Ecosystem biomonitoring with eDNA: Metabarcoding across the tree of life in a tropical marine environment
MetadataShow full item record
Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs. © 2017 The Author(s).
Showing items related by title, author, creator and subject.
Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movementJeunen, G.; Knapp, M.; Spencer, H.; Lamare, M.; Taylor, H.; Stat, M.; Bunce, Michael; Gemmell, N. (2018)While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal ...
Koziol, A.; Stat, Michael; Simpson, T.; Jarman, Simon; Di Battista, Joseph; Harvey, Euan; Marnane, M.; McDonald, J.; Bunce, Michael (2018)Effective biomonitoring is critical for driving management outcomes that ensure long-term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with metabarcoding methodologies, has ...
Challenges for assessing vertebrate diversity in turbid Saharan water-bodies using environmental DNAEgeter, B.; Peixoto, S.; Brito, J.; Jarman, Simon; Puppo, P.; Velo-Antón, G. (2018)The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful ...