Probing the living ocean with ecogenomic sensors

Abstract

This review discusses the role of ecogenomic sensors in biological oceanography. Ecogenomic sensors are instruments that can autonomously collect biological samples and perform molecular analyses. This technology reduces logistical constraints on the length and duration of biological data collection. Autonomous, robotic performance of molecular assays shows particular promise in the field of public health. Recent applications include simultaneous detection of harmful algal species and fecal markers paired with same-day remote reporting of test results. Ecogenomic instruments are also showing promise for molecular ecological studies. Autonomous collection and preservation of biological samples is facilitating high-resolution ecological studies that are expanding our understanding of marine microbial ecology and dynamics. This review discusses recent applications of these instruments and makes recommendations for future developments.

The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

“…The so-called ecogenomic sensors are instruments for DNA analysis that can be deployed outside the laboratory, providing the entire sample-to-result process without human interaction. They autonomously collect and store water samples and perform (near) real-time molecular analysis using qPCR and other molecular detection technologies (Ottesen, 2016;Scholin, 2009). The "environmental sample processor" (ESP) platform has already shown practical application and significant progress for monitoring a wide array of microorganisms (Ottesen et al, 2014;Robidart et al, 2014;Saito, Bulygin, Moran, Taylor, & Scholin, 2011) and zooplankton (Harvey et al, 2012), from diverse environments ranging from coastal to deep sea applications (Harvey et al, 2012;Ussler et al, 2013).…”

“…The "environmental sample processor" (ESP) platform has already shown practical application and significant progress for monitoring a wide array of microorganisms (Ottesen et al, 2014;Robidart et al, 2014;Saito, Bulygin, Moran, Taylor, & Scholin, 2011) and zooplankton (Harvey et al, 2012), from diverse environments ranging from coastal to deep sea applications (Harvey et al, 2012;Ussler et al, 2013). The ESP can be set to monitor either a specified geographical location, for example moored to a dockside or buoy, or be mobile, for example free drifting or carried onboard vessels to perform autonomous sampling and analysis (Ottesen, 2016). Even automated self-propelling ecogenomic sensors are currently under development (Pargett et al, 2015).…”

Considerations in Harmful Algal Bloom Research and Monitoring: Perspectives From a Consensus-Building Workshop and Technology Testing

“…Most of the technologies listed in Table 1 are discussed in greater detail in subsequent sections. Readers are directed toward additional reviews which provide a more detailed treatment of many of the technologies that are not discussed in detail (e.g., Ottesen, 2016;Doucette and Kudela, 2017;Glibert et al, 2018) and/or which focus more on classical methods for cell and/or toxin detection (e.g., Frolov et al, 2013;Trainer and Hardy, 2015;Zhang and Zhang, 2015;Otten and Paerl, 2016;Reguera et al, 2016; Association of Public Health Laboratories [APHL], 2017; Medlin and Orozco, 2017;Doucette et al, 2018;Glibert et al, 2018).…”

New High-Tech Flexible Networks for the Monitoring of Deep-Sea Ecosystems

“…92,93 Recent technical improvements concern the development of "eco-genomic" sensors capable of autonomously collect biological samples and perform molecular analyses. 94 These sensors allow the characterization of marine community composition as a whole, regardless of the faunal size classes involved. 95 One example is the environmental sample processor (ESP 96 ), designed to autonomously collect discrete water samples, concentrate microorganisms, and automate the application of molecular probe technologies.…”