Abstract
The ocean is a soup of its resident species' genetic material, cast off in the forms of metabolic waste, shed skin cells, or damaged tissue. Sampling this environmental DNA (eDNA) is a potentially powerful means of assessing whole biological communities, a significant advance over the manual methods of environmental sampling that have historically dominated marine ecology and related fields. Here, we estimate the vertebrate fauna in a 4.5-million-liter mesocosm aquarium tank at the Monterey Bay Aquarium of known species composition by sequencing the eDNA from its constituent seawater. We find that it is generally possible to detect mitochondrial DNA of bony fishes sufficient to identify organisms to taxonomic family- or genus-level using a 106 bp fragment of the 12S ribosomal gene. Within bony fishes, we observe a low false-negative detection rate, although we did not detect the cartilaginous fishes or sea turtles present with this fragment. We find that the rank abundance of recovered eDNA sequences correlates with the abundance of corresponding species' biomass in the mesocosm, but the data in hand do not allow us to develop a quantitative relationship between biomass and eDNA abundance. Finally, we find a low false-positive rate for detection of exogenous eDNA, and we were able to diagnose non-native species' tissue in the food used to maintain the mesocosm, underscoring the sensitivity of eDNA as a technique for community-level ecological surveys. We conclude that eDNA has substantial potential to become a core tool for environmental monitoring, but that a variety of challenges remain before reliable quantitative assessments of ecological communities in the field become possible.
Highlights
A key component of understanding marine ecosystems, and of implementing science-based policy in those ecosystems, is the development of comprehensive environmental monitoring programs
We find a taxonomic bias towards bony fishes, and that within amplified bony fish species, rank DNA sequence abundance correlates with rank biomass abundance, suggesting that concentration of environmental DNA (eDNA) is in part a function of species’ abundance
Mixing model We developed a mixing model to estimate the contributions of four different sources of DNA in the sampled aquarium tank: intake water, two different commercial feed sources and endogenously generated DNA shed by the species in the tank itself
Summary
A key component of understanding marine ecosystems, and of implementing science-based policy in those ecosystems, is the development of comprehensive environmental monitoring programs. Examples of current marine monitoring programs along the west coast of the United States include the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO; an academic collaboration), California Cooperative Oceanic Fisheries Investigations (CalCOFI; a public-private partnership), the nonprofit Reef Check, and programs affiliated with NOAA Fisheries (a federal agency), among others. These provide data on species diversity and community composition using visual surveys, trawls, seines and tissue biopsies. More cost-effective, and more sensitive methods are desirable for ecosystem assessments as well as for improving baseline ecological knowledge about marine ecosystems
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