Abstract
The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed toward small fragments, we evaluated the effect of removingshort DNA fragments via size selection and ethanol reconcentration using eDNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by eDNA and environmental RNA (eRNA) co-extracted from ∼2 g of sedimen at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using eRNA. With ribosomal loci, eRNA, while resolving similar spatial patterns than co-extracted eDNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to overabundance of rRNA and RNA release. With the mitochondrial locus, eRNA detected lower metazoan richness and resolved fewer spatial patterns than co-extracted eDNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (≥10 g) for accurately surveying eukaryotic diversity. We conclude that eDNA should be favored over eRNA for logistically realistic, repeatable, and reliable surveys and confirm that large sediment samples (≥10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.
Highlights
Environmental DNA metabarcoding is an increasingly used tool for biodiversity inventories and ecological surveys
Environmental RNA has been viewed as a way to avoid the problem of ancient DNA (aDNA) in Environmental DNA (eDNA) biodiversity inventories because RNA is only produced by living organisms and quickly degrades when released in the environment due to spontaneous hydrolysis and the abundance of RNases (Torti et al, 2015)
A total of 70 million 18S-V1 reads, 61 million c Oxidase I (COI) reads, 30 million 18S-V4 reads, and 45 million 16S-V4V5 reads were obtained from four Illumina HiSeq runs of pooled amplicon libraries built from triplicate PCR replicates of 75 sediment samples, two mock communities, three extraction blanks, and two to four PCR negative controls (Supplementary Table S6)
Summary
Environmental DNA (eDNA) metabarcoding is an increasingly used tool for biodiversity inventories and ecological surveys. Using high-throughput sequencing (HTS) and bioinformatic processing, it allows the detection or the inventory of target organisms using their DNA directly extracted from soil, water, or air samples (Taberlet et al, 2012a). As it does not require specimen isolation, it represents a practical and efficient tool in large and hard-to-access ecosystems, such as the marine realm. Given the increased time efficiency offered by eDNA metabarcoding and its wide taxonomic applicability, this tool is a good candidate for large-scale biodiversity surveys and environmental impact assessments (EIAs) in the deep-sea biome
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
