Remote Detection of Marine Microbes, Small Invertebrates, Harmful Algae, and Biotoxins using the Environmental Sample Processor (ESP)

Scholin, Christopher A.; Doucette, Gregory J.; Jensen, Scott; Roman, Brent; Pargett, Douglas; Marin, Roman; Preston, Christina M.; Jones, W. Monty; Feldman, Jason; Everlove, Cheri; Harris, Adeline; Alvarado, Nilo; Massion, Eugene; Birch, James M.; Greenfield, Dianne I.; Wheeler, Kevin; Vrijenhoek, Robert C.; Mikulski, Christina M.; Jones, Kelly L.

doi:10.5670/oceanog.2009.46

Cited by 140 publications

(74 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Only methods for ESP sample archival are presented here; for a full description of ESP operation, see Scholin et al (2009) and Roman et al (2007). Samples archived by the ESP for metatranscriptomic analysis were collected in titanium sample 'pucks' (filter holders) containing the following 25 mm diameter filters stacked from top to bottom: a 5 mm Durapore prefilter (Millipore, Billerica, MA, USA), a 0.22 mm Durapore sample filter, 0.45 mm Metricell backing filter (Pall Gelman Corporation, Port Washington, NY, USA) and a 10 mm sintered frit (Chand Eisenmann Metallurgical, Burlington, CT, USA); see Greenfield et al (2006) for details.…”

Section: Esp Operation For Sample Archivalmentioning

confidence: 99%

“…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). The ESP can return samples preserved in a saline-ethanol solution, but sample analysis has been primarily limited to in situ hybridization techniques (Goffredi et al, 2006;Greenfield et al, 2006Greenfield et al, , 2008Jones et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…Together with the ESP platform (Scholin et al, 2009), these protocols enable the autonomous collection of samples and their return to the laboratory for transcriptional analysis. As the ESP also incorporates standard oceanographic instrumentation and the ability to transmit collected data and receive remote commands, environmental context monitoring and event response are also possible.…”

Section: Introductionmentioning

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).…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton

et al. 2011

View full text Add to dashboard Cite

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.

show abstract

Section: Esp Operation For Sample Archivalmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton

et al. 2011

View full text Add to dashboard Cite

show abstract

“…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

View full text Add to dashboard Cite

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.

show abstract

Detection and Surveillance of Harmful Algal Bloom Species and Toxins

Doucette

Medlin

McCarron

et al. 2018

Harmful Algal Blooms

View full text Add to dashboard Cite

Remote Detection of Marine Microbes, Small Invertebrates, Harmful Algae, and Biotoxins using the Environmental Sample Processor (ESP)

Cited by 140 publications

References 10 publications

Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton

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

Detection and Surveillance of Harmful Algal Bloom Species and Toxins

Contact Info

Product

Resources

About