We are witnessing an explosion of environmental DNA (eDNA) techniques that has already revolutionized aquatic biodiversity monitoring. eDNA offers the opportunity to complement conventional methods, delivering fast, comprehensive, and traceable biodiversity assessments. This is critical in a moment where human activities constitute a direct threat to freshwater and marine ecosystems around the world. Accurate, fast, and cost-efficient molecular tools are now available for detecting the genetic material isolated from environmental samples and inferring the presence of particular species in the sampled locations, allowing us to capture and understand changes in aquatic biodiversity with unprecedented efficiency. The explosion of large volumes of molecular data has occurred in parallel with the advancement of resilience science, providing an opportunity to approach these complex phenomena from an interdisciplinary point of view (e.g., limnology, community ecology, paleolimnology, food web ecology, coastal fisheries, disturbance ecology) and combining classical and novel bioassesment methods. The time has come now to develop robust methods to infer valuable ecological information from molecular biodiversity data. Robust molecular bioindicators would allow to develop reliable and repeatable molecular biomonitoring protocols, to accurately diagnose ecosystem health status and to evaluate the performance of management policies and recovery plans. This session aims to showcase applications and methods of eDNA research focused on the development of novel ecological quality indicators from molecular biodiversity inventories, which are expected to become key tools to robustly assess resilience and recovery of aquatic ecosystems. We aim to bring contributors from different ecological backgrounds together who synthesize disparate sources of data, including any taxonomical group (or even taxonomy-free indicators), and transcending aquatic ecosystem boundaries. This also explicitly includes the assessment of long-term ecological changes inferred from sedimentary ancient DNA studies. We will favor eDNA studies profiling novel approaches to understand ecological patterns in aquatic systems, discussing how functional biodiversity traits or sequencing data can be used to infer ecological status, introducing new molecular analysis workflows to assess ecosystem health, presenting new methods to improve efficient sampling of aquatic ecosystems, as well as better harnessing the opportunities that high throughput sequencing technologies and automatization can provide. This session will welcome delegates interested in aquatic biomonitoring and molecular bioindicators and will encourage proposals for short (10-12 mins) presentations.
Lead Organizer: Xavier Benito-Granell, Institute of Agrifood Research and Technology (IRTA), Spain (xavier.benito.granell@gmail.com)
Co-organizers:
Sandra Garcés-Pastor, ICM-CSIC, Spain (sgarcespastor@gmail.com)
Owen S. Wangensteen, University of Barcelona, Spain (owenwangensteen@ub.edu)
Presentations
10:30 AM
Biomonitoring marine sanctuaries: a six-year study of Spanish National Parks using metabarcoding of benthic reef communities (5748)
Primary Presenter: Xavier Turon, Consejo Superior Inv. Cientificas (xturon@ceab.csic.es)
Metabarcoding has proven an effective method for comprehensive biodiversity assessment. However, its application in biomonitoring requires the generation of time series data, which are mostly wanting. We have obtained COI metabarcoding datasets of benthic reef communities of the two marine National Parks established in Spain, one in the Mediterranean (Cabrera Archipelago), and the other in the Atlantic (Cíes Islands) coast. These sanctuaries are under stress as a result of invasive seaweeds and warming. We have sampled four (Cabrera) and three (Cíes) time points over a six-year span (2014-2020), analyzing five community-types in each Park, with and without invasive algae. We devised a method for direct sampling of the reef communities using quadrats and size-fractionation. The generation of time series required adjustments of the bioinformatics pipelines as the volume of data grew exponentially. We chose to reduce the datasets at each time point using a denoising procedure within samples that took into account the variability of each codon position in the coding sequences. These reduced datasets can be easily assembled, and clustered into molecular operational taxonomic units, at desired time points. Our results showed a highly diverse assemblage, with ca. 270,000 sequence variants that clustered into 35,543 molecular operational taxonomic units (MOTUs). The effect of invasive algae was overall minor, while a clear effect of time was detected at the last sampling date (2020), indicating ongoing changes. Our study proves the feasibility of biomonitoring benthic reef communities over time, and our survey will continue in the forthcoming years.
10:45 AM
Metabarcoding reveals high-resolution biogeographical and metaphylogeographical patterns through marine barriers. (5866)
Primary Presenter: Adrià Antich González, Center for Advanced Studies of Blanes (CEAB-CSIC) (a.antich@ceab.csic.es)
Aim It has been predicted that there should be concordance between biogeographical and phylogeographical processes structuring multi-species regional assemblages. We hypothesise that oceanographic barriers in the marine environment affect concomitantly the distribution and the connectivity of the marine biota, thus producing congruent biogeographical and phylogeographical structures. We also predict that macro- and meio-eukaryotes will be differentially affected by hydrological features. Location The Atlanto-Mediterranean transition along the E Iberian coast marked by the Almeria-Oran Front (AOF) and the Ibiza Channel hydrological discontinuities. Taxon Eukaryotes. Methods A new analytical framework based in the metabarcoding of community DNA and a hypervariable marker is presented. This framework allows the simultaneous detection of multispecies biogeographical and phylogeographical structures. Shallow hard-bottom communities were sampled at 12 sites over the littoral zone and community-DNA metabarcoding was performed using the cytochrome c oxidase I marker. The resulting dataset was analysed at several levels: beta diversity of Molecular Operational Taxonomic Units (MOTUs) as surrogate for species, and Exact Sequence Variants as surrogate for haplotypes. We also assessed genetic differentiation within MOTUs (metaphylogeography). Analyses were performed for the combined dataset and separately for macro- and meio-eukaryotes. Results Both hydrological discontinuities had a detectable effect, more marked at all levels for the AOF than for the Ibiza Channel. The MOTU dataset provided more clear-cut patterns than the ESVs. The metaphylogeographical approach provided the highest resolution in terms of differentiating localities and identifying geographical barriers. The separate analyses of macro- and meio-eukaryotes showed a higher differentiation of the latter, both in terms of beta diversity and genetic differentiation. Main Conclusions Metabarcoding coupled with metaphylogeography allowed the characterisation of the heterogeneity in community composition and population genetic structure along the Atlanto-Mediterranean transition, coherent with known hydrological discontinuities. This methodology unlocks a vast amount of information on the geographical distribution of different components of biodiversity for basic and applied research.
11:00 AM
OPTIMIZATION OF ENVIRONMENTAL DNA METHODS FOR IMPROVING DETECTION PROBABILIITY OF MULTIPLE AQUATIC INVASICE SPECIES (AIS) IN FRESHWATER ECOSYSTEMS (5573)
Primary Presenter: Anna Totsch, University of Minnesota Duluth (totsc005@umn.edu)
Aquatic invasive species (AIS) are a threat to the ecological and economic integrity in freshwater ecosystems. Early detection and monitoring of AIS are essential to contain or eradicate a population in a timely manner and prevent spread to other waters. Physical AIS surveys require considerable effort, money, time, and by then the AIS may already be established. Environmental DNA (eDNA) is organismal DNA that originates from cellular material shed by organisms into the environment which can be detected using molecular methods. This study aims to test and compare different field and lab eDNA methods to determine which combinations maximize detection probability of our target AIS. Field sampling and traditional AIS surveys were conducted at five lakes in Minnesota, USA. Lake characteristics include sizes of large, medium, and small with one being a river system. AIS of interest includes Zebra mussels (Dreissena polymorpha), Spiny water flea (Bythotrephes cederstromii), Rusty crayfish (Faxonius rusticus), and Common carp (Cyprinus carpio). These species were chosen since they have already been established in our selected lake bodies. We compared several different ways of harvesting DNA (volume, filters, sample locations) and molecular biological detection method to see which method performed better. AIS detection using eDNA methods was more sensitive in comparison against traditional AIS detection surveys. The detection probability of eDNA methods by sampling locations (nearshore vs offshore and surface vs benthic) appears to be influenced by species and waterbody types. Our findings will provide guidance and recommendations to natural resource managers who might consider eDNA as an AIS monitoring tool.
11:15 AM
An eDNA metabarcoding survey of gelatinous zooplankton biodiversity and community composition in the rapidly changing Fram Strait (Arctic-Atlantic gateway) (6159)
Primary Presenter: Ayla Murray, Alfred Wegener Institute for Polar and Marine Research (ayla.murray@awi.de)
The Arctic is warming four times faster than the global mean, while the ‘Atlantification’ of the Arctic via Fram Strait is having growing influences on both physical and biological processes in the region. Greater understanding of how these changes are impacting local marine biodiversity is crucial for formulating accurate predictions of future Arctic ecosystems and potential management and mitigation decisions. Gelatinous zooplankton (GZP) are a highly diverse group of taxa, including cnidarians, ctenophores and pelagic tunicates and can have a wide range of ecosystem impacts. Little is known about GZP ecology in the Arctic seas, and even less about how their diversity and distributions are being impacted by climate-related changes. GZP are notoriously difficult to catch in good condition and are regularly underestimated in biodiversity, distribution and abundance. This has led to a lack of reliable and comprehensive baseline datasets, especially in the Arctic. In this study, we investigate GZP biodiversity across Fram Strait, comparing eDNA metabarcoding and net catch data from the same period and localities. We used the cytochrome c oxidase I (COI) gene for DNA metabarcoding using the Illumina NovaSeq platform. We successfully detected a wide range of GZP taxa with eDNA, across stations and depths. This dataset represents a valuable contribution to forming baseline datasets for the region, future research on changing GZP biodiversity and community composition, as well as biomonitoring of rare and range-shifting species in a changing Arctic Ocean.
11:30 AM
SPONGES AS NATURAL ENVIRONMENTAL DNA SENTINELS FOR MONITORING COASTAL MPAS (6729)
Primary Presenter: Erika Neave, Liverpool John Moores University (e.f.neave@ljmu.ac.uk)
Sponges have been identified as natural samplers of environmental DNA (eDNA) due to their filter feeding behaviour. This natural sampler DNA (nsDNA) has been obtained from opportunistic sponge samples previously collected for other purposes, and in controlled laboratory conditions to understand how nsDNA compares to aquatic eDNA methods. Yet there have still been few attempts to practically assess the effectiveness of sponges for monitoring coastal biodiversity. Here we compare traditional underwater visual census (UVC) surveys, aquatic eDNA, and sponge nsDNA to monitor diurnal fish assemblages in a marine protected area (Dafni Beach, Zakynthos, Greece) and an area of significance to tourism and culture (Korakonissi, Zakynthos, Greece). Differences in fish assemblages were apparent across the three methods. Invasive species could be detected across the three methods but only the common and very established <em>Siganus</em> spp were recorded by UVC. We found that some sponge species were less effective as natural samplers, but the ubiquitous and accessible nature of these organisms make them powerful and cost-effective solutions for monitoring MPAs, especially where the labour and taxonomic expertise required by UVC and field expertise required by eDNA are not easily available.
11:45 AM
EXPLORING ALTERNATIVE NATURAL EDNA SAMPLERS TO AID PELAGIC AND BENTHIC BIODIVERSITY ASSESSMENT (6779)
Primary Presenter: Alice Cunnington, Liverpool John Moores University (alicevcunnington@gmail.com)
Biodiversity in coastal marine environments is under unprecedented threat from the changing climate, pollution, and other anthropogenic disturbances. To better evaluate such impacts, it is imperative that more accurate, cost-effective and expedient methods of assessing biodiversity are developed. The analysis of environmental DNA (eDNA), the term used to describe genetic material shed by organisms into an environment, can paint a detailed picture of fish diversity in marine coastal environments. At present, eDNA for use in this context is typically obtained by way of water samples that have been actively passed through artificial filters; but more recently, analysis of natural sampler DNA (nsDNA) has emerged as a potential alternative. Natural samplers are usually filter-feeding invertebrates that naturally trap environmental DNA in their tissues. In this study, we explore whether two natural samplers present in differing habitats - i) benthic sea anemone (Actinia equina) ii) pelagic jellyfish (Aurelia solida, Rhizostoma pulmo, Aequorea forskalea) - are successful nsDNA candidates. Amplification of samples with fish-specific primers revealed that both these natural samplers successfully detected a range of fish and other vertebrate species expected in their respective benthic (sea anemone) and pelagic (jellyfish) environments. We also observed significant differences in the species detected through using nsDNA when directly compared to conventional eDNA samples. This indicates the value of using nsDNA alongside established eDNA methods to achieve a more comprehensive and accurate picture of an ecosystem’s biodiversity.
SS061A Novel Molecular Tools To Assess Biodiversity and Resilience of Aquatic Environments
Description
Time: 10:30 AM
Date: 9/6/2023
Room: Sala Santa Catalina