Subsurface automated samplers for eDNA (SASe) for biological monitoring and research

Formel, Nathan; Enochs, Ian C.; Sinigalliano, Christopher D.; Anderson, Sean R.; Thompson, Luke R.

doi:10.1016/j.ohx.2021.e00239

Cited by 22 publications

(14 citation statements)

References 19 publications

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“…over water tanks, river streams, green houses, aviaries and fields). This would allow to scale at the community level the existing automated single species monitoring, such as those existing for ants and fish in the laboratory (Cao et al, 2020;Lopez-Marcano et al, 2021), and directly in the field (Francisco et al, 2020;Imirzian et al, 2019), by adding a species classification layer to these automated frameworks. Furthermore, such larger-scale systems would allow the use of multiple cameras without the need to mount them on a microscope and robot, reducing the cost of the recording part of the monitoring system while allowing to record of multiple landscapes simultaneously.…”

Section: Com Bi N I Ng T Ec H Nologi E S To F U L Ly Au Tom At E T H ...mentioning

confidence: 99%

“…sample filtration, DNA extraction, purification, amplification, sequencing and sequence blasting and alignment) that were not suitable for automated remote monitoring of ecological communities. However, recent developments in miniaturised microfluidic technologies that automate the sampling and processing of eDNA samples (Dhar & Lee, 2018 ; Formel et al, 2021 ), and the advent of autonomous vehicles to carry such devices (Yamahara et al, 2019 ) have enabled the conception of environmental sample processors (ESPs) that can perform all these steps from sampling to DNA amplification and sample storage without human intervention (Hansen et al, 2020 ; Jacobsen, 2021 ) (Figure 2 ). While ESPs do not automate post‐sampling procedures such as DNA sequencing, equipping these devices with modules composed of portable nanopore sequencing devices such as the MinION and SmidgION (Ames et al, 2021 ; Jain et al, 2016 ) could allow them to achieve fully automated status in the future (Huo et al, 2021 ).…”

Section: From Automated Data Collection To Ecological Knowledgementioning

confidence: 99%

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Towards the fully automated monitoring of ecological communities

et al. 2022

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Ecosystems are increasingly exposed to stressors, leading to unprecedented rates of biodiversity decline globally (Capdevila et al., 2022;Díaz et al., 2019). Our ability to reliably forecast ecosystems dynamics is limited by our capacity to understand what governs their composition, dynamics, function and structure (Dietze et al., 2018;Petchey et al., 2015). To drive predictive ecology forward and design appropriate conservation strategies, we therefore need access to long-term, highresolution and standardised information about ecosystems' abiotic and biotic components (Farley et al., 2018;

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Section: Com Bi N I Ng T Ec H Nologi E S To F U L Ly Au Tom At E T H ...mentioning

confidence: 99%

Section: From Automated Data Collection To Ecological Knowledgementioning

confidence: 99%

Towards the fully automated monitoring of ecological communities

et al. 2022

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“…These efforts to monitor wild corals' responses to environmental variability are extremely useful, especially to characterize 'normal' behavior and common responses to multiple stressors but are also time consuming in terms of experimentation and field monitoring, validating the findings, and downstream analysis. Recently, the method of eDNA monitoring has developed into a potentially useful way of monitoring biodiversity (Leray and Knowlton, 2015;Formel et al, 2021). eDNA is a metabarcoding method to detect and quantify multiple types of DNA from environmental samples including water samples (Beng and Corlett, 2020).…”

Section: Ecological Approaches: Monitoring and 'Omicsmentioning

confidence: 99%

Advances in coral immunity ‘omics in response to disease outbreaks

et al. 2022

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Coral disease has progressively become one of the most pressing issues affecting coral reef survival. In the last 50 years, several reefs throughout the Caribbean have been severely impacted by increased frequency and intensity of disease outbreaks leading to coral death. A recent example of this is stony coral tissue loss disease which has quickly spread throughout the Caribbean, devastating coral reef ecosystems. Emerging from these disease outbreaks has been a coordinated research response that often integrates ‘omics techniques to better understand the coral immune system. ‘Omics techniques encompass a wide range of technologies used to identify large scale gene, DNA, metabolite, and protein expression. In this review, we discuss what is known about coral immunity and coral disease from an ‘omics perspective. We reflect on the development of biomarkers and discuss ways in which coral disease experiments to test immunity can be improved. Lastly, we consider how existing data can be better leveraged to combat future coral disease outbreaks.

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“…will likely be the future [65]. Ideally, devices should store DNA until it is collected, but a further advancement in the future would be the development of devices able detect strains, sequence samples, upload sequence data for remote biomonitoring and artificial assisted (AI) analyses [66].…”

Section: Box 3: Investigating Microbial Evolution Using Omics and Tem...mentioning

confidence: 99%