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Sample test suite
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Sample preparation
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Methods text section
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Shipboard community samples*
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“Onboard incubation for shore-based microbiological
cultivation experiments” |
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PFC
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5 cm3 sample in 20 cm3 gas vial with silicon stopper; handed to technician.
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“Chemical tracer” |
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DNA contamination
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2 cm3 sample from core exterior and halfway to core interior into 15 mL Falcon tubes; frozen at –20°C.
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“DNA-based contamination tracers” |
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Cell counts + FISH
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2 cm3 sample into round-bottom (13 cm3) tube, added 8 mL of 4% PFA, and shaken to slurry; stored at
4°C. Note: if too stiff to slurry by shaking, crushed in aluminum bag using hammer. If too hard to crush
with hammer, inserted into round-bottom tube and without PFA addition. |
“Cell separation and enumeration” |
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DNA for qPCR and T-RFLP
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10 cm3 into 15 mL Falcon tube; frozen at –20°C.
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“DNA extraction and purification” |
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Sulfate reduction rates
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5–10 cm WRC in gas-tight bag, flushed with N2, and sealed; stored at 4°C. Processed within 24 h.
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“Potential sulfate reduction rates” |
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Shore-based testing†
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“Sampling for shore-based investigations” |
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Cultivation
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10 cm WRC in gas-tight bag, flushed with N2, vacuumed, and sealed; stored at 4°C.
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“Cultivation experiments” |
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SIP/NanoSIMS
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10 cm WRC in gas-tight bag, flushed with N2, vacuumed, and sealed; stored at 4°C.
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“Single-cell analyses of carbon and nitrogen assimilation
rates of subseafloor microbes” |
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Extracellular DNA/functional genes/
amino acids and amino sugars
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10 cm WRC in gas-tight bag, flushed with N2, vacuumed, and sealed; stored at 4°C. Processed within 24 h.
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“Shore-based DNA extraction, functional gene
characterization, and organic acid analyses” |
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Sulfate reduction rates
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5–10 cm WRC in gas-tight bag, flushed with N2, and sealed.
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“Shore-based 35S incubations” |
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Fungi
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20+ cm3 sample in gas-tight bag, flushed with N2, and sealed; stored at 4°. Processed within 24 h.
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“Cultivation experiments” |
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Chemical degradation of coal/lignite and
release of short-chain fatty acids
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Sampled from split cores.
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“Hydrogenase activity measurements” |
* = underwent X-ray computed tomography. † = underwent X-ray computed tomography and whole-round multisensor core logging. Samples for shipboard community analyses were taken from 15 cm whole-round cores (WRCs) that were shared with other shipboard scientists for lipid biomarker, TOC = total organic carbon, iron and sulfur species, and sedimentology. PFC = perfluorocarbon, FISH = fluorescence in situ hybridization, PCR = polymerase chain reaction, T-RFLP = terminal restriction fragment length polymorphism, NanoSIMS = nanoscale secondary-ion mass spectrometry, PFA = paraformaldehyde.