Here you will be able to find resources used by the MBARI BOG group for our Environmental DNA (eDNA) work.

Monitoring ocean biodiversity is key in understanding how the marine environment is shifting in response to external influences like climate change. Traditional ocean monitoring techniques involving research cruises, visual surveys, or trawls can be very time consuming and expensive. Using environmental DNA (eDNA) collected from the water column to assess marine biodiversity is a relatively new technology that is rapidly becoming more sophisticated and widely available. eDNA allows for a non-invasive approach to monitor the biodiversity of marine environments and is capable of detecting taxa across all trophic levels (bacteria to whales), lending novel insights into marine food webs, species ranges, and community compositions.

Artist rendering of using environmental DNA and autonomous vehicles to observe life in the sea.

eDNA is genetic material that is found in the environment and can be found in many forms including skin and scales, tissue, metabolic waste, and free floating DNA. As eDNA is relatively short lived (days to a week or two) it can capture a ‘snapshot’ of what organisms are living in the sampled environment. We are able to sample water from many different marine environments ranging from kelp forest systems to deep-water benthic habitats then filter the water to capture the eDNA on a small disk filter. By utilizing molecular techniques, we are then able to isolate the eDNA from the filter and amplify the DNA of desired taxa groups through polymerase chain reactions (PCR), targeting different taxa groups based on the gene regions selected to amplify. After amplification, we sequence the DNA using Next Generation Sequencing to determine the order of the nucleotide which in turn is used to identify which taxa the DNA derived from. The use of eDNA for biomonitoring is powerful and with it we are able to detect shifts in population structure across both time and space.

Figure 2: Marine eDNA suspended in seawater may contain living cells, metabolic waste, parts of organisms, or dissolved material. As part of the Marine Biodiversity Observation Network (MBON) projects, quantitative polymerase chain reaction (qPCR) and metabarcoding have been combined with so-called next generation sequencing to determine biodiversity. On the right are the primers used by the project with a representation of the range of organisms they detect. The eDNA droplet was designed and illustrated by Kevan Yamahara.

Environmental DNA Technology

The field of eDNA has grown exponentially over the past few years. With support from NASA/NOAA (MBON) we have developed a growing number of eDNA capabilities at MBARI. These include the laboratory techniques, Illumina sequencing, MinIon sequencing and data processing capabilities for both types of eDNA sequencers. These new technologies are now being routinely used as part of environmental monitoring at MBARI and strengthen MBARI collaborations with NOAA Fisheries, MBNMS, PISCO, UCSC, USGS, and Instituto del MAR del Perú.

Towards sequencing in situ.  The ability of integrating the long-range autonomous underwater vehicle (LRAUV) with the environmental sample processor (ESP) to collect eDNA samples provides a valuable platform for autonomous collection and we have been continuing to ground truth and expand this capability at MBARI. Our team works to integrate near real-time eDNA sequencing onboard MBARI research cruises and to ultimately automate the entire workflow so the technology can be embedded onboard the LRAUV-ESP.

A map of eDNA samples we have taken (not comprehensive, but provides an example of where some of our sampling locations are).

HiPP (Hig

h Performance Processing) – Our team is developing a GPU based bioinformatics workflow for processing DNA sequence data in near-real time onboard research cruises with the goal of transferring this technology for use onboard a LRAUV. GPU processing is being used to accelerate DNA basecalling, DNA read assignment, DNA mapping, and taxonomic analysis.

These developments have the potential to dramatically increase the frequency of data collection, help increase the scale of eDNA sampling, provide biodiversity data from locations that are not easily accessible by ship, and provide species taxonomy data that can be used for real-time decision making, while at sea or on shore.

We can also use metabarcoding of mixed tissue samples to recover patterns in biogeography. Here we saw a strong break in zooplankton community composition at Punta Eugenia across both krill (Euphausiid) and copepod groups.

Citation: Pitz KJ, Guo J, Johnson SB, Campbell TL, Zhang H, Vrijenhoek RC, Chavez FP, Geller J. Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding. Plos one. 2020 Jun 25;15(6):e0235159.



Chavez, F.P., M. Min, K. Pitz, N. Truelove, J. Baker, D. LaScala-Grunewald, M. Blum, K. Walz, C. Nye, A. Djurhuus, R.J. Miller, K.D. Goodwin, F.E. Muller-Karger, H.A. Ruhl, and C.A. Scholin. 2021. Observing life in the sea using environmental DNA. Oceanography, 34: 102–119.

Lamy, T., K.J. Pitz, F.P. Chavez, C.E. York, and R.J. Miller. 2021. Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities. Scientific Reports, 11: 1–13.

Djurhuus, A., C.J. Closek, R.P. Kelly, K.J. Pitz, R.P. Michisaki, H.A. Starks, K.R. Walz, E.A. Andruszkiewicz, E. Olesin, K.A. Hubbard, E. Montes, D. Otis, F.E. Muller-Karger, F.P. Chavez, A.B. Boehm, and M. Breitbart. 2020. Environmental DNA reveals seasonal shifts and potential interactions in a marine community. Nature Communications, 11: 1–9.

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