Abstract
Abstract. The OceanSensors08 workshop held 31 March–4 April 2008 in Warnemünde, Germany, brought together an international group of marine scientists, sensor developers and technologists with a common interest in shaping the future of ocean sensing. In preparation for that meeting a series of review papers was commissioned, one of which was meant to cover Sensors for Ocean-omics. The "ocean-omics" topic was cast very broadly. The notion was to review use of genetic techniques for assessing presence and diversity of organisms, their genomic capacity and gene expression, and to provide a prospectus of how such methods could be applied in an autonomous capacity. I chose "ecogenomic sensor" as a descriptor to convey the essence of such a system – a device that integrates genetic level sensing with larger scale environmental characterization. This phrase is derived from workshops refining the US's Ocean Observatories Initiative (OOI) and visions for instrument systems that could be deployed on such a network. But what exactly are ecogenomic sensors? A clear definition is lacking and conceptualizations far outweigh actual hardware that can be deployed in the ocean. This prospectus builds from that point. I advance a definition of "ecogenomic sensor" and outline the opportunities and challenges associated with developing such instruments. Suggestions as to how this technology may be further refined and applied are offered against the backdrop of the Autonomous Microbial Genosensor (AMG) and Environmental Sample Processor (ESP). Applications that center on detection of DNA and RNA are emphasized. The word "review" appears in the title at the request of the editors.
Highlights
An internet search using the phrase “ecogenomic sensor” will return numerous references that speak broadly to the idea of detecting molecular markers indicative of specific organisms, genes or other biomarkers within an environmental context
I am aware of only two examples where the steps of sample collection and molecular analytical analyses are integrated into an ocean-deployable instrument: the Autonomous Microbial Genosensor (AMG) and Environmental Sample Processor (ESP) (Paul et al, 2007)
Development of ecogenomic sensors remains a ripe area for future investigation from science, policy and systems engineering standpoints
Summary
An internet search using the phrase “ecogenomic sensor” will return numerous references that speak broadly to the idea of detecting molecular markers indicative of specific organisms, genes or other biomarkers within an environmental context. It is a class of instrument that employs wet chemistry molecular analytical techniques to assess the presence and abundance of specified set of organisms, their genes and/or metabolites in near real-time. For the purposes of the OceanSensors workshop, the premise was to consider development of a device that would sense molecular signatures that are already known, defined sequences of DNA or RNA. This restricted view of an ecogenomic sensor was emphasized since prototypes of such instruments already exist and so provide a valuable benchmark for assessing the challenges of engineering and operating such “basic”, deployable systems. The image captures the requirement to embed such sensors within a broad ocean observatory framework
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