[Coral-List] Help us solve a fish DNA mystery -- UPDATE

Luke Thompson - NOAA Affiliate luke.thompson at noaa.gov
Mon Sep 13 14:58:26 UTC 2021


Hi all,

We want to thank the many of you who provided feedback about our eDNA work
in Bear Cut. The response to our survey was overwhelming. We received over
20 survey responses and emails from experts like you willing to share their
knowledge about South Florida fishes.

Based on this expert feedback and our own research, 31 of the top 40 most
abundant fish sequences could be accounted for as native to South Florida
waters at the genus level or lowest assigned level. Regarding the
non-native sequences, including the abundant sequence assigned as
Oncorhynchus mykiss (rainbow trout), many respondents surmised that this
DNA could be coming from fish parts being dumped nearby, with several
mentioning the Miami Seaquarium. We subsequently confirmed with the curator
of the Seaquarium that, indeed, they nightly dump leftover parts of three
feed fishes: Oncorhynchus mykiss, Clupea harengus (herring), and members of
Osmeridae (capelins and smelts), which were among the most abundant
sequences observed. Two other non-native sequences, assigned to Ammodytes
spp. (sand lance), may derive from common bait fish in fishing activities
around Bear Cut.

Our paper describing these findings as part of an updated method for
extracting DNA from Sterivex filters is out today:
Anderson, S.R. and Thompson, L.R. Optimizing an enclosed bead beating
extraction method for microbial and fish environmental DNA. Environmental
DNA (2021) http://doi.org/10.1002/edn3.251.

We took a published method by Ushio for adding beads directly to the filter
chamber and adapted it for high-throughput extraction on a KingFisher Flex
bead handling robot. Two or three people can process 96 samples in an
8-hour work day. This beats opening the filters by hand and manually
removing the filter membrane! Different bead sizes were tested for physical
lysis on a Vortex-Genie. We found that using larger or differently sized
beads for Sterivex extractions detects the widest range of marine life,
with increased water volume (>2 L per filter) improving fish eDNA capture.
And yes, after finding several non-native fish (rainbow trout, herring,
smelt) in the eDNA at our Biscayne Bay sampling site, we discovered that
the Miami Seaquarium was feeding these exact fishes to their marine mammals
and dumping the guts each night. Mystery solved thanks to the process of
science and a community of scientists.

Luke & Sean

-- 
Luke R. Thompson, Ph.D.
Associate Research Professor
Northern Gulf Institute, Mississippi State University
Atlantic Oceanographic and Meteorological Laboratory (AOML)
National Oceanic and Atmospheric Administration (NOAA)
4301 Rickenbacker Cswy, Miami, FL 33149
o:305-361-4553 c:‭305-330-9626‬
https://www.aoml.noaa.gov/omics


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