Near real‐time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA‐targeted DNA probes

Preston, Christina M.; Marin, Roman; Jensen, Scott; Feldman, Jason; Birch, James M.; Massion, Eugene; DeLong, Edward F.; Suzuki, Marcelino T.; Wheeler, Kevin R.; Scholin, Christopher A.

doi:10.1111/j.1462-2920.2009.01848.x

Cited by 60 publications

(61 citation statements)

References 46 publications

(55 reference statements)

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“…qPCR tests using surface seawater from the Coastal Data Information Program (CDIP) Station 156 in Monterey Bay and from Monterey Bay Wharf verified that quantification by all primer sets was comparable between the ESP module and a bench-top assay. A more detailed description of ESP procedures can be found elsewhere (Preston et al, 2009.…”

Section: Pre-deployment Testingmentioning

confidence: 99%

Single-taxon field measurements of bacterial gene regulation controlling DMSP fate

et al. 2015

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The 'bacterial switch' is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate (DMSP) to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere. Yet which ecological or physiological factors might control the bacterial switch remains a topic of considerable debate. Here we report the first field observations of dynamic changes in expression of DMSP pathway genes by a single marine bacterial species in its natural environment. Detection of taxon-specific gene expression in Roseobacter species HTCC2255 during a month-long deployment of an autonomous ocean sensor in Monterey Bay, CA captured in situ regulation of the first gene in each DMSP pathway (dddP and dmdA) that corresponded with shifts in the taxonomy of the phytoplankton community. Expression of the demethylation pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the cleavage pathway was greater in the presence of a mixed diatom and dinoflagellate community. These field data fit the prevailing hypothesis for bacterial DMSP gene regulation based on bacterial sulfur demand, but also suggest a modification involving oxidative stress response, evidenced as upregulation of catalase via katG, when DMSP is demethylated.

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Section: Pre-deployment Testingmentioning

confidence: 99%

Single-taxon field measurements of bacterial gene regulation controlling DMSP fate

et al. 2015

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“…Additionally, our study used a 5 mm prefilter during sample collection, while the array experiments used a 1.6 mm prefilter, which may change the representation of larger and/or particle-attached bacterial cells. Polaribacter-like sequences were identified in 16S rRNA libraries prepared from samples collected at station M0 in SeptemberOctober 2004, during development of their sandwich hybridization assay (Preston et al, 2009). …”

Section: Metatranscriptomic Analysis Of Montereymentioning

confidence: 99%

“…The ESP is an automated fluid handling system that collects and processes biological samples from seawater (Scholin et al, 2009). Current real-time capabilities include array-based detection of target organisms including harmful algal species (Greenfield et al, 2006(Greenfield et al, , 2008Haywood et al, 2007), invertebrate larvae (Goffredi et al, 2006;Jones et al, 2008) and major bacterial and archaeal clades (Preston et al, 2009). Quantitative PCR capabilities are also currently in development (Scholin et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton

et al. 2011

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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 undersampled 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.

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“…The SHA chemistry has been coupled with an in situ instrument, the Environmental Sample Processor (ESP), for autonomous environmental monitoring for a range of larval species simultaneously ). The SHA chemistry and the ESP have also been used to remotely detect marine bacterioplankton, dinoflagellates and invertebrates (Greenfield et al 2008;Preston et al 2009;Scholin et al 2009). …”

Section: Introductionmentioning

confidence: 99%

Application of a sandwich hybridisation assay for rapid detection of the Northern Pacific seastar, Asterias amurensis

Smith

Rhodes

Adamson

et al. 2011

New Zealand Journal of Marine and Freshwater Research

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A sandwich hybridisation assay (SHA) has been developed to detect Asterias amurensis (Lu¨tken 1871), commonly known as the northern Pacific seastar, which is an unwanted, and as yet undetected, pest in New Zealand waters. Probes in SHA format have been developed that target the ribosomal RNA internal transcribed spacer region of A. amurensis. The successful assay utilises the capture probe ITS-C2-110 and the combined signal probes ITS-S1-93 and ITS-S3-240. It has been successfully tested for specificity, including cross-reactivity testing against the common and related seastars, Patiriella regularis (Verrill 1867), P. mortenseni (O'Loughlin et al. 2002), Coscinasterias muricata (Verrill 1867) and Stichaster australis (Verrill 1871). The SHA is a rapid and potentially portable RNA-based test, and opens up the opportunity for direct analysis of water samples, for example, portside during surveillance of marine pests.

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Near real‐time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA‐targeted DNA probes

Cited by 60 publications

References 46 publications

Single-taxon field measurements of bacterial gene regulation controlling DMSP fate

Single-taxon field measurements of bacterial gene regulation controlling DMSP fate

Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton

Application of a sandwich hybridisation assay for rapid detection of the Northern Pacific seastar, Asterias amurensis

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