posted on 2013-08-20, 00:00authored byWilliam Ussler, Christina Preston, Patricia Tavormina, Doug Pargett, Scott Jensen, Brent Roman, Roman Marin, Sunita R. Shah, Peter R. Girguis, James
M. Birch, Victoria Orphan, Christopher Scholin
Recent advances in ocean observing
systems and genomic technologies
have led to the development of the deep-sea environmental sample processor
(D-ESP). The D-ESP filters particulates from seawater at depths up
to 4000 m and applies a variety of molecular assays to the particulates,
including quantitative PCR (qPCR), to identify particular organisms
and genes in situ. Preserved samples enable laboratory-based validation
of in situ results and expanded studies of genomic diversity and gene
expression. Tests of the D-ESP at a methane-rich mound in the Santa
Monica Basin centered on detection of 16S rRNA and particulate methane
monooxygenase (pmoA) genes for two putative aerobic
methanotrophs. Comparison of in situ qPCR results with laboratory-based
assays of preserved samples demonstrates the D-ESP generated high-quality
qPCR data while operating autonomously on the seafloor. Levels of
16S rRNA and pmoA cDNA detected in preserved samples
are consistent with an active community of aerobic methanotrophs near
the methane-rich mound. These findings are substantiated at low methane
sites off Point Conception and in Monterey Bay where target genes
are at or below detection limits. Successful deployment of the D-ESP
is a major step toward developing autonomous systems to facilitate
a wide range of marine microbiological investigations.