RubyConf_Lloyd_Nov19_2019.pdf

RubyConf

1. Slow, energy-efficient, and mysterious life deep within Earth’s crust Karen G. Lloyd, Associate Professor University of Tennessee
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.
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.
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.
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
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
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!