Journal
ISME JOURNAL
Volume 5, Issue 12, Pages 1881-1895Publisher
SPRINGERNATURE
DOI: 10.1038/ismej.2011.70
Keywords
metatranscriptomics; gene expression; automated sampling; marine bacterioplankton; RNA preservation; Monterey Bay
Categories
Funding
- Gordon and Betty Moore Foundation [ERG731]
- Office of Science
- US Department of Energy
- NSF Science and Technology Center [EF0424599]
- David and Lucille Packard Foundation
- Monterey Bay Aquarium Research Institute (MBARI)
- NSF [OCE-0314222]
- NASA Astrobiology [NNG06GB34G, NNX09AB78G]
- NASA [120409, NNX09AB78G] Funding Source: Federal RePORTER
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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. The ISME Journal (2011) 5, 1881-1895; doi: 10.1038/ismej.2011.70; published online 30 June 2011
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