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Nutrient Cycling + Prokaryotes > Carbon Cycle/Photosynthesis > Flashcards

Carbon Cycle/Photosynthesis Flashcards

1
Q

Where did carbon come from originally?

A

likely from star nucleosynthesis

this idea was established in 1957

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2
Q

Who was Messier?

A

an 18th century astronomer who listed over 100 objects in the sky that weren’t comets

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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

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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

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3
Q

what is star/stellar nucleosynthesis?

A

the creation of chemical elements from the explosion of stars

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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)

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5
Q

What are examples of radioactive C and N isotopes?

A

C14, N13

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6
Q

Examples of stable C and N isotopes?

A

C13
N15

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7
Q

Where is the largest pool of carbon on earth?

A

coal, oil, etc. and sediments

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8
Q

Which phyla of bacteria are photosynthetic?

A

filamentous green bacteria (Chloroflexi)

Green sulfur bacteria (Chlorobi)

Firmicutes

Cyanobacteria

Proteobacteria

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9
Q

What is the most ancient known ancestor of photosynthetic bacteria?

A

Thermotoga

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10
Q

Which photosynthetic bacteria evolved first?

A

Chloroflexi (filamentous green bacteria)

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11
Q

Where in BC would you expect to find green sulfur bacteria (Chlorobi)?

A

in Lake Mahoney, where there’s high sulfur concentration

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12
Q

what is an example of Chlorobi (green sulfur bacteria) you’d expect to find in Lake Mahoney, BC?

A

Chlorobium (green)

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13
Q

What type of ecosystems do Firmicutes live in?

A

rice paddies

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14
Q

What is the only species of Firmicutes?

A

Heliobacterium

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15
Q

What type of bacteria are Firmicutes?

A

gram positive

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16
Q

Of the photosynthetic bacteria, which are oxygenic? anoxygenic?

A

oxygenic: Cyanobacteria

anoxygenic: Chloroflexi, Chlorobi, Firmicutes, Proteobacteria

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17
Q

Which bacteria phylum was the origin of chloroplasts?

A

cyanobacteria

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18
Q

Where in BC would you expect to find proteobacteria?

A

Mt Doug

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19
Q

Are proteobacteria green or purple?

A

purple

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20
Q

What are Firmicutes sometimes called? why?

A

Heliobacterium because they’re only one species

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21
Q

What are proteobacteria sometimes called?

A

purple bacteria

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22
Q

What light harvesting pigments do purple bacteria (proteobacteria), green bacteria, and heliobacterium have?

A

(Bchl) Bacteriochlorophyll

and

aliphatic, monocyclic carotenoids

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23
Q

What are the main electron carriers in proteobacteria, green bacteria, and heliobacterium photosynthesis?

A

bacterial ferredoxins

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24
Q

what are ferredoxins?

A

small proteins with iron and sulfur atoms

electron carriers

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25
Q

What light harvesting pigments do cyanobacteria (and rhodophytan chloroplasts) have?

A

chlorophyll a

phycobilliproteins

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26
Q

What are the main electron carriers in cyanobacteria (and rhodophytan chloroplasts) photosynthesis?

A

plant ferredoxins
plastoquinones
plastocyanin
cytochrome f

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27
Q

What light harvesting pigments do prochlorophytes and chlorphytan chloroplasts have?

A

chlorophyll a and b
Beta-carotene and derivatives

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28
Q

What are the main electron carriers in prochlorophytes and chlorphytan chloroplasts
photosynthesis?

A

plant ferredoxins
plastoquinones
plastocyanin
cytochrome f

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29
Q

Which bacteria have photosynthetic elements more similar to plants?

A

cyanobacteria

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30
Q

describe the general structure of a photosynthetic apparatus

A

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

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31
Q

Where is the pigment antenna located in a cell?

A

its in the membrane

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32
Q

What is the function of the pigment antenna?

A

to expand the range of photons that can be captured

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33
Q

What is the RCC made of?

A

2-3 chlorophyll bound to proteins

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34
Q

What is the ET system?

A

the electron transport chain

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35
Q

What is another term for reaction center?

A

photosystem

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36
Q

Describe the photosynthetic apparatus for purple (proteo) and green bacteria (Chlorobi, chloroflexi)

A

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

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37
Q

What is ferris?

A

Fe2+, grey coloured (reduced)

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38
Q

What is ferric?

A

Fe3+, red (more oxidized)

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39
Q

What type of light do the carotenoids in the pigment antenna of green and purple bacteria absorb?

A

visible light (short)

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40
Q

What type of light do the bacteriochlorophyll in the pigment antenna of green and purple bacteria absorb?

A

red and infrared

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41
Q

What components are in the pigment antenna of purple and green bacteria?

A

carotenoids
bacteriochlorophyll

the light harvesting pigments

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42
Q

What components are in the pigment antenna of cyanobacteria and chloroplasts?

A

phycobilliproteins
chlorophyll a

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43
Q

What type of light do the light harvesting pigments of cyanobacteria and chloroplasts absorb?

A

phycobiliproteins absorb 550-660 nm

chlorophyll a absorbs > 660 nm

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44
Q

Describe the photosynthetic apparatus for cyanobacteria and chloroplasts

A

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

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45
Q

Which is the reduced version: NADPH or NADP?

A

NADPH is reduced
NADP+ is oxidized

MORE H+ = MORE REDUCED

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46
Q

What are the 2 reaction centers for cyanobacteria and chloroplasts? what do they do?

A

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

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47
Q

Which of the photosynthetic bacteria conduct oxygenic photosynthesis?

A

only cyanobacteria

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48
Q

What is the primary product of energy conversion for anoxic photosynthesis by green bacteria?

A

ATP

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49
Q

What is the primary product of energy conversion for anoxic photosynthesis by green sulfur bacteria?

A

ATP + NADH

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50
Q

What is the primary product of energy conversion for anoxic photosynthesis by purple and non-sulfur bacteria?

A

ATP

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51
Q

What is the primary product of energy conversion for anoxic photosynthesis by heliobacteria?

A

ATP + NADH

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52
Q

What is the primary product of energy conversion for oxygenic photosynthesis by cyanobacteria?

A

ATP + NADH

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53
Q

Which bacteria produce only ATP from energy conversion during photosynthesis?

A

non sulfur green and sulfur purple bacteria

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54
Q

Which bacteria produce both ATP + NADH as primary product of energy conversion during photosynthesis?

A

green sulfur bacteria
heliobacteria
cyanobacteria

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55
Q

What electron donors do green bacteria use?

A

organic
sulfur
thiosulfate (S2O3-)

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56
Q

What electron donors do green sulfur bacteria use?

A

H2
S2
So
thiosulfate (S2O3-)

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57
Q

What electron donors do purple and non-sulfur bacteria use?

A

H2
S2
So
thiosulfate

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58
Q

Describe the chemical structure of chlorophyll a

A

4 nitrogen atoms surrounding a magnesium at the center (tetrapyrrole ring)

cyclopentanone ring

phytol (long carbon chain)

reduced = more H bound

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59
Q

What is phytol?

A

a long carbon chain that anchors chlorophyll a and Bchl to cell membranes

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60
Q

What does the similarity of the tetrapyrrole ring in chlorophyll a to other cofactors (ex. heme b, heme d1, cobalamin, coenzyme F430)?

A

with 16s rRNA it can help understand the evolution of chl pigments

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61
Q

What is chlorophyll a?

A

a cofactor that is essential to oxygenic photosynthesis

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62
Q

What are cofactors? give examples

A

non-protein, inorganic chemical compounds that bind to enzymes or other proteins

these can be metals

ex. Mg, Cu, Fe, Zn, selenium

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63
Q

What are coenzymes? give examples

A

non-protein, organic molecules that carry chemicals BETWEEN enzymes

NAD
FAD
coenzyme A

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64
Q

What is heme?

A

a metal-binding compound that is incorporated into enzymes (ex. cytochromes) or other proteins (ex. hemoglobin)

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65
Q

What type of molecules contain heme?

A

enzymes and non-enzyme proteins

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66
Q

What are the 2 major reactions in oxygenic photosynthesis?

A

light reaction (absorption of photons, production and transport of e- to produce energy as ATP and NADPH)

dark reaction (Calvin cycle) (assimilation of CO2)

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67
Q

What is the model organism used to study anoxygenic photosynthesis?

A

Rhodobacter capsulatus

a purple non-S bacteria

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68
Q

What are the 6 major proteins involved in anoxygenic photosynthesis (Rhodobacter capsulatus)?

A

Light harvesting I
light harvesting II
reaction center
cytochrome bc1
cytochrome c
proton ATPase

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69
Q

Describe the protein structure of LHI for anoxygenic photosynthesis

A

composed of 2 small Bch-binding polypeptides (heterodimers with alpha and beta subunit)

each heterodimer binds to 2 bchl

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70
Q

Describe the protein structure of LHII for anoxygenic photosynthesis

A

composed of 2 small Bch-binding polypeptides (heterodimer with alpha and beta subunit)

each heterodimer binds to 3 bchl and 2 carotenoids

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71
Q

What are carotenoids? what do they do?

A

they are photosynthetic pigments in the antennae of reaction centers that expand the range of light absorption

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72
Q

Describe the protein structure of the RC for anoxygenic photosynthesis

A

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

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73
Q

What is the RC in Rhodobacter capsulatus similar to?

A

the P680 (RC II) in cyanobacteria

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74
Q

Describe the protein structure of cytochrome bc1 for anoxygenic photosynthesis

A

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)

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75
Q

T or F: cytochrome bc1 is only found in purple non-sulfur bacteria

A

false, it’s found in many bacteria and mitochondria

76
Q

What is the function of cytochrome bc1?

A

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
Q

Describe the protein structure of cytochrome c for anoxygenic photosynthesis

A

a small, water soluble protein with one heme

78
Q

What is the function of cytochrome c in anoxygenic photosynthesis?

A

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
Q

Describe the protein structure of a proton ATPase for anoxygenic photosynthesis

A

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
Q

T or F: proton ATPase are only found in some bacteria

A

false,

they are HIGHLY conserved and are a defining characteristic of bacteria

81
Q

What else shares the commonality of proton ATPases with bacteria?

A

chloroplasts and mitochondria

82
Q

Describe the function of a proton ATPase

A

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
Q

Which photosynthetic bacteria have cyclic flow in their light reactions?

A

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
Q

Which photosynthetic bacteria have linear flow of electrons in their light reactions?

A

only oxygenic have the option for linear flow = cyanobacteria

but cyanobacteria can also have cyclic

85
Q

T or F: oxygenic photosynthesis only has linear flow of e-

A

false, it can have cyclic too at ferredoxin in RS I sending e- to cytochrome bcf in RS II

86
Q

What is quinone?

A

highly abundant e- carriers in the ETC of both oxygenic and anoxygenic photosynthesis

87
Q

T or F: Q is only an e- carrier in oxygenic photosynthesis

A

false, it’s present in both oxygenic and anoxygenic

88
Q

What splits H2O to release H+ in the ETC of oxygenic photosynthesis?

A

cytochrome bf

89
Q

How many H+ ions are moved from the cytoplasm into the periplasmic space by cytochrome bc1 during anoxygenic photosynthesis?

A

2 H+

90
Q

How many H+ ions are pumped back from the periplasmic space into the cytoplasm by ATPase?

A

for every rotation of ATPase, 3 H+ ions are moved

91
Q

What is the overall reaction for photosynthesis?

A

6 CO2 + hv + 6 H2O –> C6H12O6 + 6 O2

92
Q

Describe the oxygenic dark reaction steps

A

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
Q

What is RuBP? what does it stand for?

A

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
Q

What are the products of the oxygenic light reactions?

A

18 ATP + 12 NADPH (reduced)

ENERGY to power the dark reactions

95
Q

What are the inputs for the dark reactions of oxygenic photosynthesis?

A

products of the light rxns

18 ATP + 12 NADPH (energy)

6 CO2 + 6 H2O

96
Q

What are the outputs for the dark reactions of oxygenic photosynthesis?

A

regeneration of RuBisco

6 RuBP ready to accept more CO2

2 G3P (3C) leave for gluconeogenesis

12 NADP+ and 17 ADP ready to

97
Q

Who else helped Calvin understand the oxygenic dark reactions? How did they discover it?

A

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
Q

What is the balanced reaction for the oxygenic light rxns?

A

15 H2O + hv → 7.5 O2 + 30 H+
27 H+ + 18 ADP + 18 Pi → 18 ATP
12 H+ + 12 NADP+ → 12 NADPH

99
Q

What is the balanced reaction for the oxygenic dark rxns?

A

6 CO2 + 18 ATP + 12 NADPH → C6H12O6 (PO3H2) + 12 NADP+ + 17 ADP + 17 Pi

100
Q

What is the balanced reaction for the ANoxygenic light rxns?

A

H2S + hv → S0 (in or out) + 2 H+
3H+ + 2 ADP + 2 Pi → 2 ATP

101
Q

T or F: all anoxygenic dark reactions follow the same processes

A

false

102
Q

What is the dark reactions pathway for green S bacteria?

A

reverse citric (Kreb’s) cycle

ie., CO2 is added, not removed

103
Q

What is the dark reactions pathway for non-S green bacteria?

A

hydroxypropionate (3C) cycle

104
Q

What is the dark reactions pathway for purple bacteria?

A

sine can directly assimilate organic acids from the environment

some use Calvin cycle (but not in a carboxysome with RuBisco)

105
Q

What is RuBisco? Why is it important/what is its function?

A

ribulose 1,5-bisphosphate carboxylase/oxygenase

an enzyme in the Calvin cycle that catalyzes the reaction between CO2 and RuBP (carbon fixation)

106
Q

What types of environments do purple sulfur bacteria live in?

A

high [S]

ex. hotsprings

107
Q

What types of environments do non-S purple bacteria live in?

A

low [S]

ex. Mt Doug

108
Q

What are the orders of purple S bacteria that do photosynthesis?

A

Gammaproteobacteria
Chromatiales

109
Q

What are the orders of purple non-S bacteria that do photosynthesis?

A

beta proteobacteria
alpha proteobacteria

110
Q

What are the orders of aerobic purple bacteria that do photosynthesis?

A

alpha proteobacteria

111
Q

What are 2 families of purple sulfur bacteria?

A

Chromatiaceae
Ectothiorhodospiraceae

112
Q

What type of photosynthetic pigments can purple S bacteria use?

A

either bchl a or b

113
Q

Which family of purple S bacteria accumulates elemental sulfur inside its cells?

A

Chromatiaceae

114
Q

Which family of purple S bacteria accumulates elemental sulfur outside its cells?

A

Ectothiorhodospiraceae

115
Q

What are 2 genera of purple S bacteria?

A

Chromatium and Ectothiorhodospira

116
Q

What is a local example of purple S bacteria? which family and genus is it from? Where ca n it be found?

A

Lamprocystis purpurea

Family: Chromatiaceae
Genus: Chromatium

Lake Mahoney

117
Q

What are 2 genera of purple non sulfur bacteria?

A

Rubrivivax (beta proteo)

Rhodospirillum (alpha proteo)

118
Q

Where is a local example of habitat for Rubrivivax (a genus of purple non S bacteria)?

A

Mt Doug

119
Q

What pigments do beta purple non-S bacteria use?

A

bchl a

120
Q

What pigments do alpha purple non-S bacteria use?

A

bchl a or b

121
Q

What pigments do aerobic purple bacteria use?

A

bchl a

122
Q

What is a genus of aerobic purple bacteria?

A

Roseobacter

123
Q

What is an example species from Rhodospirillum? which class of proteobacteria does it belong to?

What is special about this bacteria?

A

Rhodopseudomonas palustrius

class: alpha proteobacteria (purple non sulfur)

it is a photoheterotroph (can use both CO2 and organic C)

124
Q

Describe the steps in the dark reactions of green sulfur bacteria (Chlorobium)

A

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
Q

What is the overall net reaction for the dark reactions in Chlorobium (green S bacteria)?

A

3 CO2 + 12 H+ + 5 ATP –> G3P (aka triose-P)

126
Q

what is G3P?

A

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
Q

T or F: the dark reactions in green S bacteria follow the same pathway of glycolysis

A

false, they follow it in reverse including the reverse CAC

128
Q

Describe the steps involved in the hydroxypropionate pathway for the dark rxns of green non-S bacteria

A

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
Q

What is the net reaction for the hydroxypropionate pathway for the dark rxns of green non-S bacteria?

A

2 CO2 + 4 H+ + 3 ATP = glyoxylate

130
Q

What is glyoxylate?

A

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
Q

How are photosynthetic genes distributed in the model organism Rhodobacter capsulatus?

A

in clusters (operons) that range 45-50 kb (kilobase) of a chromosome

132
Q

What are the 9 major photosynthetic gene types in Rhodobacter capsulatus?

A

bch

crt

puf A and puf B

puc A and puc B

puf L, puf M, puh A

133
Q

What do bch genes code for?

A

bchlB and bchlH encode bacteriochlorophyll synthesis

134
Q

What do crt genes code for?

A

carotenoid synthesis

135
Q

What do puf A and puf B genes code for?

A

light harvesting I synthesis

136
Q

What do puc A and puc B genes code for?

A

light harvesting II synthesis

137
Q

What do puf L, puf M, and puh A genes code for?

A

reaction center synthesis

138
Q

Which gene is used to distinguish purple bacteria?

A

puf M

139
Q

Which genes are important to the study of photosynthetic and bacterial evolution?

A

bch B and bch H genes coding for bacteriochlorophyll

140
Q

Where would you find bch B and bch H genes along a chromosome?

A

in the H segment, near the “start” of the operon

141
Q

Where would you find puf M genes along a chromosome?

A

near the end of the operon in the M segment

142
Q

what is known about the evolution of bch genes?

A

current evidence suggests that is may have a related ancestor with chlorophyll

143
Q

What is the root gene for phylogenetic analysis on bch and chl evolution?

A

nifDKEN

144
Q

Which photosynthetic bacteria has the most ancient divergence in its evolution from the bchB/chlB-nifDKEN root gene?

A

purple bacteria

145
Q

What is the evolutionary divergence order for photosynthetic bacteria. from
the root gene bchB/chlB-nifDKEN?

A

earliest: purple bacteria
green non-S and green S (same time)
heliobacteria
cyanobacteria
latest: photosynthetic eukaryotes

146
Q

What structure is the corrin ring similar to?

A

heme
chlorophyll a
coenzyme 430
vitamin B12

147
Q

What are examples of cyanobacteria?

A

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
Q

Which 3 cyanobacteria are found in Mirror Lake?

A

Anabaena (N2 + photo)
- filamentous, colonial
- heterocyst

Chlooroccus (N2 + photo)
- no heterocyst

Merismopedia (no N2)

149
Q

What unique structure do Anabaena have that other cyanobacteria in Mirror Lake do not?

A

heterocysts = separate environments from photosynthetic cells for optimal conditions for nitrogenase to fix N2

energy for nitrogenase produced by photosynthetic cells

150
Q

How can accumulation of elemental sulfur within or outside of cells be detected?

A

it appears shiney under microscope

151
Q

Does Lamprocystis purpurea accumulate S0 inside or outside its cells?

A

inside

152
Q

What is an example of green non-S bacteria?

A

Chloronema in Michigan Lake

filamentous, colonial

153
Q

T or F: non-S green bacteria cannot oxidize H2S

A

false, all of them can

154
Q

What is an example of Heliobacteria? Describe it

A

Heliophilum fasciatum

thick, peptidoglycan wall (gram +)
fixes N2
photoheterotroph

rice paddies

155
Q

What environmental factors dictate the presence of photosynthetic bacteria?

A

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
Q

in the absence of H2S, what non Sulfur element can act as an e- donor to anoxygenic photosynthesis by Oscillatoria (cyanobacteria)?

A

Fe2+

157
Q

in the absence of H2S, what non Sulfur element can act as an e- donor to anoxygenic photosynthesis by some purple bacteria?

A

NaCl but only for the halophilic

158
Q

where is sulfide a common e- donor for anoxygenic photosynthesis?

A

marine or hot springs

159
Q

What are 4 ways to measure photosynthesis?

A

abundance (cell numbers)
activity
species
production of oxygen

160
Q

How can abundance be measured?

A

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
Q

What techniques can be used to measure photosynthetic activity?

A
  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
Q

What techniques can be used to determine photosynthetic species?

A
  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
Q

What techniques can be used to determine production of oxygen by photosynthetic bacteria?

A
  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
Q

What is Fick’s law?

A

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
Q

What did the study in Niva Bay on flux measurements of oxygen in mesophilic cyanobacterial mats show?

A

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
Q

What did the study in Niva Bay on flux measurements of oxygen in mesophilic cyanobacterial mats show about pH levels?

A

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
Q

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

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
Q

What kind of photosynthetic bacteria grow in New Pit Spring, Yellowstone National park? what was measured to determine this?

A

green sulfur bacterial mat

[sulfide] measured in light and dark

169
Q

What can inhibit oxygenic photosynthesis?

A

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
Q

T or F: DCMU inhibits both oxygenic and anoxygenic photosynthesis - why/why not?

A

false

only oxygenic because it blocks the flow e- between PSII and PSI, anoxygenic only has one PS

171
Q

If DCMU was applied to Oscillatoria (cyanobacteria), could it still photosynthesize?

A

its oxygenic pathway would be inhibited, but Oscillatoria can also conduct anoxygenic photosynthesis

172
Q

Where is Lake Mahoney?

A

south eastern BC (interior)

173
Q

What species of purple S bacteria found in Lake Mahoney?

A

at 7m depth, Lamprocystis purpurea

174
Q

How would photosynthesis by L. purpurea be measured?

A

a lake core sample to determine H2S concentration (NOT O2 because not oxygenic)

175
Q

Why would it be important to measure the photosynthetic activity of L. purpurea in Lake Mahoney?

A

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
Q

What leads to the near continuous layer of Lamprocystis purpurea mat in Lake Mahoney?

A

the lake’s high salinity and alkalinity

177
Q

How do microbial mat primary productivity compare to other ecosystems with high levels of PP (tropical rainforests, swamps, hypertrophic lakes, coastal upwellings)?

A

very high levels of primary productivity

178
Q

What is a Winogradsky column?

A

an example of a microcosm for measuring soil that shows stratified layers when settled

179
Q

What did the Winogradsky column show over time as the conditions changed from oxic to anoxic?

A

increase of purple photosynthetic bacteria

180
Q

Which gene is isolated and amplified and cloned to identify anoxygenic photosynthetic bacteria?

A

puf M - the gene that codes for the M subunit of the reaction center

181
Q

Explain the steps of analyzing Mt Doug soil collected in the Winogradsky column

A

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
Q

Which photosynthetic bacteria were found in soils ONLY around WRC at Mt Doug?

A

Alpha proteobacteria:
- Azorhizobium
- Pleomorphomonas
- Rhodomicrobium

beta proteobacteria:
- Rubrivivax

Gamma proteobacteria: Allochromatium

Firmicute:
Clostridium

183
Q

Which photosynthetic bacteria were found in soils ONLY around Garry oaks at Mt Doug?

A

Alpha proteobacteria: Rhodopseudomonas

Beta proteobacteria: Rhodocyclus

Firmicutes: Thermolithobacteria

184
Q

Which photosynthetic bacteria were found in soils around WRC AND GO at Mt Doug?

A

alpha proteobacteria:
Sphingomonas
Rhodobacter

beta proteobacteria:
rhodoferax

185
Q

Which genes were used to determine the type of photosynthetic bacteria at Mt Doug?

A

16s rRNA and puf M

186
Q

What is nanopore sequencing?

A

metagenomic analysis of Winogradksy Columns

187
Q

What did the nanopore sequencing metagenomic analysis reveal about the number of bacteria species found in WRC vs GO soil?

A

WRC > GO

shared = 3

188
Q

What did the nanopore sequencing metagenomic analysis reveal about the number of fungal species found in WRC vs GO soil?

A

WRC > GO

shared = 12

189
Q

What did the nanopore sequencing metagenomic analysis reveal about the number of archaea species found in WRC vs GO soil?

A

WRC had 3
GO had 0

190
Q

Which photosynthetic bacteria type was shared between WRC and GO at Mt Doug?

A

Rhodopseudomonas

anoxygenic phototroph and mixotroph

Nutrient Cycling + Prokaryotes (13 decks)

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