TY - JOUR
T1 - Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula
AU - Cowart, Dominique A.
AU - Murphy, Katherine R.
AU - Cheng, C. H.Christina
N1 - Funding Information:
We would like to thank the captain and crew of the R/V Laurence M. Gould, the staff at Palmer Station, Antarctica (USA), the Department of Animal Biology at the University of Illinois and the Roy J. Carver Biotechnology Center. We are sincerely thankful to the following people for their assistance in various aspects of this project: Julian Catchen, Arthur DeVries, Mateusz Grobelny, Elliot DeVries, Kevin Bilyk, Konrad Meister, Lauren Fields, Kai Zhao, Margaret Thairu, Allison Hansen, Patrick Degnan, Rebecca Fuller, Olivier Soubigou, and Huw Griffiths. We also extend our thanks to anonymous reviewers for comments that improved the manuscript. This research was supported by National Science Foundation Division of Polar Program award ANT1142158 to CHCC and a UIUC STEM postdoctoral fellowship to DAC. Any opinions, findings, conclusions or recommendations expressed in this article are those of the authors and do not necessarily reflect the views of the National Science Foundation.
Funding Information:
We would like to thank the captain and crew of the R/V Laurence M. Gould, the staff at Palmer Station, Antarctica (USA), the Department of Animal Biology at the University of Illinois and the Roy J. Carver Biotechnology Center. We are sincerely thankful to the following people for their assistance in various aspects of this project: Julian Catchen, Arthur DeVries, Mateusz Grobelny, Elliot DeVries, Kevin Bilyk, Konrad Meister, Lauren Fields, Kai Zhao, Margaret Thairu, Allison Hansen, Patrick Degnan, Rebecca Fuller, Olivier Soubigou, and Huw Griffiths. We also extend our thanks to anonymous reviewers for comments that improved the manuscript. This research was supported by National Science Foundation Division of Polar Program award ANT1142158 to CHCC and a UIUC STEM postdoctoral fellowship to DAC. Any opinions, findings, conclusions or recommendations expressed in this article are those of the authors and do not necessarily reflect the views of the National Science Foundation .
Publisher Copyright:
© 2017 The Authors
PY - 2018/2
Y1 - 2018/2
N2 - The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods. We collected water samples from four WAP shallow (≤ 300 m) shelf regions, recovered the eDNA therein, and performed metagenomic shotgun sequencing and analyses to determine the effectiveness of this method to assess marine benthic faunal diversity; this includes the detection of deep-water predatory king crabs whose potential shoreward expansion to warming shelves has sparked much concern. Using a customized bioinformatics pipeline, we identified abundant signatures of common benthic invertebrate fauna, endemic notothenioid fishes, as well as lithodid king crabs. We also uncovered species richness and diversity comparable to biological inventories compiled by the use of traditional survey methods, supporting the efficacy of the eDNA shotgun sequencing approach. As the rate of eDNA degradation affects faunal detection sensitivity, we also quantified mitochondrial ND2 gene copies in eDNA derived from a WAP icefish and found ND2 copies persisted to at least 20 days in the cold WAP water, much longer than values reported for temperate environments. We propose that eDNA metagenomic sequencing complements traditional sampling, and combining both will enable more inclusive biodiversity detection and faunal change monitoring in the vast Southern Ocean.
AB - The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods. We collected water samples from four WAP shallow (≤ 300 m) shelf regions, recovered the eDNA therein, and performed metagenomic shotgun sequencing and analyses to determine the effectiveness of this method to assess marine benthic faunal diversity; this includes the detection of deep-water predatory king crabs whose potential shoreward expansion to warming shelves has sparked much concern. Using a customized bioinformatics pipeline, we identified abundant signatures of common benthic invertebrate fauna, endemic notothenioid fishes, as well as lithodid king crabs. We also uncovered species richness and diversity comparable to biological inventories compiled by the use of traditional survey methods, supporting the efficacy of the eDNA shotgun sequencing approach. As the rate of eDNA degradation affects faunal detection sensitivity, we also quantified mitochondrial ND2 gene copies in eDNA derived from a WAP icefish and found ND2 copies persisted to at least 20 days in the cold WAP water, much longer than values reported for temperate environments. We propose that eDNA metagenomic sequencing complements traditional sampling, and combining both will enable more inclusive biodiversity detection and faunal change monitoring in the vast Southern Ocean.
KW - Antarctica
KW - Benthic invertebrates
KW - King crabs
KW - Metagenomics
KW - eDNA
UR - http://www.scopus.com/inward/record.url?scp=85042716041&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85042716041&partnerID=8YFLogxK
U2 - 10.1016/j.margen.2017.11.003
DO - 10.1016/j.margen.2017.11.003
M3 - Article
C2 - 29223543
AN - SCOPUS:85042716041
SN - 1874-7787
VL - 37
SP - 148
EP - 160
JO - Marine Genomics
JF - Marine Genomics
ER -