Unit 10: Diversity of Permafrost LECTURE LEARNING GOALS 1. Describe permafrost, and the microbial diversity of permafrost. Explain how the greatest diversity of Archaea exist in cold environments. 2. Describe the two main Archaeal phyla, and describe example species. 3. Explain how climate change is affecting permafrost and microbial diversity.

1. DIVERSITY OF PERMAFROST
Unit 10, 3.9.2021
Reading for today: Brown Ch. 15
Reading for next class: Brown Ch. 17
Dr. Kristen DeAngelis
Office Hours by appointment
deangelis@microbio.umass.edu

2. Unit 10: Diversity of Permafrost
LECTURE LEARNING GOALS
1. Describe permafrost, and the
microbial diversity of permafrost.
Explain how the greatest diversity of
Archaea exist in cold environments.
2. Describe the two main Archaeal
phyla, and describe example species.
3. Explain how climate change is
affecting permafrost and microbial
diversity.
2

3. Unit 10: Diversity of Permafrost
LECTURE LEARNING GOALS
1. Describe permafrost, and the
microbial diversity of permafrost.
Explain how the greatest diversity of
Archaea exist in cold environments.
2. Describe the two main Archaeal
phyla, and describe example species.
3. Explain how climate change is
affecting permafrost and microbial
diversity.
3

4. Permafrost
l the thermal condition in which soils and
sediments remains at or below 0°C for two or
more years in succession
4

5. Permafrost
5

6. Permafrost
l Permafrost has a depth profile and distinct
layers
- Active layer on top, soil which is seasonally frozen.
- The middle zone is permanently frozen: "permafrost”
- And the bottom layer is where the geothermal
temperature is above freezing
l Red dotted lines depict the average
temperature profile with depth of soil. The
trumpet-shaped lines show seasonal maximum
and minimum temperatures in the "active
layer”
l The active layer is the depth where the
maximum annual temperature intersects 0oC
6

7. Cryobiosphere
Seasonal
formations
Long-term
formations
Gilichinsky et al., 2008 7

8. Permafrost environments
l Temperatures – Psychrophile optimal growth is <
15˚C
l Solar radiation – snow and vegetation cover
decrease and minimize this impact
l Redox potential – aerobic to anaerobic
8

9. What is the microbial diversity of
permafrost?
• Bacteria
– Proteobacteria, Actinobacteria,
Firmicutes, Bacteroidetes
– Similar diversity as other non-
frozen soils
• Eukarya
– Mostly fungi
• Archaea
– There is a wide diversity of
psychrophilic archaea
– Methanogens and
methanotrophs
9

10. Psychrophiles
• Most (~75%) of the Earth’s biosphere is cold, and
psychrophiles can be found in permanently cold
environments (≤5°C), such as alpine and polar
habitats, the deep ocean, caves, terrestrial and
ocean subsurface, and the upper atmosphere.
• Psychrophiles are also found in seasonally and
artificially cold environments (≤5°C), such as
refrigerated appliances and products.
• Psychrophiles are particularly abundant in the cold
ocean depths (1–5°C; below ~1,000 m) which cover
~70% of the surface of the planet.
Cavicchioli, Nature Reviews Microbiology, 2006
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11. Psychrophiles can live in ice
Deming, Current Opinion in Microbiology 2002, 5:301–309
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12. Psychrophiles can live in ice
• If T <0˚C, microbes can grow between
ice crystals or in the pore spaces of ice.
– Bacteria visualized microscopically by DAPI (4,6-
diamidino-2-phenylindole-2HCl) stain directly
within a brine pocket of Arctic winter sea ice at –
15°C. The transmitted light image in (a) shows ice
crystals and the brine-filled veins between them
(bar = 100 µm).
– Enlarged images (bar = 10 µm) of a brine pocket
in (a) show, (b) by transmitted light, the
microscale habitat and, (c) by epifluorescence
microscopy, its bacterial inhabitants.
Deming, Current Opinion in Microbiology 2002, 5:301–309
12

13. Cell processes common for cold adaptation
Maayer, EMBO Reports, 2014
13

14. Physiological adaptations of Psychrophiles
• Membrane function
– increased polyunsaturated to saturated fatty acid ratios in
membrane phospholipids
– changes in lipid class composition
– reduced size and charge of lipid head groups, which
affects phospholipid packing
– conversion of trans- to cis-isomeric fatty acids
• Cryoprotectants and antifreeze proteins
– compatible solutes glycine, betaine, sucrose, mannitol
– protein 'antifreezes' to keep their internal space liquid and
protect their DNA even in temperatures below freezing
– Exopolysaccharide (EPS) can trap water, and protect
extracellular enzymes against cold denaturation and
autolysis
14

15. Archaeal
membranes have
unique lipids
• Membrane lipids are
ether linked (not ester-
linked like bacteria)
• no peptidoglycans
• Exist as monolayers
(not bilayers)
• Unsaturations in the
lipids are generally
conjugated
15
Valentine 2007

16. Activity for Review of
Unit 10.1 Permafrost
• Which statements are true about permafrost?
a) It has an active layer which freezes and thaws in
cycles.
b) It is colonized by bacteria, archaea and eukarya.
c) Soils frozen for two or more weeks are
permafrost.
d) Permafrost can be frozen soils but not frozen
sediments.
16

17. Unit 10: Diversity of Permafrost
LECTURE LEARNING GOALS
1. Describe permafrost, and the
microbial diversity of permafrost.
Explain how the greatest diversity of
Archaea exist in cold environments.
2. Describe the two main Archaeal
phyla, and describe example species.
3. Explain how climate change is
affecting permafrost and microbial
diversity.
17

18. Domain Archaea
• Woesian tree (top)
– Based on 16S
ribosomal RNA
• Alternative 3-domain
ToL (middle)
– Based on protein
structures
• Eocyte ToL (bottom)
– Based on
metagenomic
sequencing
18
18
Bacteria
Archaea Eukaryotes
BacteriaArchaea Eukaryotes
Bacteria
Eukaryotes
Euryarchaea
Crenarchaea

19. Archaea: phylogenetic diversity
19
Thaumarchaeota

20. Archaea: functional diversity
• Methanogens— archaeans that produce
methane gas as a waste product of their
"digestion," or process of making energy.
• Halophiles— those archaeans that live in
salty environments.
• Thermophiles— the archaeans that live at
extremely hot temperatures.
• Psychrophiles— those that live at
unusually cold temperatures.
20

21. Archaea: genetic diversity
• Like bacteria…
q Similar metabolic
proteins
q Similar gene and
chromosome structure
q Process of replication,
transcription and
translation, e.g., one
or a few replication
origins
q Genes are arranged
in operons
q Cytoskeleton
• Like eukaryotes…
q Information-processing
machinery (replication,
transcription, translation)
q Nucleosomes, nucleolar
enzymes, and cell-cycle
proteins
q no peptidoglycans
• Unique to archaea…
q Ether-linked membrane
lipids (bacteria are ester-
linked)
q Flagellar structure
21

22. Phylum Crenarchaeota
22

23. Phylum Crenarchaeota
• Diversity is phylogenetically low, with few
isolates
• Metabolism
– Sulfur reduction coupled with C fixation
– Sulfur respiration with both C and energy
gained from organic compounds
– Sulfur oxidation under aerobic conditions
paired with heterotrophy
• Habitat includes many environments, with
cultivated examples mostly from extreme
hot environments
23

24. Phylum Crenarchaeota:
Sulfolobus sulfatericus
• Lobed coccus with budding
scars from reproduction
• Grow on sulfur granules
– Obligate aerobe or
microaerophile
– Autotrophic sulfur oxidation,
chemolithoheterotrophy (Sulfur
oxidation for energy) or oxidative
heterotrophy
• Common organisms of
solfataras (fumarole which
emits H2S and SO2) and boiling
mud pots
24

25. Phylum Euryarchaeota
25

26. Phylum
Euryarchaeota
26

27. Phylum Euryarchaeota
• Diversity is more diverse phylogenetically and phenotypically
than Crenarchaeota
• Metabolism
– Methanogens are Euryarchaeota, gaining their energy by
reduction of C1 compounds (formate, CO, CO2)
– Some methanogens can make methane from acetate
and/or methanol
– Most methanogens are autotrophs, gaining biomass and
energy from C fixation
• Habitat
– Methanogenic enzymes are extremely oxygen sensitive
– Euryarchaeota are found in a wide diversity of anaerobic
habitats including sediments, soils, animal gastrointestinal
tracts, wastewater, landfills, and oil deposits
27

28. Phylum Euryarchaeota:
Methanocaldococcus janashii
• Motile coccus with a
single “tuft” of many
flagella (aka
lophotrichous)
• Obligate autotroph (using
Calvin cycle for C fixation)
• Capable of reducing CO2
or CO with H2 to produce
methane
• Extreme thermophile
28

29. Activity for Review of
Unit 10.2 Archaea
1. Name one phylum or class of Archaea.
2. For the list of Archaeal traits below,
circle which ones are shared with the
Eukarya
a) Information-processing machinery
b) Ether-linked membrane lipids
c) Cytoskeleton
d) Nucleosomes
e) Flagellar structure
29

30. Unit 10: Diversity of Permafrost
LECTURE LEARNING GOALS
1. Describe permafrost, and the
microbial diversity of permafrost.
Explain how the greatest diversity of
Archaea exist in cold environments.
2. Describe the two main Archaeal
phyla, and describe example species.
3. Explain how climate change is
affecting permafrost and microbial
diversity.
30

31. Permafrost
Where is permafrost
31

32. Permafrost extent
l In the Northern Hemisphere, 24% of the ice-
free land area, or 19 million km2, is
influenced by permafrost.
l The Antarctic continent is mostly covered
by glaciers (not permafrost)
l Permafrost stores ~1500 Gt of the world's C,
that's twice what's in the atmosphere right
now. Storage forms are mostly peat
(partially decayed organic matter) and
methane.
32

33. Tundra
33

34. Taiga
34

35. Permafrost is found in tundra
and taiga ecosystems or biomes
l The word "tundra" usually refers only to the areas
where the subsoil is permafrost, or permanently
frozen soil.
l Boreal forests, or taiga, are the largest terrestrial
biome. Occurring between 50 and 60 degrees
north latitudes.
l Continuous permafrost typically forms in any
climate where the mean annual air temperature is
less than the freezing point of water.
l Discontinuous permafrost forms if the mean annual
air temperature is only slightly below 0 °C (32 °F)
35

36. Thawing permafrost
l Permafrost melting can cause the release of
greenhouse gasses such as CO2, CH4 and N2O
36

37. Thawing permafrost
l Permafrost melting releases greenhouse
gasses such as CO2, CH4 and N2O
l Increased microbial activity
l Release of methane hydrates which experience
increased permeability in thawed permafrost
l Thermokarst/permafrost degradation
l Increased plant growth causes both increased
photosynthesis and more root C inputs into the soil
l Increased forest fires
l Liquid water causes increased leaching, litter fall,
and erosion
37

38. Permafrost thaw increases microbial activity
38

39. Permafrost thaw increases microbial activity
• Permafrost thaw releases methane
– Most is stored, generated long ago
– this large release of methane that occurs within
days of thaw is from stored methane present in
permafrost before the thaw; we know this
because 2-bromoethane sulphonic acid (BES)
prevents methanogenesis
– Increased microbial activity occurs with thaw, as
methanogenesis with accelerated
methanotrophy and methylotrophy
• Drunken forests form where discontinuous
permafrost or ice wedges have melted,
causing trees to tilt at various angles.
39

40. Carbon balance in tundra over time
40

41. Permafrost thaw will release
mercury
• Mercury is a naturally
occurring metal and
neurotoxin
• It accumulates as it
moves up the food
chain
• Thousands of years
worth of accumulation
are stored in
permafrost
41
https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2017GL075571

42. Permafrost thaw will release
dormant viruses and microbes
• Mostly no evidence that new
old pathogens are being
released
• Thawing permafrost disturbed
historic cattle burial grounds in
East Siberia
– Associated with an outbreak of
anthrax
– Bacillus anthracis, spore-forming
soil-dwelling Firmicutes
• Some giant viruses have been
found active after 30,000 years
in permafrost
42
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222928/
http://www.pnas.org/content/111/11/4274

43. Activity for Review of
Unit 10.3 Climate crisis
• What are the effects of thawing
permafrost?
43

44. Unit 10: Diversity of Permafrost
LECTURE LEARNING GOALS
1. Describe permafrost, and the microbial
diversity of permafrost. Explain how the
greatest diversity of Archaea exist in
cold environments.
2. Describe the two main Archaeal phyla,
and describe example species.
3. Explain how climate change is affecting
permafrost and microbial diversity.
Next class is Unit 11: Viruses and prions
Reading for next class: Brown Ch. 17
44