RubyConf_Lloyd_Nov19_2019.pdf

Transcript

1. Slow, energy-efficient, and mysterious life deep within Earth’s crust Karen

   G. Lloyd, Associate Professor University of Tennessee
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3. 2.9 x 1029 living microbial cells are buried in Earth’s

   seafloor. Kallmeyer et al., 2012, PNAS

4. 2.9 x 1029 living microbial cells are buried in Earth’s

   seafloor. That’s a third of the microbes on the planet. And 10,000 Imes more than the number of stars in the universe. Kallmeyer et al., 2012, PNAS

5. 2.9 x 1029 living microbial cells are buried in Earth’s

   seafloor. That’s a third of the microbes on the planet. And 10,000 Imes more than the number of stars in the universe. Kallmeyer et al., 2012, PNAS

6. 2.9 x 1029 living microbial cells are buried in Earth’s

   seafloor. That’s a third of the microbes on the planet. And 10,000 Imes more than the number of stars in the universe. Much of the life on Earth actually lives inside Earth. Kallmeyer et al., 2012, PNAS

7. How do we learn about these deep subsurface microbes? • 

   We go out into nature and get samples. •  We measure all the chemicals around them to see what they might be eaIng and breathing. •  We extract their DNA or other biomolecules directly from a natural sample. •  We bring them home and grow them in our laboratories.

8. How do we learn about these deep subsurface microbes? • 

   We go out into nature and get samples. •  We measure all the chemicals around them to see what they might be eaIng and breathing. •  We extract their DNA or other biomolecules directly from a natural sample. •  We bring them home and grow them in our laboratories.

9. How do we learn about these deep subsurface microbes? • 

   We go out into nature and get samples. •  We measure all the chemicals around them to see what they might be eaIng and breathing. •  We extract their DNA or other biomolecules directly from a natural sample. •  We bring them home and grow them in our laboratories.

10. How do we learn about these deep subsurface microbes? • 

    We go out into nature and get samples. •  We measure all the chemicals around them to see what they might be eaIng and breathing. •  We extract their DNA or other biomolecules directly from a natural sample. •  We bring them home and grow them in our laboratories.
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12. There are a LOT of different microbes on this planet.

13. There are a LOT of different microbes on this planet.

    Most of them don’t know how to kill us.

14. There are a LOT of different microbes on this planet.

    Most of them don’t know how to kill us. Yet.
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16. 88 84 84 81 85 84 88 81 79 82

    83 82 81 8 5 79 81 Same strain that some other microbiologist discovered

17. 88 84 84 81 85 84 88 81 79 82

    83 82 81 8 5 79 81 Different strain, species, genus, family, order, class than anything that has ever been grown in a lab Same strain that some other microbiologist discovered

18. Oerskovia Bacteriodales Desulfomicrobium Thioclava Agrobacterium Brevundimonas Psychrobacter Alkaliphilus Panibacillus Micrococcus

    Kocuria 98 94 99 93 90 99 99 99 99 97 99 99 99 99 Isolates in liquid Same strain that some other microbiologist discovered Different strain, species, genus, family, order, class than anything that has ever been grown in a lab DNA sequences Data are all from ODP Leg 201: Parkes et al. 2005 Nature, Biddle et al. 2006 PNAS, Biddle et al. 2006 Geobiology, Batzke et al. 2007 Geomicrobiology Journal

19. Oerskovia Bacteriodales Desulfomicrobium Thioclava Agrobacterium Brevundimonas Psychrobacter Alkaliphilus Panibacillus Micrococcus

    Kocuria 98 94 99 93 90 99 99 99 99 97 99 99 99 99 Isolates on plates Isolates in liquid Same strain that some other microbiologist discovered Different strain, species, genus, family, order, class than anything that has ever been grown in a lab DNA sequences Data are all from ODP Leg 201: Parkes et al. 2005 Nature, Biddle et al. 2006 PNAS, Biddle et al. 2006 Geobiology, Batzke et al. 2007 Geomicrobiology Journal

20. Isolates on plates Isolates in liquid Same strain that some

    other microbiologist discovered Different strain, species, genus, family, order, class than anything that has ever been grown in a lab DNA sequences Data are all from ODP Leg 201: Parkes et al. 2005 Nature, Biddle et al. 2006 PNAS, Biddle et al. 2006 Geobiology, Batzke et al. 2007 Geomicrobiology Journal

21. Isolates on plates Isolates in liquid Data are all from

    ODP Leg 201: Parkes et al. 2005 Nature, Biddle et al. 2006 PNAS, Biddle et al. 2006 Geobiology, Batzke et al. 2007 Geomicrobiology Journal Same strain that some other microbiologist discovered Different strain, species, genus, family, order, class than anything that has ever been grown in a lab DNA sequences “Microbial Dark MaPer”

22. •  Microbes grow in cultures. •  We know what microbes

    do on this planet. Microbiology 101

23. •  Microbes grow in cultures. •  We know what microbes

    do on this planet.

24. Let’s think about this from the microbe’s perspecTve.

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29. The number of microbial cells should decrease with depth.

30. Kallmeyer et al. 2012, Proc. Nat. Acad. Sci

31. Kallmeyer et al. 2012, Proc. Nat. Acad. Sci But, how

    fast do they grow?

32. Starnawski et al., 2017, PNAS

33. Starnawski et al., 2017, PNAS

34. Starnawski et al., 2017, PNAS

35. Starnawski et al., 2017, PNAS They’re not really dividing and

    making new cells at all!

36. “It’s not a biome, Karen, it’s a die-ome.” -Jordan Bird,

    in his first year as my PhD student

37. If this ecosystem is just dying, why am I dedicaIng

    my professional life to learning about it?

38. The goal in most ecology: increasing popula.on size

39. (Maybe) The goal in deep marine sediment ecology: exis.ng

40. (Maybe) The goal in deep marine sediment ecology: exis.ng

41. (Maybe) The goal in deep marine sediment ecology: exis.ng

42. So, WHAT does a microbial cell have to do to

    “just exist” for thousands of years?

43. Baltic Sea Sites in IODP Expedition 347 60 63 59

    Jordan Bird Joy Buongiorno

44. What are the potenIal mechanisms that allow bacteria and archaea

    to persist in a near- zero growth state for 8,000 years, 50 meters deep into BalIc Sea sediments?

45. Mixed environmental populaIon of microbes in whole sediments Single cell

    genomics

46. Mixed environmental populaIon of microbes in whole sediments Physically separate

    one cell Single cell genomics

47. Mixed environmental populaIon of microbes in whole sediments Physically separate

    one cell Break it open to get its genome Single cell genomics

48. Mixed environmental populaIon of microbes in whole sediments Physically separate

    one cell Break it open to get its genome Single cell genomics Copy its genome with an enzyme so there’s enough to sequence

49. Mixed environmental populaIon of microbes in whole sediments Physically separate

    one cell Break it open to get its genome Single cell genomics Copy its genome with an enzyme so there’s enough to sequence Sequence all the DNA

50. Mixed environmental populaIon of microbes in whole sediments Physically separate

    one cell Break it open to get its genome Single cell genomics Copy its genome with an enzyme so there’s enough to sequence Assemble genome in a computer Sequence all the DNA

51. Mixed environmental populaIon of microbes in whole sediments Physically separate

    one cell Break it open to get its genome Single cell genomics Copy its genome with an enzyme so there’s enough to sequence Assemble genome in a computer Sequence all the DNA Then you analyze the genes present in a microbe. Genes are like a menu for what the microbe is capable of doing.

52. These deep subsurface microbes contained a TON of toxin-anItoxin systems.

53. Anantharaman and Aravind 2013 Genome Biology Tuberculosis contains the same

    amount of toxin- anItoxin systems

54. Everyone’s starving, because the food is 8,000 years old.

55. Everyone’s starving, because the food is 8,000 years old. But,

    that’s OK, because they are geneIcally programmed to avoid growing too fast.

56. Everyone’s starving, because the food is 8,000 years old. But,

    that’s OK, because they are geneIcally programmed to avoid growing too fast. So, what do they actually eat in order to stay alive for so long????

57. hhp://www.imsb.ethz.ch/research/sauer/research/metabolomics.html Metabolomics Shawn Campagna Eric Tague Hector Castro

58. Depth (mbsf) UMP 4.6 14.3 77.92 74.72 68.02 54.82 48.3

    43.15 37.4 7.65 14.3 78.3 67.05 60.4 53.9 47.25 40.65 20.85 Depth (mbsf) Bird et al., 2019, mBio

59. Depth (mbsf) UMP 4.6 14.3 77.92 74.72 68.02 54.82 48.3

    43.15 37.4 7.65 14.3 78.3 67.05 60.4 53.9 47.25 40.65 20.85 Depth (mbsf) Bird et al., 2019, mBio

60. Atribacteria were the only microbes that could take up allantoin

    from the environment and eat it. Depth (mbsf) UMP 4.6 14.3 77.92 74.72 68.02 54.82 48.3 43.15 37.4 7.65 14.3 78.3 67.05 60.4 53.9 47.25 40.65 20.85 Depth (mbsf) Bird et al., 2019, mBio

61. If Atribacteria are the best at eaIng all the food,

    then why they don’t just kill everyone else and “win” the deep subsurface game?

62. Bird et al., 2019, mBio Atribacterial have a fully funcIonal

    metabolism, including the ability to make all their own amino acids.

63. Which of Atribacteria’s cellular processes was most heavily in-use? Look

    at the metatranscriptomes Laura Zinke, USC Brandi Reese, Texas A&M Corpus ChrisI

64. Bird et al., 2019, mBio The 2nd most acIve gene

    in their genome encodes a protein that exports amino acids.

65. Zombieland

66. Bird et al., 2019, mBio The 2nd most acIve gene

    in their genome encodes a protein that exports amino acids. Maybe they get rid of their amino acids to keep from dividing?

67. Bird et al., 2019, mBio The 2nd most acIve gene

    in their genome encodes a protein that exports amino acids. Maybe they get rid of their amino acids to keep from dividing? This would have the effect of feeding the other organisms in the environment.

68. How can adaptaIons to deep subsurface marine sediments arise when

    there’s no chance to pass your genes along to the next generaIon?

69. D. Giovannelli and P. Barcala Dominguez Maybe microbes come back

    up early in the subducIon zones of volcanic arcs

70. Maybe deep microbial life is connected across long scales of

    Tme and space
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72. Photo: D. Giovannelli

73. Inside an acIve volcano, Poas. Photo: D. Giovannelli Photo: T.

    Owens Photo: C. PraE

74. Inside an acIve volcano, Poas. Photo: D. Giovannelli

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76. It’s hard to imagine life on other planets and moons

    because they lack thick atmospheres. Our solar system may teem with subsurface biospheres.

77. It’s hard to imagine life on other planets and moons

    because they lack thick atmospheres. But nothing is stopping their subsurfaces from teeming with life!
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