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Lecture 10 (4 26-2018) archaea

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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.

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Lecture 10 (4 26-2018) archaea

  1. 1. DIVERSITY OF PERMAFROST Unit 10, 4.26.2018 Reading for today: Brown Ch. 15 Reading for next class: Brown Ch. 17 Review Session: Mon May 7, 2018, 11:30 am – 1:00 pm, LSL N610 Final Exam Wed May 9, 2018, 10:30 am – 12:30 pm, 222 Morrill 2 Dr. Kristen DeAngelis Life Science Labs (LSL) N435 Office Hours Tu & Th 12:30 to 1:30 pm OR by appointment (RSVP appreciated) deangelis@microbio.umass.edu, 413-577-4669 1
  2. 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. 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. 4. Permafrost !! the thermal condition in which soils and sediments remains at or below 0°C for two or more years in succession 4
  5. 5. Permafrost 5
  6. 6. Permafrost l  Permafrost has a depth profile and distinct layers, which form due to variation in temperature stability over time -  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 in a permafrost region. The trumpet-shaped lines show seasonal maximum and minimum temperatures in the "active layer", the depth where the maximum annual temperature intersects 0oC 6
  7. 7. Cryobiosphere Seasonal formations Long-term formations Gilichinsky et al., 2008 7
  8. 8. Cryobiosphere l  Cryobiosphere is the part of the cyrosphere containing microorganisms l  The number of viable, mostly airborne, cells in snow and seasonal ice covers are in the same order of magnitude as within the ancient Ice Sheet cores. l  The most colonized part of Cryosphere is represented by modern frost-affected soils and permafrost l  The number of viable cells in these cores increases sharply with the presence of dust particles. l  The abundance of viable cells in Antarctic Ice Sheet decreases with increasing age of the ice 8
  9. 9. Permafrost environments l  Temperatures l  Solar radiation l  Redox potential 9
  10. 10. Permafrost environments •  Most of the Earth's biosphere is cold, and psychrophilic microorganism can be found in these permanently cold environments (5°C). •  Psychrophilic microorganisms proliferate at 0– 10°C, metabolize in snow and ice at –20°C, are predicted to metabolize at –40°C and can survive at –45°C. •  There are many stresses associated with life in permafrost –  Temperatures – Psychrophiles grow optimally below 15˚C. 80% of Earth’s biosphere is < 15˚C. –  Redox potential – aerobic to anaerobic –  Solar radiation – covers of snow and vegetation decrease and minimize this impact 10
  11. 11. 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 •  All psychrophiles 11
  12. 12. 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 12
  13. 13. Psychrophiles can live in ice Deming,  Current  Opinion  in  Microbiology  2002,  5:301–309   13
  14. 14. Psychrophiles can live in ice •  The lower temperature limit for metabolic activity (as opposed to preserved life) is sought in various forms of ice, particularly freshwater forms, because of astrobiology-defined interests in habitat analogues for soil-covered Mars (Arctic tundra) and ice-covered Europa (Antarctica’s Lake Vostok buried deep below glacial 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   14
  15. 15. Cell processes common for cold adaptation Maayer,  EMBO  Reports,  2014   15
  16. 16. 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 such as glycine, betaine, sucrose, mannitol –  protein 'antifreezes' to keep their internal space liquid and protect their DNA even in temperatures below water's freezing point. –  Exopolysaccharide (EPS) can trap water, and protect extracellular enzymes against cold denaturation and autolysis 16
  17. 17. 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 17ValenDne  2007  
  18. 18. 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." 18
  19. 19. 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. 19
  20. 20. Archaea: phylogenetic diversity 20 Thaumarchaeota  
  21. 21. Archaea: taxonomic diversity •  Archaea are ubiquitous microorganisms that are present in most terrestrial and aquatic environments. •  Major archaeal phyla: – Euryarchaeota – Crenarchaeota – Nanoarchaeum – Koryarchaeum – Thaumarchaeota 21
  22. 22. 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. 22
  23. 23. 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 q Small (0.5 – 5 um), unicellular organisms with asexual reproduction •  Like eukaryotes… q Information-processing machinery (replication, transcription, translation), e.g. binding sites are for transcription factors (not RNApol like bacteria) q Nucleosomes, nucleolar enzymes, and cell-cycle proteins •  Unique to archaea… q Membrane lipids are ether linked (not ester-linked like bacteria) q no peptidoglycans q Flagellar structure 23
  24. 24. Phylum Crenarchaeota 24
  25. 25. 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 25
  26. 26. 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 26
  27. 27. Crenarchaeota oxidize and/or reduce sulfur compounds •  Sulfur reduction –  Sulfur + H2 à H2S + H+ –  Hydrogen is the electron donor for ETC –  Sulfur is the terminal electron acceptor •  Sulfur respiration –  Sulfur + organics à CO2 + H2S –  Like aerobic respiration with heterotrophy –  Sulfur is the terminal electron acceptor (t.e.a.) •  Sulfur oxidation –  Sulfur + O2 à H2SO4 –  Aerobic heterotrophy or autotrophy –  Sulfur is the electron donor and O2 the t.e.a. 27
  28. 28. Phylum Euryarchaeota 28
  29. 29. Phylum Euryarchaeota 29
  30. 30. 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 30
  31. 31. 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 31
  32. 32. Methanogenesis from C1 compounds, acetate, or methanol 32
  33. 33. 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" 33
  34. 34. 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. 34
  35. 35. PermafrostPermafrostWhere is permafrost( 35
  36. 36. Permafrost extent l  In the Northern Hemisphere, 24% of the ice-free land area, or 19 million km2, is influenced by permafrost. l  Most of this area is found in Siberia, northern Canada, Alaska and Greenland. l  Most of the Arctic is covered by permafrost (including discontinuous permafrost). l  The arctic is defined as north of the Arctic Circle (66° 33'N), the approximate limit of the midnight sun and the polar night. 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. 36
  37. 37. Tundra 37
  38. 38. Taiga 38
  39. 39. 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  Seasons are divided into short, moist, and moderately warm summers and long, cold, and dry winters. 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) 39
  40. 40. Thawing permafrost l  Permafrost melting can cause the release of greenhouse gasses such as CO2, CH4 and N2O 40
  41. 41. 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 41
  42. 42. Permafrost thaw increases microbial activity 42
  43. 43. 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. 43
  44. 44. 44
  45. 45. Carbon balance in tundra over time •  In healthy ecosystems, C in equals C out •  As permafrost starts to thaw, plants will grow in the soil and the land will act as a net C sink, drawing C in through photosynthesis •  As permafrost continues to thaw, more stored, deep or old C will be released (e.g., diagram at right), and the land will act as a net C source 45
  46. 46. 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 46 hHps://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2017GL075571  
  47. 47. Permafrost thaw will release dormant viruses and microbes •  Thawing of permafrost may disturb 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 –  GC-rich dsDNA genomes up to 2.8 Mbp 47 hHps://www.ncbi.nlm.nih.gov/pmc/arDcles/PMC3222928/   hHp://www.pnas.org/content/111/11/4274  
  48. 48. Activity for Review of ! Unit 10.3 Climate crisis •! What are the effects of thawing permafrost?" 48
  49. 49. 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 49

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