy)
6 CO2 + 6 H2O
96
What are the outputs for the dark reactions of oxygenic photosynthesis?
regeneration of RuBisco
6 RuBP ready to accept more CO2
2 G3P (3C) leave for gluconeogenesis
12 NADP+ and 17 ADP ready to
97
Who else helped Calvin understand the oxygenic dark reactions? How did they discover it?
Benson and Bassham
labelled CO2 with 14C isotope to measure [CO2] over time to determine where and how much C was being traded and by what molecules
98
What is the balanced reaction for the oxygenic light rxns?
15 H2O + hv → 7.5 O2 + 30 H+
27 H+ + 18 ADP + 18 Pi → 18 ATP
12 H+ + 12 NADP+ → 12 NADPH
99
What is the balanced reaction for the oxygenic dark rxns?
6 CO2 + 18 ATP + 12 NADPH → C6H12O6 (PO3H2) + 12 NADP+ + 17 ADP + 17 Pi
100
What is the balanced reaction for the ANoxygenic light rxns?
H2S + hv → S0 (in or out) + 2 H+
3H+ + 2 ADP + 2 Pi → 2 ATP
101
T or F: all anoxygenic dark reactions follow the same processes
false
102
What is the dark reactions pathway for green S bacteria?
reverse citric (Kreb's) cycle
ie., CO2 is added, not removed
103
What is the dark reactions pathway for non-S green bacteria?
hydroxypropionate (3C) cycle
104
What is the dark reactions pathway for purple bacteria?
sine can directly assimilate organic acids from the environment
some use Calvin cycle (but not in a carboxysome with RuBisco)
105
What is RuBisco? Why is it important/what is its function?
ribulose 1,5-bisphosphate carboxylase/oxygenase
an enzyme in the Calvin cycle that catalyzes the reaction between CO2 and RuBP (carbon fixation)
106
What types of environments do purple sulfur bacteria live in?
high [S]
ex. hotsprings
107
What types of environments do non-S purple bacteria live in?
low [S]
ex. Mt Doug
108
What are the orders of purple S bacteria that do photosynthesis?
Gammaproteobacteria
Chromatiales
109
What are the orders of purple non-S bacteria that do photosynthesis?
beta proteobacteria
alpha proteobacteria
110
What are the orders of aerobic purple bacteria that do photosynthesis?
alpha proteobacteria
111
What are 2 families of purple sulfur bacteria?
Chromatiaceae
Ectothiorhodospiraceae
112
What type of photosynthetic pigments can purple S bacteria use?
either bchl a or b
113
Which family of purple S bacteria accumulates elemental sulfur inside its cells?
Chromatiaceae
114
Which family of purple S bacteria accumulates elemental sulfur outside its cells?
Ectothiorhodospiraceae
115
What are 2 genera of purple S bacteria?
Chromatium and Ectothiorhodospira
116
What is a local example of purple S bacteria? which family and genus is it from? Where ca n it be found?
Lamprocystis purpurea
Family: Chromatiaceae
Genus: Chromatium
Lake Mahoney
117
What are 2 genera of purple non sulfur bacteria?
Rubrivivax (beta proteo)
Rhodospirillum (alpha proteo)
118
Where is a local example of habitat for Rubrivivax (a genus of purple non S bacteria)?
Mt Doug
119
What pigments do beta purple non-S bacteria use?
bchl a
120
What pigments do alpha purple non-S bacteria use?
bchl a or b
121
What pigments do aerobic purple bacteria use?
bchl a
122
What is a genus of aerobic purple bacteria?
Roseobacter
123
What is an example species from Rhodospirillum? which class of proteobacteria does it belong to?
What is special about this bacteria?
Rhodopseudomonas palustrius
class: alpha proteobacteria (purple non sulfur)
it is a photoheterotroph (can use both CO2 and organic C)
124
Describe the steps in the dark reactions of green sulfur bacteria (Chlorobium)
reverse citric acid cycle
2 H+ binds to oxaloacetate
a succession of intermediates
addition of ATP
addition of 2x CO2 and Ferredoxin
= isocitrate = citrate
citrate is split into oxaloacetate (cycle continues) and
with the addition of ATP = Acetyl CoA is produced
Reverse glycolysis:
Acetyl CoA + Fd + CO2 = pyruvate
ATP = AMP
ATP + H+ = ADP
= Triose-P (G3P)
Hexose-P
cell material
125
What is the overall net reaction for the dark reactions in Chlorobium (green S bacteria)?
3 CO2 + 12 H+ + 5 ATP --> G3P (aka triose-P)
126
what is G3P?
glyceraldehyde 3-phosphate
it is the product of the dark rxn for green S bacteria and is involved in the dark rxns for purple and cyanobacteria
127
T or F: the dark reactions in green S bacteria follow the same pathway of glycolysis
false, they follow it in reverse including the reverse CAC
128
Describe the steps involved in the hydroxypropionate pathway for the dark rxns of green non-S bacteria
acetyl CoA + ATP + CO2 + H+ combine to form intermediate
another ATP + 2 H+ = hydropropionyl-CoA
+ 2H+ = propionyl-CoA
+ CO2 + ATP = methylmalonyl CoA
loss of 2H+ = malyl CoA
malyl CoA is split into acetyl CoA (cycle continues) and
glyoxylate and then cell material
129
What is the net reaction for the hydroxypropionate pathway for the dark rxns of green non-S bacteria?
2 CO2 + 4 H+ + 3 ATP = glyoxylate
130
What is glyoxylate?
an intermediate of amino acids that can be assimilated into cells
it is the product of the hydroxypropionate pathway in green non-S bacteria
131
How are photosynthetic genes distributed in the model organism Rhodobacter capsulatus?
in clusters (operons) that range 45-50 kb (kilobase) of a chromosome
132
What are the 9 major photosynthetic gene types in Rhodobacter capsulatus?
bch
crt
puf A and puf B
puc A and puc B
puf L, puf M, puh A
133
What do bch genes code for?
bchlB and bchlH encode bacteriochlorophyll synthesis
134
What do crt genes code for?
carotenoid synthesis
135
What do puf A and puf B genes code for?
light harvesting I synthesis
136
What do puc A and puc B genes code for?
light harvesting II synthesis
137
What do puf L, puf M, and puh A genes code for?
reaction center synthesis
138
Which gene is used to distinguish purple bacteria?
puf M
139
Which genes are important to the study of photosynthetic and bacterial evolution?
bch B and bch H genes coding for bacteriochlorophyll
140
Where would you find bch B and bch H genes along a chromosome?
in the H segment, near the "start" of the operon
141
Where would you find puf M genes along a chromosome?
near the end of the operon in the M segment
142
what is known about the evolution of bch genes?
current evidence suggests that is may have a related ancestor with chlorophyll
143
What is the root gene for phylogenetic analysis on bch and chl evolution?
nifDKEN
144
Which photosynthetic bacteria has the most ancient divergence in its evolution from the bchB/chlB-nifDKEN root gene?
purple bacteria
145
What is the evolutionary divergence order for photosynthetic bacteria. from
the root gene bchB/chlB-nifDKEN?
earliest: purple bacteria
green non-S and green S (same time)
heliobacteria
cyanobacteria
latest: photosynthetic eukaryotes
146
What structure is the corrin ring similar to?
heme
chlorophyll a
coenzyme 430
vitamin B12
147
What are examples of cyanobacteria?
Gloeothece (slimey on wet rocks)
Oscillatoria*
- can do anoxic but usually linear oxygenic
- colonial, filamentous
Fischerella (tropical)
*Nostoc
- symbiotic with lichen (Lobaria pulmonaria) on big leaf maple
- can also fix N2
*Anabaena
- symbiotic with Azolla ferns
- found in rice paddies
- found in Mirror Lake
148
Which 3 cyanobacteria are found in Mirror Lake?
Anabaena (N2 + photo)
- filamentous, colonial
- heterocyst
Chlooroccus (N2 + photo)
- no heterocyst
Merismopedia (no N2)
149
What unique structure do Anabaena have that other cyanobacteria in Mirror Lake do not?
heterocysts = separate environments from photosynthetic cells for optimal conditions for nitrogenase to fix N2
energy for nitrogenase produced by photosynthetic cells
150
How can accumulation of elemental sulfur within or outside of cells be detected?
it appears shiney under microscope
151
Does Lamprocystis purpurea accumulate S0 inside or outside its cells?
inside
152
What is an example of green non-S bacteria?
Chloronema in Michigan Lake
filamentous, colonial
153
T or F: non-S green bacteria cannot oxidize H2S
false, all of them can
154
What is an example of Heliobacteria? Describe it
Heliophilum fasciatum
thick, peptidoglycan wall (gram +)
fixes N2
photoheterotroph
rice paddies
155
What environmental factors dictate the presence of photosynthetic bacteria?
quality and quantity of light
nutrient availability (N, P, K, Mg, etc.)
anoxygenic photosynthesizers limited by presence of sulfide for an e-donor or limited by the type of S available
156
in the absence of H2S, what non Sulfur element can act as an e- donor to anoxygenic photosynthesis by Oscillatoria (cyanobacteria)?
Fe2+
157
in the absence of H2S, what non Sulfur element can act as an e- donor to anoxygenic photosynthesis by some purple bacteria?
NaCl but only for the halophilic
158
where is sulfide a common e- donor for anoxygenic photosynthesis?
marine or hot springs
159
What are 4 ways to measure photosynthesis?
abundance (cell numbers)
activity
species
production of oxygen
160
How can abundance be measured?
epifluorescence microscopy to determine pigments (will appear different colours chl a v. bchl)
do this by extracting with organic solvents (usually ether)
and use fiber optics on microbial mats
161
What techniques can be used to measure photosynthetic activity?
1. determine O2 concentration
- use microcosms (cores, bottles)
- profile cores using microelectrodes
2. determine H2S concentration with microcosms (cores, bottles) or microelectrodes (cores)
3. incorporate 14CO2 (radio) or 13CO2 (stable) in microcosms
4. use RNA genes involved in photosynthesis (puf M)
162
What techniques can be used to determine photosynthetic species?
1. isolate organism with mineral media (absence of carbon) (conventional)
2. extract DNA, PCR amplify, clone, sequence
3. use metagenomics (Nextgen) sequencing) (extracting DNA without PCR)
163
What techniques can be used to determine production of oxygen by photosynthetic bacteria?
1. microcosms with light and dark incubation and electrodes to measure O2
2. determine oxygen gradient and use Fick's law to measure vertical fluxes
3. incorporate 14C CO2 under light and dark
164
What is Fick's law?
used to measure oxygen gradient
J = -DdC/dx
where
J = # molecules passing a unit area by unit time
D = diffusion coefficient
dC = change in concentration
dX = change in depth
165
What did the study in Niva Bay on flux measurements of oxygen in mesophilic cyanobacterial mats show?
with decreasing depth from the mat's surface:
in dark:
[O2] decreased rapidly and became 0/negligible around 1.5mm
in light:
[O2] increased with the first 2 mm then very slowly decreased with increasing depth until ~5mm = 0
166
What did the study in Niva Bay on flux measurements of oxygen in mesophilic cyanobacterial mats show about pH levels?
follows same trends as [O2] concentration
dark: pH drops with depth until 1-1.5 mm then remains relatively constant with depth
light: pH increases with first 1-2 mm then slowly decreases
167
What kind of photosynthetic bacteria grow in Octopus Spring, Yellowstone National park? what do studies reveal about the type of photosynthesis they're doing?
a cyanobacterial mat conducting oxygenic photosynthesis
[O2] concentration increases with depth in the mat = oxygenic and then drops off as O2 depletes
pH follows same trend
168
What kind of photosynthetic bacteria grow in New Pit Spring, Yellowstone National park? what was measured to determine this?
green sulfur bacterial mat
[sulfide] measured in light and dark
169
What can inhibit oxygenic photosynthesis?
DCMU (aka 3,4-Dichlorophenyl-1,1-dimethylurea) at 50 uM concentration - blocks e- flow between PSII and PSI
DCCD (dicyclohexylcarbodiimide) inhibits electron transport phosphorylation
nitrophenol
170
T or F: DCMU inhibits both oxygenic and anoxygenic photosynthesis - why/why not?
false
only oxygenic because it blocks the flow e- between PSII and PSI, anoxygenic only has one PS
171
If DCMU was applied to Oscillatoria (cyanobacteria), could it still photosynthesize?
its oxygenic pathway would be inhibited, but Oscillatoria can also conduct anoxygenic photosynthesis
172
Where is Lake Mahoney?
south eastern BC (interior)
173
What species of purple S bacteria found in Lake Mahoney?
at 7m depth, Lamprocystis purpurea
174
How would photosynthesis by L. purpurea be measured?
a lake core sample to determine H2S concentration (NOT O2 because not oxygenic)
175
Why would it be important to measure the photosynthetic activity of L. purpurea in Lake Mahoney?
they play a key role in primary productivity as they are (photosynthetic bacteria) capable of fixing inorganic carbon (CO2)
Lake Mahoney has unique limnological characteristics
it is meromictic (does not mix)
no outlet, so evaporation causes high concentrations of minerals and salts (high salinity and alkalinity)
176
What leads to the near continuous layer of Lamprocystis purpurea mat in Lake Mahoney?
the lake's high salinity and alkalinity
177
How do microbial mat primary productivity compare to other ecosystems with high levels of PP (tropical rainforests, swamps, hypertrophic lakes, coastal upwellings)?
very high levels of primary productivity
178
What is a Winogradsky column?
an example of a microcosm for measuring soil that shows stratified layers when settled
179
What did the Winogradsky column show over time as the conditions changed from oxic to anoxic?
increase of purple photosynthetic bacteria
180
Which gene is isolated and amplified and cloned to identify anoxygenic photosynthetic bacteria?
puf M - the gene that codes for the M subunit of the reaction center
181
Explain the steps of analyzing Mt Doug soil collected in the Winogradsky column
western red cedar or garry oak soils collected in Winogradsky columns
16s rDNA extracted from soil (can go straight to metagenomics)
puf M gene isolated and amplified with PCR
clone
compare clones to:
community fingerprinting (using DGGE, TRFLP) or PCR clone library or metagenomic comparison
sequence and use sequence analysis
develop phylogenetic tree
182
Which photosynthetic bacteria were found in soils ONLY around WRC at Mt Doug?
Alpha proteobacteria:
- Azorhizobium
- Pleomorphomonas
- Rhodomicrobium
beta proteobacteria:
- Rubrivivax
Gamma proteobacteria: Allochromatium
Firmicute:
Clostridium
183
Which photosynthetic bacteria were found in soils ONLY around Garry oaks at Mt Doug?
Alpha proteobacteria: Rhodopseudomonas
Beta proteobacteria: Rhodocyclus
Firmicutes: Thermolithobacteria
184
Which photosynthetic bacteria were found in soils around WRC AND GO at Mt Doug?
alpha proteobacteria:
Sphingomonas
Rhodobacter
beta proteobacteria:
rhodoferax
185
Which genes were used to determine the type of photosynthetic bacteria at Mt Doug?
16s rRNA and puf M
186
What is nanopore sequencing?
metagenomic analysis of Winogradksy Columns
187
What did the nanopore sequencing metagenomic analysis reveal about the number of bacteria species found in WRC vs GO soil?
WRC > GO
shared = 3
188
What did the nanopore sequencing metagenomic analysis reveal about the number of fungal species found in WRC vs GO soil?
WRC > GO
shared = 12
189
What did the nanopore sequencing metagenomic analysis reveal about the number of archaea species found in WRC vs GO soil?
WRC had 3
GO had 0
190
Which photosynthetic bacteria type was shared between WRC and GO at Mt Doug?
Rhodopseudomonas
anoxygenic phototroph and mixotroph
