scholarly journals Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies

2022 ◽  
Author(s):  
Annette F. Govindarajan ◽  
Luke McCartin ◽  
Allan Adams ◽  
Elizabeth Allan ◽  
Abhimanyu Belani ◽  
...  
Keyword(s):  
Large Volume ◽  
Small Volume ◽  
Deep Ocean ◽  
Environmental Dna ◽  
Marine Biodiversity ◽  
Robotic Vehicle ◽  
Seawater Samples ◽  
Biodiversity Changes ◽  
Collection Strategies

Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large-volume eDNA sampler with in situ filtration, capable of taking up to 12 samples per deployment. We conducted three deployments of our sampler on the robotic vehicle Mesobot in the Flower Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico and collected samples from 20 to 400 m depth. We compared the large volume (~40-60 liters) samples collected by Mesobot with small volume (~2 liters) samples collected using the conventional CTD-mounted Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which detects a broad range of invertebrate taxa, and found that while both methods detected biodiversity changes associated with depth, our large volume samples detected approximately 66% more taxa than the CTD small volume samples. We found that the fraction of the eDNA signal originating from metazoans relative to the total eDNA signal decreased with sampling depth, indicating that larger volume samples may be especially important for detecting metazoans in mesopelagic and deep ocean environments. We also noted substantial variability in biological replicates from both the large volume Mesobot and small volume CTD sample sets. Both of the sample sets also identified taxa that the other did not; although the number of unique taxa associated with the Mesobot samples was almost four times larger than those from the CTD samples. Large volume eDNA sampling with in situ filtration, particularly when coupled with robotic platforms, has great potential for marine biodiversity surveys, and we discuss practical methodological and sampling considerations for future applications.

scholarly journals Utilization of eDNA metabarcoding to assess coral reef health in Okinawa, Japan

2018 ◽  
Author(s):  
James D Reimer ◽  
Joseph DiBattista ◽  
Piera Biondi ◽  
Giovanni D Masucci ◽  
Michael Stat ◽  
...  
Keyword(s):  
Coral Reef ◽  
Environmental Dna ◽  
Global Scale ◽  
Coastal Development ◽  
Marine Biodiversity ◽  
Critical Data ◽  
Coral Reef Ecosystems ◽  
Reef Health ◽  
Seawater Samples ◽  
Over Exploitation

Environmental DNA (eDNA) metabarcoding has great potential in assessing comparative total biodiversity, and facilitating robust comparisons across a wide variety of sites and taxa. In particular, eDNA combined with next-generation sequencing can help address the huge critical data gaps in our understanding of marine biodiversity, especially in regions with high levels of understudied diversity such as the coral reefs of the Indo-Pacific region. Within this region, Okinawa is known for its high levels of marine biodiversity and endemicity, and also for the threats shallow coral reef ecosystems face from a variety of stressors including local-scale coastal development and over-exploitation to global scale threats such as climate change. In this study, we generated eDNA metabarcoding sequences from sediment and seawater samples from various reefs in Okinawa, Japan. At the same time, we developed a simple methodology to assess the relative health of these reefs based on anthropogenic and natural stressors. We discuss our eDNA results in comparison to coral reef health, identify potential bioindicator taxa, and explore the relative biodiversity of coral reef communities across sites. Our results indicate that taxa asides from the corals (Scleractinia) can provide robust information on coral reef health.

scholarly journals Utilization of eDNA metabarcoding to assess coral reef health in Okinawa, Japan

2018 ◽  
Author(s):  
James D Reimer ◽  
Joseph DiBattista ◽  
Piera Biondi ◽  
Giovanni D Masucci ◽  
Michael Stat ◽  
...  
Keyword(s):  
Coral Reef ◽  
Environmental Dna ◽  
Global Scale ◽  
Coastal Development ◽  
Marine Biodiversity ◽  
Critical Data ◽  
Coral Reef Ecosystems ◽  
Reef Health ◽  
Seawater Samples ◽  
Over Exploitation

Environmental DNA (eDNA) metabarcoding has great potential in assessing comparative total biodiversity, and facilitating robust comparisons across a wide variety of sites and taxa. In particular, eDNA combined with next-generation sequencing can help address the huge critical data gaps in our understanding of marine biodiversity, especially in regions with high levels of understudied diversity such as the coral reefs of the Indo-Pacific region. Within this region, Okinawa is known for its high levels of marine biodiversity and endemicity, and also for the threats shallow coral reef ecosystems face from a variety of stressors including local-scale coastal development and over-exploitation to global scale threats such as climate change. In this study, we generated eDNA metabarcoding sequences from sediment and seawater samples from various reefs in Okinawa, Japan. At the same time, we developed a simple methodology to assess the relative health of these reefs based on anthropogenic and natural stressors. We discuss our eDNA results in comparison to coral reef health, identify potential bioindicator taxa, and explore the relative biodiversity of coral reef communities across sites. Our results indicate that taxa asides from the corals (Scleractinia) can provide robust information on coral reef health.

scholarly journals Integrating Biodiversity and Environmental Observations in Support of National Marine Sanctuary and Large Marine Ecosystem Assessments

Oceanography ◽  
2021 ◽  
Vol 34 (2) ◽  
Author(s):  
Henry Ruhl ◽  
◽  
Jennifer Brown ◽  
Alexandra Harper ◽  
Elliot Hazen ◽  
...  
Keyword(s):  
Marine Ecosystem ◽  
Deep Ocean ◽  
Environmental Dna ◽  
Noise Pollution ◽  
Marine Biodiversity ◽  
Underwater Imaging ◽  
Science Data ◽  
Metadata Standards ◽  
Large Marine Ecosystem ◽  
Ocean Observing

Species and habitats are the subjects of legislation that mandates reporting of information on ecosystem conditions. Improvements in sensors, sampling platforms, information systems, and collaborations among experts and information users now enables more effective and up-to-date information to meet regional and national needs. Specifically, advances in environmental DNA (eDNA)-based assessments of biodiversity, community science data, various underwater imaging devices, and environmental, behavioral, and physiology observations from animal telemetry provide new opportunities to address multiple requirements for reporting status and trends, including insights into life in the deep ocean. Passive and active acoustic sensors help monitor marine life, boat traffic, and noise pollution. Satellites provide repeated, frequent, and long-term records of many relevant variables from global to local scales and, when combined with numerical computer simulations, allow planning for future scenarios. Metadata standards facilitate the transfer of data from machine to machine, thus streamlining assessments and forecasting and providing knowledge directly to the public. The Marine Biodiversity Observation Network (MBON) facilitates this exchange of information on life in the sea. The collaborative efforts of the Central and Northern California Ocean Observing System (CeNCOOS) of the US Integrated Ocean Observing System and its partners provide an example of a regional MBON process for information delivery. This includes linking policy and management needs, prioritizing observing data from various platforms and methods, streamlining data handling practices, and delivery of information for management such as for the Monterey Bay National Marine Sanctuary and the California Current Large Marine Ecosystem, with iterative process adaptation.

scholarly journals Autonomous in situ sampling and analysis of eDNA using an Environmental Sample Processor (ESP)

2021 ◽  
Vol 4 ◽  
Author(s):  
Magnus Jacobsen
Keyword(s):  
Environmental Sample ◽  
Sea Water ◽  
Detection System ◽  
Environmental Dna ◽  
Temporal Analysis ◽  
Marine Biodiversity ◽  
Biological Communities ◽  
Interesting Candidate ◽  
Good Proxy

Monitoring of marine offshore biodiversity is expensive and has traditionally relied on invasive techniques like net fishing or direct observations that can only be conducted in calm seas by experts. Analysis of environmental DNA (eDNA) is a non-invasive method and can easily be collected from sea water by water filtration followed by DNA extraction. Due to the fast degradation time in sea water it is considered a good proxy for present living biodiversity. It allows direct identification of species based on their unique DNA sequence and is cheaper compared to traditional methods, which often are carried out from dedicated fishing or research vessels. However, while eDNA collection may reduce operational cost of offshore sampling, it still relies on boat time. Thus, traditional eDNA sampling still presents substantial costs for offshore biodiversity monitoring. This may reduce the number of samples that can be collected and analysed, limiting the sampling to single ‘time shots’, which may not give an adequate picture of the present biodiversity. The 2nd generation Environmental Sample Processor (2G-ESP) is an autonomous sampler/analyser of eDNA. It can collect, extract and analyse eDNA samples in situ using quantitative PCR (qPCR) or store filters for subsequent laboratory analysis after deployment. The instrument can be deployed directly on the seabed or in pelagic configuration where it can operate for several months depending on power supply and power consumption, while it is controlled by, and sends back results to scientists on land. These unique features make the 2G-ESP an interesting candidate for offshore monitoring of marine biodiversity, as well as a potential early warning/detection system e.g. for invasive species. Moreover, the possibility to preserve filters aboard makes it possible to investigate temporal changes of full biological communities by applying metabarcoding techniques on the collected samples. Here we present the major results of three years of work testing the potential use of a second generation Environmental Sample Processor (2G-ESP) for marine monitoring. These include both practical and analytical issues that we have encountered along the way, as well as results on target species detection and temporal analysis using qPCR and metabarcoding methods.

scholarly journals An Improved Algorithm for Measuring Nitrate Concentrations in Seawater Based on Deep-Ultraviolet Spectrophotometry: A Case Study of the Aoshan Bay Seawater and Western Pacific Seawater

Sensors ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 965
Author(s):  
Xingyue Zhu ◽  
Kaixiong Yu ◽  
Xiaofan Zhu ◽  
Juan Su ◽  
Chi Wu
Keyword(s):  
Weighted Average ◽  
Measuring Method ◽  
Western Pacific ◽  
Nitrate Concentrations ◽  
Deep Ultraviolet ◽  
Ultraviolet Spectrometer ◽  
Seawater Samples ◽  
Reflection Probe

Nowadays, it is still a challenge for commercial nitrate sensors to meet the requirement of high accuracy in a complex water. Based on deep-ultraviolet spectral analysis and a regression algorithm, a different measuring method for obtaining the concentration of nitrate in seawater is proposed in this paper. The system consists of a deuterium lamp, an optical fiber splitter module, a reflection probe, temperature and salinity sensors, and a deep-ultraviolet spectrometer. The regression model based on weighted average kernel partial least squares (WA-KPLS) algorithm together with corrections for temperature and salinity (TSC) is established. After that, the seawater samples from Western Pacific and Aoshan Bay in Qingdao, China with the addition of various nitrate concentrations are studied to verify the reliability and accuracy of the method. The results show that the TSC-WA-KPLS algorithm shows the best results when compared against the multiple linear regression (MLR) and ISUS (in situ ultraviolet spectrophotometer) algorithms in the temperatures range of 4–25 °C, with RMSEP of 0.67 µmol/L for Aoshan Bay seawater and 1.08 µmol/L for Western Pacific seawater. The method proposed in this paper is suitable for measuring the nitrate concentration in seawater with higher accuracy, which could find application in the development of in-situ and real-time nitrate sensors.

scholarly journals Biodiversity of echinoids and their epibionts around the Scotia Arc, Antarctica

2008 ◽  
Vol 20 (3) ◽  
pp. 227-244 ◽  
Author(s):  
Katrin Linse ◽  
Lisa J. Walker ◽  
David K.A. Barnes
Keyword(s):  
Southern Ocean ◽  
Current Knowledge ◽  
Sea Urchins ◽  
Marine Biodiversity ◽  
Current View ◽  
Depth Range ◽  
Tissue Mass ◽  
Scotia Arc ◽  
Biodiversity Changes ◽  
Study Species

AbstractThe Scotia Arc, linking the Magellan region with the Antarctic Peninsula, comprises young and old islands both near continents and isolated, and is the only semi-continuous link between cool temperate and Antarctic environments. It is an ideal region for studies on how marine biodiversity changes across an extended transition zone. Echinoids (sea urchins) and their associated epibionts were found across depths from 91–1045 m, with 19 species from shelf and four from slope depths. The 23 species from 38 trawls represent 31% of all echinoid species known from the Southern Ocean and 38% of the shelf/upper slope echinoids. The specimens collected comprise representatives of the five families Cidaridae, Echinidae, Temnopleuridae, Schizasteridae and Pourtalesiidae. Echinoids are probably a good model for how well we know Antarctic shelf and slope megabenthos; none of the species we report are new to science but we found nine (39%) of our study species present at new localities, some thousands of kilometres from previous findings. New biogeographic ranges are illustrated forCtenocidaris gigantea,C. nutrix,C. spinosa,Abatus curvidens,A. ingens,A. shackletoni,Amphineustes rostratus,Tripylaster philippiandPourtalesia aurorae. Southern Ocean echinoids show eurybathy as the mean depth range of our study species was 1241 m and only one was at less than 500 m. The current view of echinoid dominance of super-abundance in the shallows seems to be not transferable to shelf and slope depths as only one of 38 trawls was dominated by echinoids. Current knowledge on maximum sizes in Antarctic echinoids seems to be good as our morphometric measurements were mainly within known size ranges. Regular echinoids increased predictably in mass with increasing test length, apart fromCtenocidaris spinosa. Tissue mass of cidaroid species was ~17%, but across irregular species varied from 17.7–8.9%. No epibionts were found on irregular echinoids or Echinidae but 70 cidaroids examined carried 51 species representing ten classes. Many of these species are reported as cidaroid epibionts for the first time. Cidaroids and their epibionts constituted > 38% of the total macrofaunal richness in the trawls they were present in. Echinoids and their epibionts clearly contribute significantly to Southern Ocean biodiversity but are minor components of biomass except in the shallows.

An SiOx anode strengthened by the self-catalytic growth of carbon nanotubes

Nanoscale ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 3808-3816
Author(s):  
Hongjin Xue ◽  
Yong Cheng ◽  
Qianqian Gu ◽  
Zhaomin Wang ◽  
Yabin Shen ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Volume Change ◽  
Large Volume ◽  
The Self ◽  
Catalytic Growth ◽  
Large Volume Change

A close-knit CNTs coating that in-situ grown on the SiOx particles realizes the “soft-combination” between SiOx and CNTs, thus conquering the long-lasting issues of poor conductivity and large volume change of SiOx faced.

Sign in / Sign up

Export Citation Format

Share Document