Nathan Robert Geraldi

Documenting large-scale patterns of animals in the ocean and determining the drivers of these patterns is needed for conservation efforts given the unprecedented rates of change occurring within marine ecosystems. We used existing datasets from two global expeditions, Tara Oceans and Malaspina , that circumnavigated the oceans and sampled down to 4000 m to assess metazoans from environmental DNA (eDNA) extracted from seawater. We describe patterns of taxonomic richness within metazoan phyla and orders based on metabarcoding and infer the relative abundance of phyla using metagenome datasets, and relate these data to environmental variables. Arthropods had the greatest taxonomic richness of metazoan phyla at the surface, while cnidarians had the greatest richness in pelagic zones. Half of the marine metazoan eDNA from metagenome datasets was from arthropods, followed by cnidarians and nematodes. We found that mean surface temperature and primary productivity were positively related to metazoan taxonomic richness. Our findings concur with existing knowledge that temperature and primary productivity are important drivers of taxonomic richness for specific taxa at the ocean’s surface, but these correlations are less evident in the deep ocean. Massive sequencing of eDNA can improve understanding of animal distributions, particularly for the deep ocean where sampling is challenging.

The hadopelagic environment remains highly understudied due to the inherent difficulties in sampling at these depths. The use of sediment environmental DNA (eDNA) can overcome some of these restrictions as settled and preserved DNA represent an archive of the biological communities. We use sediment eDNA to assess changes in the community within one of the world's most productive open‐ocean ecosystems: the Atacama Trench. The ecosystems around the Atacama Trench have been intensively fished and are affected by climate oscillations, but the understanding of potential impacts on the marine community is limited. We sampled five sites using sediment cores at water depths from 2400 to ~8000 m. The chronologies of the sedimentary record were determined using ²¹⁰Pb_ex. Environmental DNA was extracted from core slices and metabarcoding was used to identify the eukaryote community using two separate primer pairs for different sections of the 18S rRNA gene (V9 and V7) effectively targeting pelagic taxa. The reconstructed communities were similar among markers and mainly composed of chordates and members of the Chromista kingdom. Alpha diversity was estimated for all sites in intervals of 15 years (from 1842 to 2018), showing a severe drop in biodiversity from 1970 to 1985 that aligns with one of the strongest known El Niño events and extensive fishing efforts during the time. We find a direct impact of sea surface temperature on the community composition over time. Fish and cnidarian read abundance was examined separately to determine whether fishing had a direct impact, but no direct relation was found. These results demonstrate that sediment eDNA can be a valuable emerging tool providing insight in historical perspectives on ecosystem developments. This study constitutes an important step toward an improved understanding of the importance of environmental and anthropogenic drivers in affecting open and deep ocean communities.

Our ability to assess biodiversity at relevant spatial and temporal scales for informing management is of increasing importance given this is foundational to identify and mitigate the impacts of global change. Collecting baseline information and tracking ecological changes are particularly important for areas experiencing rapid changes and representing data gaps such as Arctic marine ecosystems. Environmental DNA has the potential to provide such data. We extracted environmental DNA from 90 surface sediment samples to assess eukaryote diversity around Greenland and Svalbard using two separate primer pairs amplifying different sections of the 18S rRNA gene. We detected 27 different phyla and 99 different orders and found that temperature and the change in temperature explained the most variation in the community in a single linear model, while latitude, sea ice cover and change in temperature explained the most variation in the community when assessed by individual non-linear models. We identified potential indicator taxa for Arctic climate change, including a terebellid annelid worm. In conclusion, our study demonstrates that environmental DNA offers a feasible method to assess biodiversity and identifies warming as a key driver of differences in biodiversity across these remote ecosystems.

Anthropogenic impacts on marine ecosystems have led to a decline of biodiversity across the oceans, threatening invaluable ecosystem services on which we depend. Ecological temporal data to track changes in diversity are relatively rare, and the few long-term datasets that exist often only date back a few decades or less. Here, we use eDNA taken from dated sediment cores to investigate changes over approximately the last 100 years of metazoan communities in native (Cymodocea nodosa and Posidonia oceanica) and exotic (Halophila stipulacea) seagrass meadows within the eastern Mediterranean Sea, at two locations in Greece and two in Cyprus. Overall, metazoan communities showed a high turnover of taxa during the past century, where losses of individual taxa in a seagrass meadow were compensated by the arrival of new taxa, probably due to the arrival of exotic species introduced in the Mediterranean Sea from the Suez Canal or the Gibraltar Strait. Specifically, bony fishes (Class Actinopteri) and soft corals (Class Anthozoa) presented significantly higher richness in the past (before the 1980s) than in the most recent time periods (from 1980–2017) and some Cnidarian orders were solely found in the past, whereas sponges and Calanoids (Class Hexanauplia), an order of copepods, showed an increase in richness since the 1980s. Moreover, the Phyla Porifera, Nematoda and the Classes Staurozoa, Hydrozoa and Ophiuroidea were detected in P. oceanica meadows but not in C. nodosa and H. stipulacea, which led to P. oceanica meadows having twice the richness of other seagrasses. The greater richness resulted from the more complex habitat provided by P. oceanica. The combination of eDNA and sediment cores allowed us to reconstruct temporal patterns of metazoan community diversity and provides a novel approach to follow natural communities back in time in the absence of time series and baseline data. The ongoing loss of P. oceanica meadows, likely to be compounded with future warming, might lead to a major loss of biodiversity and the replacement by other seagrass species, whether native or exotic, does not compensate for the loss.

Predation affects community structure and functioning within marine habitats. Predator–prey interactions can change through space and time. Documenting how these interactions change is essential to improve our understanding of food web dynamics and to enhance our ability to manage preferred species. In this study, our goals were to determine whether the density of subtidal oysters (Crassostrea virginica) differed spatially by looking at three separate restored oyster sanctuaries within Pamlico Sound (North Carolina, USA), whether oyster density changed over an interval of 16 months, and whether oyster density was related to the presence of different‐sized predators by using an experimental approach. Multiple exclusion treatments were used in situ to exclude, selectively, different predator guilds from consuming oysters. Predator densities were also measured both within experimental treatments and on the restored oyster reefs by using multiple survey techniques. We found that oyster abundance differed among the four sample dates over the 16‐month study and differed among the three sites. Mud crabs—one of the smallest predators measured—had the greatest predator biomass per unit of area, but the presence of other predators was largely site‐dependent. Oyster abundance was affected by the exclusion of all predators, but this was dependent on sample date and location, which may suggest that mud crabs were the only predator to reduce oyster abundance in this study. In addition, large predators may have affected small predators, such as mud crabs and oyster drills, which were more abundant in treatments where large predators were excluded. The strongest evidence for top‐down effects on oyster reefs occurred at one of the three field sites at the first and final sampling time, suggesting that predator effects are complex, as well as spatially and temporally variable. Field experiments that assess variables through time and at multiple locations are needed as this information could improve the success of oyster reef conservation and restoration efforts.

Macroalgae are key primary producers in North Atlantic and Arctic coastal ecosystems, and tracing their fate and distribution is vital to improve our understanding of their ecological role and provision of ecosystem services. Recent advances from environmental DNA (eDNA) have added a new capacity to fingerprint and trace macroalgae. However, further development of resources for amplifying and identifying macroalgal eDNA are much needed. Here, we examined the performance in terms of resolution and specificity of two 18S primers (18S‐V7 and 18S‐V9) recently applied in identifying macroalgae from eDNA. We also built a local barcode database for primer 18S‐V7 with 31 widespread Arctic and North Atlantic macroalgal species to complement the existing DNA databases. Furthermore, we applied metabarcoding of eDNA to identify macroalgae in Arctic marine sediments (Disko Bay, W. Greenland) and evaluated the contributions from our local barcode database. We identified macroalgal DNA from 19 families across 11 orders in surface (0–1 cm, with both primers) and sub‐surface (5–10 cm, with 18S‐V7 primer) sediments. The barcode database developed here with the 18S‐V7 primer improved the identification of unique families, from 16 to 19 families, thereby strengthening the taxonomic assignment possible relative to pre‐existing barcode reference sequences. Overall, this study demonstrates the feasibility of eDNA to resolve contributions of macroalgae in Arctic marine sediments, and enhances the fingerprinting resolution. We thereby document a novel pathway to answer key questions on the ecological role and fate of macroalgae in the Arctic.

Background: Quantifying metabolic rate in free-living animals is invaluable in understanding the costs of behaviour and movement for individuals and communities. Dynamic body acceleration (DBA) metrics, such as vectoral DBA (VeDBA), are commonly used as proxies for the energy expenditure of movement but are of limited applicability for slow-moving species. It has recently been suggested that metrics based on angular velocity might be better suited to characterise their energetics. We investigated whether a novel metric—the ‘Rate of change of Rotational Movement (RocRM)’, calculated from the vectoral sum of change in the pitch, roll and yaw/heading axes over a given length of time, is a suitable proxy for energy expenditure. Results: We found that RocRM can be used as an alternative energy expenditure proxy in a slow-moving benthic invertebrate. Eleven Giant spider conchs Lambis truncata (collected in the Red Sea) were instrumented with multiple channel (Daily Diary) tags and kept in sealed chambers for 5 h while their oxygen consumption, V̇O₂, was measured. We found RocRM to be positively correlated with V̇O₂, this relationship being affected by the time-step (i.e. the range of the calculated differential) of the RocRM. Time steps of 1, 5, 10 and 60 s yielded an explained variability of between 15 and 31%. The relationship between V̇O₂ and VeDBA was not statistically significant, suggesting RocRM to provide more accurate estimations of metabolic rates in L. truncata. Conclusions: RocRM proved to be a statistically significant predictor of V̇O₂ where VeDBA did not, validating the approach of using angular-based metrics over dynamic movement-based ones for slower moving animals. Further work is required to validate the use of RocRM for other species, particularly in animals with minimally dynamic movement, to better understand energetic costs of whole ecosystems. Unexplained variability in the models might be a consequence of the methodology used, but also likely a result of conch activity that does not manifest in movement of the shell. Additionally, density plots of mean RocRM at each time-step suggest differences in movement scales, which may collectively be useful as a species fingerprint of movement going forward.

Our understanding of the response of reef‐building corals to changes in their physical environment is largely based on laboratory experiments, analysis of long‐term field data, and model projections. Experimental data provide unique insights into how organisms respond to variation of environmental drivers. However, an assessment of how well experimental conditions cover the breadth of environmental conditions and variability where corals live successfully is missing. Here, we compiled and analyzed a globally distributed dataset of in‐situ seasonal and diurnal variability of key environmental drivers (temperature, pCO₂, and O₂) critical for the growth and livelihood of reef‐building corals. Using a meta‐analysis approach, we compared the variability of environmental conditions assayed in coral experimental studies to current and projected conditions in their natural habitats. We found that annual temperature profiles projected for the end of the 21st century were characterized by distributional shifts in temperatures with warmer winters and longer warm periods in the summer, not just peak temperatures. Furthermore, short‐term hourly fluctuations of temperature and pCO₂ may regularly expose corals to conditions beyond the projected average increases for the end of the 21st century. Coral reef sites varied in the degree of coupling between temperature, pCO₂, and dissolved O₂, which warrants site‐specific, differentiated experimental approaches depending on the local hydrography and influence of biological processes on the carbonate system and O₂ availability. Our analysis highlights that a large portion of the natural environmental variability at short and long timescales is underexplored in experimental designs, which may provide a path to extend our understanding on the response of corals to global climate change.

Over this century, coral reefs will run the gauntlet of climate change, as marine heatwaves (MHWs) become more intense and frequent, and ocean acidification (OA) progresses. However, we still lack a quantitative assessment of how, and to what degree, OA will moderate the responses of corals to MHWs as they intensify throughout this century. Here, we first projected future MHW intensities for tropical regions under three future greenhouse gas emissions scenario (representative concentration pathways, RCP2.6, RCP4.5 and RCP8.5) for the near‐term (2021–2040), mid‐century (2041–2060) and late‐century (2081–2100). We then combined these MHW intensity projections with a global data set of 1,788 experiments to assess coral attribute performance and survival under the three emissions scenarios for the near‐term, mid‐century and late‐century in the presence and absence of OA. Although warming and OA had predominately additive impacts on the coral responses, the contribution of OA in affecting most coral attributes was minor relative to the dominant role of intensifying MHWs. However, the addition of OA led to greater decreases in photosynthesis and survival under intermediate and unrestricted emissions scenario for the mid‐ and late‐century than if intensifying MHWs were considered as the only driver. These results show that role of OA in modulating coral responses to intensifying MHWs depended on the focal coral attribute and extremity of the scenario examined. Specifically, intensifying MHWs and OA will cause increasing instances of coral bleaching and substantial declines in coral productivity, calcification and survival within the next two decades under the low and intermediate emissions scenario. These projections suggest that corals must rapidly adapt or acclimatize to projected ocean conditions to persist, which is far more likely under a low emissions scenario and with increasing efforts to manage reefs to enhance resilience.