Underwater application of quantitative PCR on an ocean mooring.
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 th...
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Public Library of Science (PLoS)
2011
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oai:doaj.org-article:cf03f0ba62de4e3f9bd58d8d372d8f732021-11-18T06:48:56ZUnderwater application of quantitative PCR on an ocean mooring.1932-620310.1371/journal.pone.0022522https://doaj.org/article/cf03f0ba62de4e3f9bd58d8d372d8f732011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21829630/?tool=EBIhttps://doaj.org/toc/1932-6203The 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.Christina M PrestonAdeline HarrisJohn P RyanBrent RomanRoman MarinScott JensenCheri EverloveJames BirchJohn M DzenitisDouglas PargettMasao AdachiKendra TurkJonathon P ZehrChristopher A ScholinPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 8, p e22522 (2011) |
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DOAJ |
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EN |
| topic |
Medicine R Science Q |
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Medicine R Science Q Christina M Preston Adeline Harris John P Ryan Brent Roman Roman Marin Scott Jensen Cheri Everlove James Birch John M Dzenitis Douglas Pargett Masao Adachi Kendra Turk Jonathon P Zehr Christopher A Scholin Underwater application of quantitative PCR on an ocean mooring. |
| description |
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. |
| format |
article |
| author |
Christina M Preston Adeline Harris John P Ryan Brent Roman Roman Marin Scott Jensen Cheri Everlove James Birch John M Dzenitis Douglas Pargett Masao Adachi Kendra Turk Jonathon P Zehr Christopher A Scholin |
| author_facet |
Christina M Preston Adeline Harris John P Ryan Brent Roman Roman Marin Scott Jensen Cheri Everlove James Birch John M Dzenitis Douglas Pargett Masao Adachi Kendra Turk Jonathon P Zehr Christopher A Scholin |
| author_sort |
Christina M Preston |
| title |
Underwater application of quantitative PCR on an ocean mooring. |
| title_short |
Underwater application of quantitative PCR on an ocean mooring. |
| title_full |
Underwater application of quantitative PCR on an ocean mooring. |
| title_fullStr |
Underwater application of quantitative PCR on an ocean mooring. |
| title_full_unstemmed |
Underwater application of quantitative PCR on an ocean mooring. |
| title_sort |
underwater application of quantitative pcr on an ocean mooring. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2011 |
| url |
https://doaj.org/article/cf03f0ba62de4e3f9bd58d8d372d8f73 |
| work_keys_str_mv |
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| _version_ |
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