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

Abstract

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.

Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

“…The development of eDNA as a reliable method to monitor biodiversity and evaluate anthropogenic impacts is crucial because important changes in biodiversity might currently occur under our radar [39,57]. Depending on the organisms of interest, eDNA can be used to sample whole eukaryote assemblages [58] or more specific taxonomic groups ranging from sponges and corals [59] to larger taxa such as sharks [30]. In our case, we potentially missed some native and common species in the Mediterranean Sea since the teleo marker cannot distinguish the wrasses Symphodus rostratus, S. cinnereus, S. mediterraneus, and S. roissali from each other, or Labrus merula from L. viridis, as well as the rarer pipefishes Syngnathus abaster and S. sp cfr taenionotus.…”

Airborne eDNA Reflects Human Activity and Seasonal Changes on a Landscape Scale

“…Additionally, Buxton et al (2018) found, when examining eDNA of the great crested newt (Triturus cristatus) in aquatic and sediment samples, that detection varied throughout the year based on habitat suitability and species ecology. Work has also been done in ocean systems with studies ranging from examining shark diversity response to anthropogenic disturbance to understanding how anthropogenic activities such as oil spills and development impact micro and macro coastal communities (Bakker et al, 2017;Xie et al, 2018;DiBattista et al, 2020). Sun et al (2019) used eDNA metabarcoding to understand Dipteria and other organism populations in human caused roadside stormwater ponds.…”

Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States

“…As the name indicates, eDNA is genetic material that has been deposited into the environment via numerous sources, such as skin, feces, urine, larvae, and gametes. DNA extracted directly from environmental samples (e.g., filtered seawater, soil, and sand) can be sequenced to identify source organisms occupying the proximate area of the collected sample (Laramie et al, 2015;Minamoto et al, 2016;Hinlo et al, 2017;Dibattista et al, 2020). Accordingly, eDNA-based investigations have proven to be as valuable as traditional survey methods that require capture and subsampling of target organisms.…”

“…Importantly, eDNA methods are a less-intrusive approach to studying invasive or declining species (Zhou et al, 2013;Bucklin et al, 2016;Holman et al, 2019;Nelson-Chorney et al, 2019), documenting the distribution of difficult to sample taxa (Parsons et al, 2018), and estimating relative seasonal biomass of target species (Takasu et al, 2019;Stoeckle et al, 2020). Marine-derived eDNA has also been likened to a "barometer of disturbance" with respect to its potential to assess anthropogenic effects on ecosystems (Dibattista et al, 2020).…”