Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems

• Published in: Scientific reports 2020-05, Vol.10 (1), p.8365, Article 8365
• Main Authors: DiBattista, Joseph D., Reimer, James D., Stat, Michael, Masucci, Giovanni D., Biondi, Piera, De Brauwer, Maarten, Wilkinson, Shaun P., Chariton, Anthony A., Bunce, Michael
• Format: Article
• Language: English
• Subjects: 631/158/2452; 631/158/2464; 631/158/670; 704/172/4081; 704/829/826; Anthropogenic factors; Biodiversity; Biodiversity loss; Biota; Biota - genetics; Chemical analysis; Coastal ecosystems; Coral Reefs; Deoxyribonucleic acid; DNA; DNA Barcoding, Taxonomic; DNA, Ribosomal Spacer - genetics; DNA, Ribosomal Spacer - isolation & purification; Environmental DNA; Environmental DNA - genetics; Environmental DNA - isolation & purification; Environmental Monitoring - methods; Genetic Markers - genetics; Humanities and Social Sciences; Learning algorithms; Machine learning; Marine ecosystems; multidisciplinary; Nucleotide sequence; Oceans; Oceans and Seas; RNA, Ribosomal, 18S - genetics; rRNA; Science; Science (multidisciplinary); Seawater; Spatio-Temporal Analysis; Trophic levels; Water analysis
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-64858-9

Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities.