Evidence of dark oxygen production at the abyssal seafloor

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Abstract

Deep-seafloor organisms consume oxygen, which can be measured by in situ benthic chamber experiments. Here we report such experiments at the polymetallic nodule-covered abyssal seafloor in the Pacific Ocean in which oxygen increased over two days to more than three times the background concentration, which from ex situ incubations we attribute to the polymetallic nodules. Given high voltage potentials (up to 0.95 V) on nodule surfaces, we hypothesize that seawater electrolysis may contribute to this dark oxygen production.

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Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples.

Alma Parada, David M Needham, Jed Fuhrman (2016)

Microbial community analysis via high-throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer pair 515F (515F-C) and 806R greatly underestimated (e.g. SAR11) or overestimated (e.g. Gammaproteobacteria) common marine taxa. We evaluated marine samples and mock communities (containing 11 or 27 marine 16S clones), showing alternative primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT) yield more accurate estimates of mock community abundances, produce longer amplicons that can differentiate taxa unresolvable with 515F-C/806R, and amplify eukaryotic 18S rRNA. Mock communities amplified with 515F-Y/926R yielded closer observed community composition versus expected (r(2) = 0.95) compared with 515F-Y/806R (r(2) ∼ 0.5). Unexpectedly, biases with 515F-Y/806R against SAR11 in field samples (∼4-10-fold) were stronger than in mock communities (∼2-fold). Correcting a mismatch to Thaumarchaea in the 515F-C increased their apparent abundance in field samples, but not as much as using 926R rather than 806R. With plankton samples rich in eukaryotic DNA (> 1 μm size fraction), 18S sequences averaged ∼17% of all sequences. A single mismatch can strongly bias amplification, but even perfectly matched primers can exhibit preferential amplification. We show that beyond in silico predictions, testing with mock communities and field samples is important in primer selection.