Towards In Situ Sequencing for Life Detection

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Apr 5, 2017 - Weak Panspermia: Common building blocks of life. – Synthesis of prebiotic molecules in early solar nebula (Nuevo et al. 2009, 2012; Ciesla &.
FISO Seminar – May 3, 2017

Towards In Situ Sequencing for Life Detection

Christopher E. Carr Research Scientist, MIT Research Fellow, MGH Science PI, Search for Extra-Terrestrial Genomes (SETG)

[email protected] | setg.mit.edu | @carr_lab Image: Jenny Mo-ar/NASA

Search for Extra-Terrestrial Genomes (SETG) Team

Not pictured: Levon Avakian, John Cashion, SETG Alumni 5/3/17

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“I believe we are going to have strong indica@ons of life beyond Earth in the next decade and defini@ve evidence in the next 10 to 20 years” – Ellen Stofan, (then) Chief Scien3st (NASA) April 7, 2015

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Today •  •  •  • 

What is life? Where should we search for it? How should we detect it? What comes next?

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Today •  •  •  • 

What is life? Where should we search for it? How should we detect it? What comes next?

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Life As We Know It DNA RNA Proteins

Proper@es EvoluHon Growth ReproducHon Metabolism 5/3/17

Poten@al Features InformaHonal polymers Cell and populaHon growth Cell division Metabolites

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“RNA World”

NASA “A self-sustaining chemical system capable of Darwinian evoluHon” 6

Origin(s) of Life Astrochemistry

ArHficial Life

Volcanism

UV-driven synthesis

Hydrothermal Vents Mural at NASA Ames Research Center 5/3/17

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Requirements for Life (as we know it) •  •  •  •  • 

CHNOPS elements Liquid water / water activity > 0.61 Redox gradient (energy flux) Moderate temperatures pH, salinity, pressure, etc.

What environments meet the requirements? NAP h-ps://goo.gl/110XN5

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Today •  •  •  • 

What is life? Where should we search for it? How should we detect it? What comes next?

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Searching for Life Beyond Earth Other Ocean Worlds…

Exoplanets

Mars

A direct search for life

Enceladus

James Webb Space Telescope

Europa

Credits: NASA/JPL-Caltech/SETI 5/3/17

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Is Carbon Based Life Universal? “Weak Panspermia” Sugars (Ribose)

Nucleobases

Comet (simulated) Meteorite(s)

ESA/Rose-a/NAVCAM, CC BY-SA IGO 3.0

CC BY-SA 3.0 h-ps://goo.gl/SGBkXz

Synthesis of prebio3c molecules in early solar nebula (Nuevo et al. 2009, 2012; Ciesla & Sandford, 2012), ribose and other sugars in late solar nebula (Meinert et al. 2016); Meteori3c amino acids & nucleobases (Engel et al. 1997; Mar3ns et al. 2008; SchmiL-Kopplin et al. 2010; Cooper et al. 2011; Callahan et al. 2011)

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Shared Ancestry? ~4 billion years ago … “Lithopanspermia”

Calcula3on/Simula3on (Gladman & Burns, 1996; Gladman et al. 1996; Gladman et al. 1997; Mileikowsky et al. 2000); Low temperature meteori3c transfer (Weiss et al. 2000); Microbes survive ejec3on shock (Burchell et al. 2004; Stöffler et al. 2007; Horneck et al. 2008; Meyer et al. 2011) Credit: ESO/M. Kornmesser CC 4.0 h-ps://goo.gl/7Vz5eS 5/3/17

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Potential Refugia for Life on Mars Poten@al Near-Surface Zones of Extant Life

Low Exposure Age Regions

Recurring Slope Lineae (RSLs) - Liquid Brines?

Fresh Impact Craters

Water Ice Fog / AcHve Water Cycle?

HRSC/MEX/ESA

HiRISE NASA/JPL/ASU/MSSS

Subsurface Regions

Extensive overlap between Mars and Earth of zones habitable for life as we know it (Jones et al., 2011) 5/3/17

Mars Odyssey / Mars Global Surveyor / NASA/JPL/ASU

Example: Subsurface environments offer UV and radiaHon shielding, heat, moisture

HiRISE NASA/JPL/ASU/MSSS

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Lava Tube

h-p://goo.gl/GupK1H

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How universal is biochemistry? 4.6 Ga Gya

4.1

ets

Com

Venus Earth Mars

Complex organics form, mix in the solar nebula

• 

Me

teo r

ites

3.8

Titan Europa Enceladus

Late Heavy Bombardment: Meteoritic transfer between Earth and Mars (and Venus?)

3.5

Extant life?

Isotopic evidence of life on Earth Start of transition from wet to dry on Mars Fossil evidence of life on Earth

Mars: Enceladus: Related life? 2nd genesis? Shadow biosphere on Earth?

Weak Panspermia: Common building blocks of life –  Synthesis of prebiotic molecules in early solar nebula (Nuevo et al. 2009, 2012; Ciesla & Sandford, 2012), ribose and other sugars in late solar nebula (Meinert et al. 2016) –  Meteoritic amino acids & nucleobases (Engel et al. 1997; Martins et al. 2008; SchmittKopplin et al. 2010; Cooper et al. 2011; Callahan et al. 2011)

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Lithopanspermia: Shared ancestry between Earth and Mars?

–  Calculation/Simulation (Gladman & Burns, 1996; Gladman et al. 1996; Gladman et al. 1997; Mileikowsky et al. 2000) –  Low temperature meteoritic transfer (Weiss et al. 2000) –  Microbes survive ejection shock (Burchell et al. 2004; Stöffler et al. 2007; Horneck et al. 2008; Meyer et al. 2011)

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Today •  •  •  • 

What is life? Where should we search for it? How should we detect it? What comes next?

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Searching for Life Beyond Earth Proper@es of Life •  Metabolism •  Growth •  ReproducHon •  EvoluHon

e.g., Klein 1978; Klein 1979

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Biomarkers •  Biofabrics •  BiomineralizaHon •  Body fossils •  SpaHal chemical pa-erns •  Biogenic gases (methane) e.g. Grotzinger et al. 2012 •  Isotope raHos •  Future missions: Biogenic organic molecules (amino acids, lipids, nucleic acids) •  Need definiHve biomarkers! Charged linear informa7onal polymers likely universal for aqueous-based life. 18

Priority: Biogenic Organic Molecules

On icy moons: biogenic organic molecules even more important, because some biosignatures are not present or are inaccessible.

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Why nucleic acids?

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Survival Time of DNA Model of DNA Hydrolysis

Survival of the coldest adapted from Millar & Lambert, 2013

Mars

Mars temperature preserves DNA on longer 3mescales versus Earth 5/3/17

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Search for Extra-Terrestrial Genomes (SETG) Data Processing

Rover Icy Moon Orbiter

Ocean Explorer

Sequence Analysis

Proteobacteria Firmicutes

DNA/RNA XNA extraction

Biologically -based Nanopore Sequencing

Archaea Bacteroidetes Chloroflexi

Current TRL 4

ValidaHon using hard to lyse spores (Bacillus sub3lis)

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Non-standard bases (Inosine nucleoside)

RadiaHon Resistant Memory (CBRAM)

Neural Network-based Data Processing

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Extraction Modules (4)

Volume-accurate Pre-TRL6 SETG Model: •  4 extracHon modules •  2 sequencers

Sequencing (internal) Data Processing (internal) Fluidics

9.5 cm

22 cm 14cm

Current Best Estimate

Average Contingency

Allocation

System Volume

2.7 L

28%

3.4 L

System Mass

3.7 kg

28%

4.8 kg

130 W-hr

31%

170 W-hr

Budget

Energy (Per Sample)

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Carr et al. 2017 IEEE Aerospace (In Press)

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System Margin

Specification 4.3 L

25%

6.0 kg 210 W-hr

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Abundance & Sensitivity 1

10

102

103

104

105

106

107

108

109 Cell Density (#/g)

Europa Ocean energetic upper limit?

2.5 · 105 Low-moisture a

1 ppb

terrestrial analogs of Mars (Atacama)

Saturated bacterial culture DNA (mass/mass)

10-15 10-14 10-12 10-11 10-10

10-9

10-8

TRL6 Target Carr et al. (2017) AbSciCon Abstract #3395 5/3/17

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10-7

10-6

10-5 B. subtilis ATCC 6633 spores

500 ng DNA for 50 mg sample 25

Subsystem Requirements Sample Delivery

Extraction

Sequencing

1 ml/50 mg after any concentration

Current Best

104 spores 40 pg DNA

5% Yield

Achieved: B. subtilis spores in Mars analog soils

Forward Contamination? Putative (Mars) Life?

OmniLyse ®

Target

Analysis

0.06% Yield

0.0001% (typical) 0.0025% (optimal)

>1M bases called

Detection of known Earth organism with