From Sea Surface to Seafloor: A Benthic Allochthonous eDNA Survey for the Abyssal Ocean
Environmental DNA (eDNA) metabarcoding could facilitate rapid and comprehensive biotic surveys in the deep ocean, yet many aspects of the sources and distribution of eDNA in the deep sea are still poorly understood. In order to examine the influence of the water column on benthic eDNA surveys in reg...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2020-09-01
|
| Series: | Frontiers in Marine Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fmars.2020.00682/full |
| _version_ | 1819060002845884416 |
|---|---|
| author | Olivier Laroche Olivier Laroche Oliver Kersten Craig R. Smith Erica Goetze |
| author_facet | Olivier Laroche Olivier Laroche Oliver Kersten Craig R. Smith Erica Goetze |
| author_sort | Olivier Laroche |
| collection | DOAJ |
| description | Environmental DNA (eDNA) metabarcoding could facilitate rapid and comprehensive biotic surveys in the deep ocean, yet many aspects of the sources and distribution of eDNA in the deep sea are still poorly understood. In order to examine the influence of the water column on benthic eDNA surveys in regions targeted for deep-sea polymetallic nodule mining, we investigated the occurrence of pelagic eDNA across: (1) two different deep-sea habitat types, abyssal plains and seamounts, (2) benthic sample types, including nodules, sediment, and seawater within the benthic boundary layer (BBL), and (3) sediment depth horizons (0–2 and 3–5 cm). Little difference was observed between seamounts and the adjacent abyssal plains in the proportion of legacy pelagic eDNA sampled in the benthos, despite >1,000 m depth difference for these habitats. In terms of both reads and amplicon sequence variants (ASVs), pelagic eDNA was minimal within sediment and nodule samples (<2%), and is unlikely to affect benthic surveys that monitor resident organisms at the deep seafloor. However, pelagic eDNA was substantial within the BBL (up to 13% ASVs, 86% reads), derived both from the high-biomass upper ocean as well as deep pelagic residents. While most pelagic metazoan eDNA found in sediments and on nodules could be sourced from the epipelagic, protist legacy eDNA sampled on these substrates appeared to originate across a range of depths in the water column. Some evidence of eDNA degradation across a vertical sediment profile was observed for protists, with higher diversity in the 0–2 cm layer and a significantly lower proportion of legacy pelagic eDNA in deeper sediments (3–5 cm). Study-wide, our estimated metazoan sampling coverage ranged from 40 to 74%, despite relatively large sample size. Future deep-sea eDNA surveys should examine oceanographic influences on eDNA transport and residence times, consider habitat heterogeneity at a range of spatial scales in the abyss, and aim to process large amounts of material per sample (with replication) in order to increase the sampling coverage in these diverse deep ocean communities. |
| first_indexed | 2024-12-21T14:20:04Z |
| format | Article |
| id | doaj.art-314dd015ffd841a7a08c4222f382bff3 |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-12-21T14:20:04Z |
| publishDate | 2020-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-314dd015ffd841a7a08c4222f382bff32022-12-21T19:00:48ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452020-09-01710.3389/fmars.2020.00682567688From Sea Surface to Seafloor: A Benthic Allochthonous eDNA Survey for the Abyssal OceanOlivier Laroche0Olivier Laroche1Oliver Kersten2Craig R. Smith3Erica Goetze4Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai‘i at Mānoa, Honolulu, HI, United StatesInstitute of Marine Research, Tromsø, NorwayCentre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, NorwayDepartment of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai‘i at Mānoa, Honolulu, HI, United StatesDepartment of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai‘i at Mānoa, Honolulu, HI, United StatesEnvironmental DNA (eDNA) metabarcoding could facilitate rapid and comprehensive biotic surveys in the deep ocean, yet many aspects of the sources and distribution of eDNA in the deep sea are still poorly understood. In order to examine the influence of the water column on benthic eDNA surveys in regions targeted for deep-sea polymetallic nodule mining, we investigated the occurrence of pelagic eDNA across: (1) two different deep-sea habitat types, abyssal plains and seamounts, (2) benthic sample types, including nodules, sediment, and seawater within the benthic boundary layer (BBL), and (3) sediment depth horizons (0–2 and 3–5 cm). Little difference was observed between seamounts and the adjacent abyssal plains in the proportion of legacy pelagic eDNA sampled in the benthos, despite >1,000 m depth difference for these habitats. In terms of both reads and amplicon sequence variants (ASVs), pelagic eDNA was minimal within sediment and nodule samples (<2%), and is unlikely to affect benthic surveys that monitor resident organisms at the deep seafloor. However, pelagic eDNA was substantial within the BBL (up to 13% ASVs, 86% reads), derived both from the high-biomass upper ocean as well as deep pelagic residents. While most pelagic metazoan eDNA found in sediments and on nodules could be sourced from the epipelagic, protist legacy eDNA sampled on these substrates appeared to originate across a range of depths in the water column. Some evidence of eDNA degradation across a vertical sediment profile was observed for protists, with higher diversity in the 0–2 cm layer and a significantly lower proportion of legacy pelagic eDNA in deeper sediments (3–5 cm). Study-wide, our estimated metazoan sampling coverage ranged from 40 to 74%, despite relatively large sample size. Future deep-sea eDNA surveys should examine oceanographic influences on eDNA transport and residence times, consider habitat heterogeneity at a range of spatial scales in the abyss, and aim to process large amounts of material per sample (with replication) in order to increase the sampling coverage in these diverse deep ocean communities.https://www.frontiersin.org/article/10.3389/fmars.2020.00682/fullenvironmental DNAmetabarcodinglegacy eDNAdeep seaabyssal plainsClarion Clipperton Zone (CCZ) |
| spellingShingle | Olivier Laroche Olivier Laroche Oliver Kersten Craig R. Smith Erica Goetze From Sea Surface to Seafloor: A Benthic Allochthonous eDNA Survey for the Abyssal Ocean Frontiers in Marine Science environmental DNA metabarcoding legacy eDNA deep sea abyssal plains Clarion Clipperton Zone (CCZ) |
| title | From Sea Surface to Seafloor: A Benthic Allochthonous eDNA Survey for the Abyssal Ocean |
| title_full | From Sea Surface to Seafloor: A Benthic Allochthonous eDNA Survey for the Abyssal Ocean |
| title_fullStr | From Sea Surface to Seafloor: A Benthic Allochthonous eDNA Survey for the Abyssal Ocean |
| title_full_unstemmed | From Sea Surface to Seafloor: A Benthic Allochthonous eDNA Survey for the Abyssal Ocean |
| title_short | From Sea Surface to Seafloor: A Benthic Allochthonous eDNA Survey for the Abyssal Ocean |
| title_sort | from sea surface to seafloor a benthic allochthonous edna survey for the abyssal ocean |
| topic | environmental DNA metabarcoding legacy eDNA deep sea abyssal plains Clarion Clipperton Zone (CCZ) |
| url | https://www.frontiersin.org/article/10.3389/fmars.2020.00682/full |
| work_keys_str_mv | AT olivierlaroche fromseasurfacetoseafloorabenthicallochthonousednasurveyfortheabyssalocean AT olivierlaroche fromseasurfacetoseafloorabenthicallochthonousednasurveyfortheabyssalocean AT oliverkersten fromseasurfacetoseafloorabenthicallochthonousednasurveyfortheabyssalocean AT craigrsmith fromseasurfacetoseafloorabenthicallochthonousednasurveyfortheabyssalocean AT ericagoetze fromseasurfacetoseafloorabenthicallochthonousednasurveyfortheabyssalocean |