eDNA Presentation at Ocean Sciences, 2016
Anni Djurhuus, post-doctoral research associate at USF in Mya Breibart's genomics lab, presented “Which animals are in the Zoo? Estimating the diversity of Florida Keys zooplankton using environmental DNA methods” based on her MBON research which compared three methods to assess zooplankton diversity: microscopy, amplicon sequencing of zooplankton tissue, and environmental DNA (eDNA).
eDNA team sequences mesopelagic fishes from the Davidson Seamount
In 2015, Andrew DeVogelaere, Research Director of the Monterey Bay National Marine Sanctuary and MBON eDNA collaborators at the Stanford Center for Ocean Solutions Jesse Port, Rebecca Martone, and Collin Closek successfully sequenced DNA extracted from mesopelagic fishes collected with a midwater trawl during a research cruise over the Davidson Seamount in Monterey Bay National Marine Sanctuary. The Genomics Team is comparing the DNA sequences from trawl-caught fish to water samples collected during the same cruise. The cruise was on the NOAA Ship Bell M. Shimada.
NOAA Funds New "eAUV" project for Environmental DNA
The "eAUV" project led by Kelly D. Goodwin and James Hendee at the National Oceanic and Atmospheric Administration-AOML & NOAA Southwest Fisheries Science Center was funded by NOAA 's Office of Ocean Exploration & Research, and other NOAA programs, under a larger FY16 NOAA/OAR 'omics initiative. This is a collaboration between NOAA-AOML (Goodwin), NOAA-SWFSC (Thompson), MBARI (Birch), and JCVI (Allen). The project is focused on testing an AUV equipped with an environmental sample processor (eAUV) in conjunction with a CalCOFI cruise track in North California.
The objectives of the overarching initiative include comparing sequence analysis for microbes and fish (16/18/12s) for samples derived from shipboard seawater filtration, eAUV sampling, and Bongo Net sampling in order to a) evaluate the suitability of the eAUV for NOAA needs; b) providing proof-of-concept testing for eDNA, and c) investigating the connection between lower food web and fisheries dynamics. The successful development and transition of eDNA techniques and eAUV technology would reduce sample processing time, ship time needs, and reliance on tissue sample collection. Understanding the connection between lower trophic levels and fisheries outcomes will improve the ability to monitor and predict ecosystem impacts resulting from stress and change.
phytoplankton, zooplankton, vertebrates). Methods for morphological zooplankton identification were completed in Feb 2015, which will enable comparison of zooplankton data between the Florida Keys and Monterey Bay sites.
To support consistent sample process and analysis, Stanford and MBARI established a bioinformatic pipeline, and USF and FWRI are testing parts of the system. This pipeline will provide a standardized data analysis framework for different gene markers used by the Sanctuaries MBON genomics teams.
The Stanford team is also comparing two library prep methods for Next Generation Sequencing data (NGS). The analysis will help to determine whether this step should become standardized in all three MBON projects, as they work in collaboration with the AMBON and SBC MBON genomics researchers.
Florida Keys Sampling Overview
The USF/FKNMS genomics team is collecting monthly samples in the Florida Keys near major coral reefs at the designated MBON stations. Samples are collected with help of the USF remote sensing group and scientists at the FKNMS during cruises on the R/V Walton Smith and on small boats.
The USF/FKNMS is collecting three samples from surface and bottom at each of the three key MBON stations - 18 samples per cruise. In 2015, the team collected 198 samples from the three MBON stations and an additional
To test if water volume is related to vertebrate eDNA concentration in offshore waters, the team collected and filtered 1-L, 10-L, and 100-L seawater samples at station M1 using tangential flow filtration (TFF). The researchers are comparing species richness and diversity across these volumes, and, to conventional vacuum filtration. Samples have been processed and the experiment may be repeated in another location.
286 samples from the surrounding ocean. The USF group has also collected samples for zooplankton morphological identifications, eDNA genomics, and for sequencing tissue of whole zooplankton communities. The goal is to ground-truth the eDNA method for zooplankton and move forward to eventually use only eDNA to assess zooplankton diversity and seasonal oscillations in the Florida keys.
Each of the three U.S. MBON projects are conducting intensive sampling campaigns. Collecting environmental DNA is one of the innovative sampling strategies being implemented to evaluate its role as a practical tool for monitoring biodiversity at multiple trophic levels.
The MBON teams developed standardized techniques for sea water sample collection, filtering, extraction and sequencing to ensure results can be compared across trophic levels, regions, and time. Each MBON Genomics team brings unique expertise and is exploring different approaches and issues. Read about the: Arctic MBON, Santa Barbara Channel MBON Program and the Sanctuaries MBON program below.
Monterey Bay Sampling Program Overview
The effort and expense associated with sample and data collections for long oceanographic time series are, in part, driving the development of autonomous platforms, sensors and sample collectors. MBARI is testing means to autonomously collect, preserve, and process discrete samples. The MBARI team has validated oceanographic samples collected by an autonomous underwater vehicle.
In fall 2015, samples were collected during the MBARI CANON cruise to assess the spatial distribution of vertebrate eDNA across nearshore and offshore locations (Figure 9). The six-month time-series at station M1 in Monterey Bay (6 cruises,10 depths sampled per cruise from 0-200 m) has yielded very low/absent amplification for 12S mt DNA (vertebrate eDNA). Stanford provided aliquots of this time-series to MBARI researchers who successfully amplified phytoplankton and zooplankton eDNA.
Article in Molecular Ecology -- Jesse Port, former postdoctoral researcher MBON collaborator at Stanford University, is the lead author of a new article in the journal Molecular Ecology. This study examines the utility of eDNA (as compared to SCUBA diver surveys) to assess biodiversity in a kelp forest in Monterey Bay.
Sanctuaries Genomics Team Overview
The Sanctuaries MBON Genomics team includes researchers at Stanford, Monterey Bay Aquarium Research Institute (MBARI), the University of South Florida (USF), and the Florida Fish and Wildlife Research Institute (FWRI). The Sanctuaries Genomic team is led by Francisco Chavez at MBARI and Mya Breitbart at USF. The MBARI research group has extensive expertise in methods development and instrumentation engineering. Breitbart’s lab uses molecular techniques to examine the diversity, distribution, and ecological roles of viruses and bacteria in a wide range of environments - including seawater, animals, plants, insects, zooplankton, coral reefs, and stromatolites.
The Sanctuaries Genomic team has developed standardized sample collection plans and methodologies for use in the Florida Keys and Monterey Bay National Marine Sanctuaries locations. The researchers are conducting tests to determine the most effective choices of filter type and DNA extraction method to capture eDNA from multiple trophic levels simultaneously (i.e. bacteria
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The U.S. MBON projects are funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803) in partnership between NOAA, BOEM, and NASA, with the U.S. Integrated Ocean Observing System (U.S. IOOS) program pioneering the implementation.