Deep Life Rick Colwell, Oregon State University Deep Carbon Observatory Summer School 2016 Yellowstone

The nature of microbial life •  Fundamental properties of life: –  Organization, heredity, growth, adaptation •  But microbial life is distinctive: –  Unicellular life allows niche exploitation of small space –  Intimate association with environment –  Well distributed through the habitable planet –  Adapted to a range of temperatures, pressures, pH, salinities, and toxins –  Numerous redox couples are exploited for energy –  Reproduction by simple cell division –  Long-term dormancy possible –  Vast genetic diversity and exchange of information between individuals O’Dors Law of Biology: Physics and chemistry have laws, while biology only has lawyers looking for loopholes.

Hug et al. 2016 Microbial life: as we know it •  Remarkable diversity of microbial life •  Uncultured (i.e., unisolated) organisms are a major component •  Large evolutionary divergence is present in the uncultured fraction •  Huge physiological potential and activity apparently absent from biogeochemical models •  Many of the uncultivated groups are in Earth environments

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Technologies enable sampling, analysis, engagement Enabling technologies mature–progressing-nascent cell staining techniques (FISH) DNA extraction/sequencing lipidomics RNA extraction/analysis metagenomics biogeophysics stable isotope probing bioreactor design reaction path modeling thermodynamic modeling bioinformatics proteomics metabolomics high-throughput cultivation single cell genomics data science visualization engagement Davis et al. 1992 CORKs drill ships mines drill rigs

hydrocarbons repositories remediation biohydrometallurgy basic science Subsurface microbiology research and sampling

Kallmeyer et al. 2012 Microbes are abundant in the subsurface - Biomass decrease with depth - Numbers are lower than early estimates - Span 5 orders of magnitude - Strong correlation to mean sedimentation rate and distance from land (ocean productivity) Non-sedimentary crustal seafloor and continental settings progressing Fractures Priscu: “…vein volume in Antarctic continent is 144 km3” For seafloor sediments…

…but even they have their limits! Life disappears if the subsurface becomes too: - Hot (c.f., Roussel et al. 2008; highest temperature?) - Impermeable (Pedersen 2000; Colwell et al. 1997) - Dry (Colwell et al. 1992) - Compacted (Rebata-Landa and Santamarina, 2006) - Deprived of energy flux or supply of redox couples (Fredrickson et al. 1997; Røy et al. 2012) ….combined factors Endospores need to be considered Rebata-Landa and Santamarina, 2006

What are we looking for? Who are those guys? – Butch Cassidy

Molecular characteristics determine microbial diversity G G C G A U G A C CC U A U A C G AC U G AG G C G G G A U C A A A A G U U U A U A A G U A A A G A A C C U G C U U A U G C G C U A U U G C C G A C C U G G U A A U G G C G A U G A C C C U A U A C G AC UG AG G C G G G A U C A A A A G U U U A U A A G U A A A G A A C C U G C U U A U G C G C U A U U G C C G A C C U G G U A A U Ribosomes in a microbial cell George Rice Ribosome A fragment of ribosomal RNA Central Dogma of Molecular Biology: “DNA makes RNA makes protein” F. Crick 1958 0.025 µm 1 x 5 µm 0.002 x 0.100 µm

Feature frequency profiles Sung-Hou Kim, LBNL and UC Berkeley For microbes use: - Short sequences of DNA - Compare genes shared by all life

Chivian et al. 2008 Desulforudis audaxviator: a keystone subsurface species? 2.8 km deep fracture Thermophilic Archaeal genes to fix N and C Uses H2 , CO >99.9% of the community Capable of independent existence Similar phylotypes detected in seafloor sediments

= terrestrial subsurface = marine subsurface = samples considered in this study Rocks, sediments, waters Census of Deep Life Cratons, metamorphic rocks, basalts, sediments, near hydrothermal vents, karst caves, serpentinites, hydrates, springs, subglacial, sub ice shelf, BIFs, sapropels, tectonically active, sulfidic caves, mud volcanoes, seamounts

CoDL: Juan de Fuca Ridge Microbial communities governed by mineralogy Smith et al. in press

Deep microbiogeography ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● −2 −1 0 1 −1 0 1 MDS1 MDS2 group ● ● ● laboratory marine terrestrial Bacterial communities by biome Lake Groundwater Terrestrial water Rock Basement Sediment Stress = 0.24 Groundwater Sediment lab marine terrestrial MDS1 MDS2 NMDS plot based off the Morisita- Horn distance matrix of the bacterial sequences from all of the samples

examples: carbohydrates hydrogen methane sulfide examples: carbon dioxide sulfate nitrate oxygen From Gaidos et al., 1999 Redox potential at 1 atm, pH 7, 25 C Reduced to oxidized half-reaction: energy rich (electrons to spare) to energy poor Oxidized to reduced half-reaction: energy poor (they crave electrons) to energy rich Physics and chemistry have laws, while biology only has lawyers looking for loopholes. Ron O’Dor Life needs a thermodynamic disequilibrium to survive

Microbial physiologies in the subsurface Heterotrophy, lithoautotrophy, and latent redox processes Valentine 2011

Microbial activity in the subsurface Surface world Figure modified from Onstott et al. 1999 •  Mostly low activities in the subsurface; estimates by geochemical modeling •  Subsurface rates range from 100 to 10-13 moles of CO2 /L/yr •  Doubling times as low as 1013 sec; growth less typical than cell maintenance •  Dependent upon balanced supply of electron donors and acceptors ….and many other factors

Contaminant migration Chemical Physical* Subsurface gradients determine where microbes might survive Nuclear waste repository Geological CO2 storage Roll front Groundwater fluctuation Hydrocarbon retort Hydrate formation/decomposition Seismicity Volcanism Permafrost formation/thawing Natural processes Human-induced processes Hydrothermal vents Redox reactions Glacial compression/rebound Mining Conventional oil/gas recovery Mass wasting Subduction Human-induced or natural processes N-cycle perturbation Nuclear testing Serpentinization Infrared radiation Radiolysis Unconventional oil/gas recovery Tides Meteorite impact Sea level rise Geothermal energy modified from Colwell and D’Hondt, 2013 * chemical-physical axis is arbitrary

Delaney et al. 1998 Surface-subsurface connections Westbrook et al. 2009 Microbial implications in bioremediation, biohydrometallurgy, repositories, reservoirs

= Haury et al. 1978 Envisioning life in a geological context •  Change the setting to an Earth system •  Consider biomass variability, activity, key functional genes

Questions… •  We have the tools •  Subsurface life is abundant, diverse, and metabolically tuned to long-term survival •  Metabolic strategies for using redox couples are diverse and latent processes are likely more important than we have yet imagined •  Understanding subsurface life as it is integrated with spatially and temporally expansive geological and chemical processes is an area of discovery

Synthesis

Deep Carbon Observatory Summer School 2016

Details… GoPros? Reimbursement Travel to Bozeman… Tomorrow morning 7:30

Field trips Context, inspiration Field study Sampling, experience Discussions Lightning talks, posters, presentations Instruments Making the measurements Data Processing, synthesis, analysis Next steps… involvement Using the tools

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