Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton
Planktonic microbial activity and community structure is dynamic, and can change dramatically on time scales of hours to days. Yet for logistical reasons, this temporal scale is typically under-sampled in the marine environment. In order to facilitate higher-resolution, long-term observation of micr...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2012
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| Online Access: | http://hdl.handle.net/1721.1/69247 |
| _version_ | 1826201173558820864 |
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| author | Ottesen, Elizabeth Marin, Roman, III Preston, Christina M. Young, Curtis Robert, III Ryan, John P. Scholin, Christopher A. DeLong, Edward |
| author2 | Massachusetts Institute of Technology. Department of Civil and Environmental Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Civil and Environmental Engineering Ottesen, Elizabeth Marin, Roman, III Preston, Christina M. Young, Curtis Robert, III Ryan, John P. Scholin, Christopher A. DeLong, Edward |
| author_sort | Ottesen, Elizabeth |
| collection | MIT |
| description | Planktonic microbial activity and community structure is dynamic, and can change dramatically on time scales of hours to days. Yet for logistical reasons, this temporal scale is typically under-sampled in the marine environment. In order to facilitate higher-resolution, long-term observation of microbial diversity and activity, we developed a protocol for automated collection and fixation of marine microbes using the Environmental Sample Processor (ESP) platform. The protocol applies a preservative (RNALater) to cells collected on filters, for long-term storage and preservation of total cellular RNA. Microbial samples preserved using this protocol yielded high-quality RNA after 30 days of storage at room temperature, or onboard the ESP at in situ temperatures. Pyrosequencing of complementary DNA libraries generated from ESP-collected and preserved samples yielded transcript abundance profiles nearly indistinguishable from those derived from conventionally treated replicate samples. To demonstrate the utility of the method, we used a moored ESP to remotely and autonomously collect Monterey Bay seawater for metatranscriptomic analysis. Community RNA was extracted and pyrosequenced from samples collected at four time points over the course of a single day. In all four samples, the oxygenic photoautotrophs were predominantly eukaryotic, while the bacterial community was dominated by Polaribacter-like Flavobacteria and a Rhodobacterales bacterium sharing high similarity with Rhodobacterales sp. HTCC2255. However, each time point was associated with distinct species abundance and gene transcript profiles. These laboratory and field tests confirmed that autonomous collection and preservation is a feasible and useful approach for characterizing the expressed genes and environmental responses of marine microbial communities. |
| first_indexed | 2024-09-23T11:47:22Z |
| format | Article |
| id | mit-1721.1/69247 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T11:47:22Z |
| publishDate | 2012 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/692472022-09-27T21:54:56Z Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton Ottesen, Elizabeth Marin, Roman, III Preston, Christina M. Young, Curtis Robert, III Ryan, John P. Scholin, Christopher A. DeLong, Edward Massachusetts Institute of Technology. Department of Civil and Environmental Engineering DeLong, Edward Young, Curtis Robert, III DeLong, Edward Ottesen, Elizabeth Planktonic microbial activity and community structure is dynamic, and can change dramatically on time scales of hours to days. Yet for logistical reasons, this temporal scale is typically under-sampled in the marine environment. In order to facilitate higher-resolution, long-term observation of microbial diversity and activity, we developed a protocol for automated collection and fixation of marine microbes using the Environmental Sample Processor (ESP) platform. The protocol applies a preservative (RNALater) to cells collected on filters, for long-term storage and preservation of total cellular RNA. Microbial samples preserved using this protocol yielded high-quality RNA after 30 days of storage at room temperature, or onboard the ESP at in situ temperatures. Pyrosequencing of complementary DNA libraries generated from ESP-collected and preserved samples yielded transcript abundance profiles nearly indistinguishable from those derived from conventionally treated replicate samples. To demonstrate the utility of the method, we used a moored ESP to remotely and autonomously collect Monterey Bay seawater for metatranscriptomic analysis. Community RNA was extracted and pyrosequenced from samples collected at four time points over the course of a single day. In all four samples, the oxygenic photoautotrophs were predominantly eukaryotic, while the bacterial community was dominated by Polaribacter-like Flavobacteria and a Rhodobacterales bacterium sharing high similarity with Rhodobacterales sp. HTCC2255. However, each time point was associated with distinct species abundance and gene transcript profiles. These laboratory and field tests confirmed that autonomous collection and preservation is a feasible and useful approach for characterizing the expressed genes and environmental responses of marine microbial communities. 2012-02-28T20:55:48Z 2012-02-28T20:55:48Z 2011-06 2011-04 Article http://purl.org/eprint/type/JournalArticle 1751-7370 1751-7362 http://hdl.handle.net/1721.1/69247 Ottesen, Elizabeth A et al. “Metatranscriptomic Analysis of Autonomously Collected and Preserved Marine Bacterioplankton.” The ISME Journal 5.12 (2011): 1881–1895. en_US http://dx.doi.org/10.1038/ismej.2011.70 ISME Journal Creative Commons Attribution-Noncommercial-Share Alike 3.0 http://creativecommons.org/licenses/by-nc-sa/3.0/ application/pdf Nature Publishing Group Delong via Anne Graham |
| spellingShingle | Ottesen, Elizabeth Marin, Roman, III Preston, Christina M. Young, Curtis Robert, III Ryan, John P. Scholin, Christopher A. DeLong, Edward Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton |
| title | Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton |
| title_full | Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton |
| title_fullStr | Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton |
| title_full_unstemmed | Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton |
| title_short | Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton |
| title_sort | metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton |
| url | http://hdl.handle.net/1721.1/69247 |
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