Exploring Environmental DNA (eDNA) to Assess Biodiversity of Hard Substratum Faunal Communities on the Lucky Strike Vent Field (Mid-Atlantic Ridge) and Investigate Recolonization Dynamics After an Induced Disturbance

Type Article
Date 2020-01
Language English
Author(s) Cowart Dominique1, Matabos MarjolaineORCID1, Brandt Miriam2, Marticorena Julien1, Sarrazin Jozee1
Affiliation(s) 1 : Ifremer Centre de Bretagne, REM/EEP, Laboratoire Environnement Profond, Plouzané, France
2 : IRD, CNRS, MARBEC, Ifremer, Université de Montpellier, Sète, France
Source Frontiers in Marine Science (2296-7745) (Frontiers Media SA), 2020-01 , Vol. 6 , N. 783 , P. 21p.
DOI 10.3389/fmars.2019.00783
Keyword(s) natural regeneration, clearance, Bathymodiolus azoricus, monitoring, hard substratum, active and inactive vent sites
Abstract

Deep ocean hydrothermal vent ecosystems face physical disturbances from naturally occurring volcanic and tectonic activities and are at increasing risk of mineral resource exploitation, raising concerns about the resilience of endemic biological communities. Following destructive events, efficient and rapidly applicable surveys of organisms are required to monitor the state, evolution and a possible return of these ecosystems to their original baseline status. In this study, we explored the environmental DNA (eDNA) approach as a tool (1) to assess biodiversity of benthic communities associated with deep-sea hard substrata and (2) tracked the recolonization dynamics of benthic invertebrate communities living on the Montségur edifice within the Lucky Strike vent field (Mid-Atlantic Ridge), after an induced disturbance that consisted of faunal clearance within experimental quadrats. Hard substratum samples were collected prior to and one year after the disturbance, for eDNA metabarcoding using one marker of the mitochondrial Cytochrome Oxidase I (COI) gene and three markers of the nuclear 18S ribosomal RNA (18S) gene. We also generated a DNA barcoding inventory that consisted of taxa physically collected from Montségur and morphologically identified. This inventory contained amplified barcodes from COI, 18S and the nuclear large subunit ribosomal RNA (28S) gene. The resulting sequence information from the COI and 18S were used for eDNA taxonomic assignment. The eDNA datasets uncovered a high diversity of metazoan OTUs, which included macro- and meiofauna common to Lucky Strike. Baseline data collected at the start of the experiment identified higher OTU richness at sites peripheral to the active edifice, as well as at inactive sites. One year following the initial disturbance, analysis of recolonization data found no statistical difference in presence/absence from baseline communities. The eDNA protocols provide a reproducible strategy to quickly assess biodiversity associated with deep sea hard substratum, enabling comparisons across various habitats. To follow recolonization dynamics at small spatial scales, however, we recommend an approach that uses both molecular and morphological-based traditional methods. Finally, we present original data on the “unseen” diversity of the fauna inhabiting the poorly studied inactive sites, locations that are targeted by commercial mining. Continued monitoring of these sites is currently ongoing and will bring new insight on recovery potential over time, with the ultimate goal of informing conservation and management decisions in relation to the protection of hydrothermal vent ecosystems.

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Publisher's official version 21 2 MB Open access
MATERIAL S1 | PCR protocols for DNA barcoding of animal tissue. 4 231 KB Open access
TABLE S1 | Sequencing depth values for all taxa and metazoan taxa only, for the four eDNA datasets and across the 18 collected samples. 1 422 KB Open access
FIGURE S1 | Sequencing depth of non-metazoans and metazoans combined (“overall”) for the four eDNA datasets. The number of reads in each OTU (right) and 18 samples (left) are shown for each gene ... 839 KB Open access
FIGURE S2 | Sequencing depth of metazoans only for the four eDNA datasets. The number of reads in each OTU (right) and 18 samples (left) are shown for each gene marker. 1 MB Open access
FIGURE S3 | The top 10 most common species, in terms of sequence abundance, for the 18S-V4 and 18S-V9 eDNA datasets. “DNA barcode” are those species that were physically collected ... 235 KB Open access
FIGURE S4 | Accumulation curves for the 18S-V4 eDNA dataset, for both baseline (left) and recolonization (right) data across all taxa (non-metazoans and metazoans) and metazoan taxa only. 628 KB Open access
FIGURE S5 | Accumulation curves for the 18S-V9 eDNA dataset, for both baseline (left) and recolonization (right) data across all taxa (non-metazoans and metazoans) and metazoan taxa only. 666 KB Open access
FIGURE S6 | Canonical correspondence analysis (CCA) plots for 18S-V4 and 18S-V9, illustrating metazoan community distributions by active, periphery or inactive habitats. 240 KB Open access
FIGURE S7 | Taxonomic characterizations of 18S-V4 and 18S-V9 eDNA datasets by phylum, based on number of OTUs (incidence) and identified from samples distributed... 432 KB Open access
FIGURE S8 | Taxonomic characterizations of the four eDNA datasets by phylum, based on number of OTUs (incidence) and identified from samples collected in 2017 and 2018, for ... 870 KB Open access
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How to cite 

Cowart Dominique, Matabos Marjolaine, Brandt Miriam, Marticorena Julien, Sarrazin Jozee (2020). Exploring Environmental DNA (eDNA) to Assess Biodiversity of Hard Substratum Faunal Communities on the Lucky Strike Vent Field (Mid-Atlantic Ridge) and Investigate Recolonization Dynamics After an Induced Disturbance. Frontiers in Marine Science, 6(783), 21p. Publisher's official version : https://doi.org/10.3389/fmars.2019.00783 , Open Access version : https://archimer.ifremer.fr/doc/00600/71176/