Methods ARTICLE

Front. Microbiol., 07 November 2011 | doi: 10.3389/fmicb.2011.00215

Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection

Mak A. Saito1*, Vladimir V. Bulygin1, Dawn M. Moran1, Craig Taylor2 and Chris Scholin3
  • 1 Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
  • 2 Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
  • 3 Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA

Improvements in temporal and spatial sampling frequency have the potential to open new windows into the understanding of marine microbial dynamics. In recent years, efforts have been made to allow automated samplers to collect microbial biomass for DNA/RNA analyses from moored observatories and autonomous underwater vehicles. Measurements of microbial proteins are also of significant interest given their biogeochemical importance as enzymes that catalyze reactions and transporters that interface with the environment. We examined the influence of five preservatives solutions (SDS-extraction buffer, ethanol, trichloroacetic acid, B-PER, and RNAlater) on the proteome integrity of the marine cyanobacterium Synechococcus WH8102 after 4 weeks of storage at room temperature. Four approaches were used to assess degradation: total protein recovery, band integrity on an SDS detergent polyacrylamide electrophoresis (SDS-PAGE) gel, and number of protein identifications and relative abundances by 1-dimensional LC–MS/MS proteomic analyses. Total protein recoveries from the preserved samples were lower than the frozen control due to processing losses, which could be corrected for with internal standardization. The trichloroacetic acid preserved sample showed significant loss of protein band integrity on the SDS-PAGE gel. The RNAlater preserved sample showed the highest number of protein identifications (103% relative to the control; 520 ± 31 identifications in RNAlater versus 504 ± 4 in the control), equivalent to the frozen control. Relative abundances of individual proteins in the RNAlater treatment were quite similar to that of the frozen control (average ratio of 1.01 ± 0.27 for the 50 most abundant proteins), while the SDS-extraction buffer, ethanol, and B-PER all showed significant decreases in both number of identifications and relative abundances of individual proteins. Based on these findings, RNAlater was an effective proteome preservative, although further study is warranted on additional marine microbes.

Keywords: proteome, preservation, autonomous sampling, cyanobacteria, alkaline phosphatase, proteomics, Synechococcus WH8102

Citation: Saito MA, Bulygin VV, Moran DM, Taylor C and Scholin C (2011) Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection. Front. Microbio. 2:215. doi: 10.3389/fmicb.2011.00215

Received: 13 July 2011; Accepted: 10 October 2011;
Published online: 07 November 2011.

Edited by:

Julie LaRoche, Leibniz Institute of Marine Sciences (IFM-GEOMAR), Germany

Reviewed by:

Claire Mahaffey, University of Liverpool, UK
Tom Bibby, University of Southampton, UK
Rachael Marie Morgan-Kiss, Miami University, USA
Heather Bouman, University of Oxford, UK

Copyright: © 2011 Saito, Bulygin, Moran, Taylor and Scholin. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and other Frontiers conditions are complied with.

*Correspondence: Mak A. Saito, Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA. e-mail: msaito@whoi.edu

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