Underwater Application of Quantitative PCR on an Ocean Mooring

Preston, Christina M.; Harris, Adeline; Ryan, John P.; Roman, Brent; Marin III, Roman; Jensen, Scott; Everlove, Cheri; Birch, James; Dzenitis, John M.; Pargett, Douglas; Adachi, Masao; Turk, Kendra; Zehr, Jonathon P.; Scholin, Christopher A.

doi:10.1371/journal.pone.0022522

Title: Underwater Application of Quantitative PCR on an Ocean Mooring

Journal Article · Mon Aug 01 00:00:00 EDT 2011 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0022522· OSTI ID:1627466

Preston, Christina M. ^[1]; Harris, Adeline ^[1]; Ryan, John P. ^[1]; Roman, Brent ^[1]; Marin III, Roman ^[1]; Jensen, Scott ^[1]; Everlove, Cheri ^[1]; Birch, James ^[1]; Dzenitis, John M. ^[2]; Pargett, Douglas ^[1]; Adachi, Masao ^[3]; Turk, Kendra ^[4]; Zehr, Jonathon P. ^[4]; Scholin, Christopher A. ^[1]

Monterey Bay Aquarium Research Inst., Moss Landing, CA (United States)
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Kochi Univ. (Japan). Lab. of Aquatic Environmental Science
Univ. of California, Santa Cruz, CA (United States). Dept. of Ocean Sciences and Earth and Marine Sciences

The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions.

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Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); David and Lucille Packard Foundation; National Science Foundation (NSF); Gordon and Betty Moore Foundation; National Aeronautics and Space Administration (NASA)

Grant/Contract Number:: AC52-07NA27344; OCE-0314222; EF-0424599; NNG06GB34G; NNX09AB78G

OSTI ID:: 1627466

Report Number(s):: LLNL-JRNL-480573

Journal Information:: PLoS ONE, Vol. 6, Issue 8; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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