This document covers the diversity of microbial mats, including the definitions and characteristics of microbial mats, their layers, and functional guilds of microbes. It also contrasts the carbon fixation methods and energy acquisition strategies of three photosynthetic bacterial phyla and describes adaptations of two thermophilic bacterial phyla. The learning goals are aimed at understanding how these microbial communities interact and the implications for early life on Earth.

1. DIVERSITY OF MICROBIAL MATS
Unit 06, 2.23.2021
Reading for today: Brown Ch. 8 & 9
Reading for next class: Brown Ch. 10 & 11
Dr. Kristen DeAngelis
Office Hours by appointment
deangelis@microbio.umass.edu
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2. Introducing the Microbial Zoo
• 13 Bacterial Phyla,
Archaea,
Eukaryotes and
Acellular life
• General
characteristics of
the phyla with 1-2
example species
2

3. 3

4. Unit 6: Diversity of Microbial Mats
LECTURE LEARNING GOALS
1. Define microbial mats. Describe the
functional guilds of microbes in the
different layers, and how they interact.
2. For each of the three phyla of
photosynthetic bacteria, contrast how
each fixes C and gains energy and
reducing equivalents from light.
3. For the two thermophilic bacterial phyla,
describe their adaptations to life at high
temperature. Explain how they are primitive
and deeply-branching.
4

5. Unit 6: Diversity of Microbial Mats
LECTURE LEARNING GOALS
1. Define microbial mats. Describe the
functional guilds of microbes in the
different layers, and how they interact.
2. For each of the three phyla of
photosynthetic bacteria, contrast how
each fixes C and gains energy and
reducing equivalents from light.
3. For the two thermophilic bacterial phyla,
describe their adaptations to life at high
temperature. Explain how they are primitive
and deeply-branching.
5

7. Microbial mats

8. Microbial mat
• Bacteria, archaea & microbial eukaryotes
– The first life on earth existed as photosynthetic mats
– Mats are food and encouraged evolution of “higher” life
• Multi-layered, stratified sheet of microbes
– Usually a few centimeters thick at most
– a wide range of internal chemical environments
– Close physical proximity of microbes facilitates interspecies
transfers, sometimes known as cross-feeding
• Microbial mats are a biofilm that you can see
– the three kinds of biofilm (simple monolayer, stratified, and
complex) are also found in mats
– held together by “slime” or EPS and filamentous
microorganisms
– Usually prefer interfaces e.g., liquid-air or solid-air

9. Biological soil
crusts
• Cyanobacteria, mosses,
and lichens
• Can cover all soil spaces
not occupied by vascular
plants
– hold soils in place, preventing
erosion
– Blowing sand can bury and kill
crusts
• Crusts grow very slowly, so
walking on them can kill
them and take decades to
recover

10. Stromatolites

11. Stromatolites
• Network of syntrophic relationships
– cyanobacteria, other photosynthetic bacteria
– anaerobic heterotrophs (including fermenters)
– sulfate reducers and sulfur-oxidizers
• grow through sediment and sand, bound by
EPS, & new layers grow up towards the sun
• Over time, layers harden to form rock
– This process is called lithification.
• Stromatolites built reefs in the first least three-
quarters of the earth's history = “molecular
fossils”

12. Lithification in Stromatolites
• Extracellular polysaccharides (EPS) have
carboxyl groups that can bind divalent
cations, including calcium (Ca++)
• Biofilms have cation binding capacity

13. Lithification in Stromatolites
• Lithification = when precipitation of
minerals outweighs dissolution.
• Carbonate precipitation is possibly the
most important process that impacts
global carbon cycling
• Microbes determine precipitation
– EPS production
– pH

14. Photoautotrophy
Depth
(m)
100
200
300

15. Photoautotrophy
• There are several types of chlorophyll
(L), but all share the chlorin
magnesium ligand (R)
• Water is a natural attenuator of light,
absorbing most of the infrared
wavelengths within the first meter
• Longer wavelengths penetrate further
into water sediments

16. Photosynthetic microbial mat
from top to bottom
1. macro- and micro- green algae
– Fix C by photosynthesis
– Filter light, exude some extra sugars
2. cyanobacteria & diatom species
– Cyanobacteria fix C
– Diatoms are heterotrophs or
photosynthetic
3. purple sulfur bacteria
– Photosynthetic C fixers
– Use reduced sulfur to oxidize to S or SO4
4. Spirochaetes
– Microaerophilic heterotrophs
5. green sulfur bacteria
– Photsynthetic
– Oxidize sulfide
6. sulfate reducers
– Reduce SO4 to H2S (“rotten egg” smell)
7. Iron sulfide-rich sediments and
remnants of decaying mats
– Below the mat

17. Activity for Review of
Unit 06.1 Microbial mats
1. A new phototrophic
microbe you’ve
discovered was
isolated from low in
the water column.
What light-
harvesting
pigments is it likely
to have, and why?
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18. Unit 6: Diversity of Microbial Mats
LECTURE LEARNING GOALS
1. Define microbial mats. Describe the
functional guilds of microbes in the
different layers, and how they interact.
2. For each of the three phyla of
photosynthetic bacteria, contrast how
each fixes C and gains energy and
reducing equivalents from light.
3. For the two thermophilic bacterial phyla,
describe their adaptations to life at high
temperature. Explain how they are primitive
and deeply-branching.
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19. Green phototrophic bacteria
• …
19
Chlorobi
Chloroflexi
(“blue-green algae”)

20. Phylum Chlorobi
(green sulfur bacteria)
Fig. 9.9 Chlorobium tempidum
Fig. 9.10 Chlorobium limicola

21. Phylum Chlorobi
(green sulfur bacteria)
• Small number of closely related species, most
are poorly characterized
• All are strict photolithoautotrophs
• Hydrogen or sulfur are electron donors for
reverse TCA cycle to fix C
• Energy via cyclic photophosphorylation
• Most can fix N
• Chlorosomes are inclusion bodies with high
concentrations of accessory photopigments
e.g. bacteriochlorophylls or carotenoids

22. Carbon fixation mechanism:
Reverse (reductive) TCA cycle
• Used by Chlorobi
(green sulfur bacteria)
• It consumes CO2, ATP,
NADH/NADPH, and
reduced ferredoxin to
produce pyruvate

23. Obtaining ATP from light:
Cyclic photophosphorylation
• Most common way
for bacteria to
convert light into
energy (ATP)
– Chlorobi
– Chloroflexi
• Single photosystem
• ATP produced via
proton motive force
(PMF) generated by
the electron transport
chain (ETC)
RC, reaction center
Bph, bacteriopheophytin
Q, quinone
ETC, electron transport chain
CytC, cytochrome c

24. Reducing equivalents for C fixation:
sulfur-dependent photosynthesis
• Chlorobi have strongly
reducing RCs
• Electrons passed from
Chl a to FeS proteins
are able to generate
reducing power as
Fdred
• External sources of
reductant (sulfide etc)
replace the electrons
removed from the ETC
to generate ATP via
PMF
Chl a, chlorophyll a
FeS, iron-sulfur proteins
Fd, ferredoxin
S=, sulfide
SO, elemental sulfur

25. Symbiotic consortia
Chlorobium (seen) encapsulating a
flagellated betaproteobacterium (unseen)
Fig 9.10 Chlorobium symbiotic consortium

26. Symbiotic consortia
Chlorobium (seen) encapsulating a
flagellated betaproteobacterium (unseen)
• The heterotroph (inside) is provided
resources by the Chlorobi
• The Chlorobi are provided motility by
the heterotroph
• The two cell types divide synchronously
• The symbiont can swim phototactically
(towards light)

27. Phylum Cyanobacteria
(blue-green algae)
Fig. 9.17
Fig. 9.16
Fig. 9.15
Fig 9.15 Dermocarpa violacea,
Fig. 9.16 Oscillatoria,
Fig. 9.17 Anabaena, freshwater species in the family Nostoc

28. Phylum Cyanobacteria
(blue-green algae)
• Not “algae,” these bacteria are functionally
diverse but phylogenetically closely related
– All do oxygenic photosynthesis with two
photosystems to get energy and reducing power
for fixing CO2 via the Calvin cycle
– Chl-a as their only chlorophyll, but many also
have phycobillins as accessory photopigments
• Most can fix N
– remember the NanoSIMS where we mapped the
C fixation in vegetative cells of anabaena and N
fixation to the heterocysts

29. ATP & reducing equivalents from light:
Oxygenic photosynthesis
• Cyanobacteria
(including chloroplasts
in plant cells) carry out
oxygenic
photosynthesis
• Light activates the RC
and reducing power is
generated with
ferredoxin reduction
• A second reaction
center (PS II) transfers
electrons to the ETC to
generate ATP via PMF
Fdox, oxidized ferredoxin
Fdred, reduced ferredoxin
PSII, Photosystem II

30. Carbon fixation mechanism:
Calvin cycle
• Used by Cyanobacteria
• Rubisco is the key
enzyme in this pathway
(ribulose bis-phosphate
carboxylase/oxidase)
• Rubisco carboxylates
ribulose 1,5-
bisphosphate to make
two molecules of 3-
phosphoglycerate
• Rubisco is the most
abundant enzyme on
Earth

31. Chloroplasts

32. Chloroplasts
• Found only in plant cells to provide
energy from light
• Derived from endosymbiosis of a
cyanobacteria of the Prochlorales
• Primary chloroplasts have 2
membranes
• Secondary chloroplasts have 3 or 4
membranes

33. Phylum Chloroflexi
(green nonsulfur bacteria)
Fig 9.3 Chloroflexus aurantiacus
Fig 9.4 Roseiflexus castenholzii
Fig 9.5 Herpetosiphon aurantiacus

34. Phylum Chloroflexi
• Generally include thermophilic phototrophs
and heterotrophs which are sometimes
thermophilic
• Single type of photosystem & carry out
Cyclic photophosphorylation to get energy
(ATP) from light
• Need to use reverse electron flow for NADH
• Most can fix C via the unusual
hydroxypropionate pathway

35. Reducing equivalents for C fixation:
reverse electron flow
• Purple non-sulfur bacteria
& Chloroflexi get their
NADH from this pathway
• Requires a strong
chemical reductant:
sulfide, thiosulfate,
elemental sulfur, a ferrous
cation or H2
• Running the ETC in reverse
drains the proton gradient
& costs ATP
Q, quinone
ETC, electron transport chain
CytC, cytochrome c
S=, sulfide
S0, elemental sulfur

36. Carbon fixation mechanism:
Hydroxypropionate pathway
• Used by
Chloroflexi
• Some of the
same reactions
as the TCA
cycle, but
generates
glyoxylate

38. Chloroflexus-rich microbial mat
• in the outflow of Excelsior Geyser,
Yellowstone NP.
• C. aurantiacus was isolated here &
seems to be the primary producer.
• You can see some patches of green
cyanobacteria interspersed with the
orange Chloroflexi
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39. Green
phototrophic
bacteria
Chlorobi (aka green
sulfur bacteria)
Cyanobacteria (aka
blue-green algae)
Chloroflexi (aka
green non-sulfur
bacteria)
lifestyle Photo-
lithoautotrophs,
some are N-fixers
Oxygenic
phototrophs,
some are N-fixers
Anoxic phototrophs
& photo-
heterotrophs
C-fixation Reverse TCA cycle Calvin cycle Hydroxypropionate
pathway
Energy (ATP) Cyclic photo-
phosphorylation
Oxygenic
photosynthesis
Cyclic photo-
phosphorylation
Reducing
equivalents
(NADH)
Ferridoxin from the
ETC (aka sulfur-
dependent
photosynthesis
Oxygenic
photosynthesis
(two PS “Z-scheme”)
Reverse electron
flow via S2- or H2
oxidation
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Chlorobi
Chloroflexi
(“blue-green algae”)

40. Activity for Review of
Unit 06.2: Phototrophic bacteria
1. Chloroplasts are derived from an ancient
endosymbiotic event, and have genomes. To
what phylogenetic group to they belong?
a. Phylum Chloroflexi (green nonsulfur bacteria)
b. Phylum Chlorobi (green sulfur bacteria)
c. Phylum Cyanobacteria (blue-green algae)
2. Based on the phylum that chloroplasts belong
to, how do they
a. gain energy from light?
b. make reducing equivalents from light?
c. fix carbon?
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41. Unit 6: Diversity of Microbial Mats
LECTURE LEARNING GOALS
1. Define microbial mats. Describe the
functional guilds of microbes in the
different layers, and how they interact.
2. For each of the three phyla of
photosynthetic bacteria, contrast how
each fixes C and gains energy and
reducing equivalents from light.
3. For the two thermophilic bacterial phyla,
describe their adaptations to life at high
temperature. Explain how they are primitive
and deeply-branching.
41

42. Thermophilic bacteria
42

43. Thermophilic bacteria
• Primitive – have changed less than other
organisms since their common ancestry
– They are NOT ancestors of other bacteria
– They are NOT less complex
• Deeply branching – branches connect
closer to the root compared to other
branches
– This is a reflection of when this phylum
(assumed to be a distinct group) emerged or
evolved
43

44. Phylum Aquifex
Fig. 8.3 Aquifex pyrophilus
Fig. 8.4 Thermocrinus ruber

45. Phylum Aquifex
• Phylogenetic relationships between
representative members of the Aquifex
• There are only a few dozen species in
total
• All are thermophilic or extremely
thermophilic
45

46. Phylum Thermotoga
Fig 8.7 Thermotoga maritima
Fig 8.8 Thermosipho melanesiense
Fig 8.9 Fervidobacterium islandicum
Fig 8.7
Fig 8.8 Fig 8.9

47. Phylum Thermotoga
• Fewer than three dozen species are
described
• All are thermophilic, anaerobic
fermentative organisms
• Their distinguishing feature is a loose
sheath (or “toga”) snug over the sides but
protruding at one or both ends
• The toga is an outer membrane, rich in
porin-like proteins, full of periplasm, with
function otherwise unknown

48. Obsidian pool is an
acidic, boiling spring

49. Life at high temperatures
1. Membrane fluidity: the membrane lipids have higher melting
points
2. DNA structure: most organisms negatively supercoil their DNA
but extreme thermophiles positively supercoil their DNA;
there is actually no GC enrichment at high temp
3. RNA structure: some RNAs are GC rich, but enhanced
stability comes from folding
4. Protein structure: we cannot predict how proteins are
stabilized at high temp, but enzymes do function well under
high temp conditions
5. Small molecule stability: many small molecules (e.g., GTP or
NAD) are not heat resistant, so it is thought that they are
consumed as they are produced

50. Activity for Review of
Unit 06.3 Thermophilic bacteria
• The Aquificae and Thermotogae are both primitive and
deep-branching phyla. Can you draw a tree with deep
branches that are not primitive, and with primitive
branches that are not deep? Do you know of any
examples of either?
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51. Unit 6: Diversity of Microbial Mats
LECTURE LEARNING GOALS
1. Define microbial mats. Describe the functional
guilds of microbes in the different layers, and how
they interact.
2. For each of the three phyla of photosynthetic
bacteria, contrast how each fixes C and gains
energy and reducing equivalents from light.
3. For the two thermophilic bacterial phyla, describe
their adaptations to life at high temperature.
Explain how they are primitive and deeply-
branching.
Next class is Unit 7: Diversity soils and sediments
Reading for next class: Brown Ch. 10 & 11
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