Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures

Deep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their integration in an expanding network of marine infrastructures for the exploration of the seas, such as cabled observatories. While still in its infancy, the application of environmental DNA (eDNA) metabarcoding approaches is revolutionizing marine biodiversity monitoring capability. Indeed, the analysis of eDNA in conjunction with the collection of multidisciplinary optoacoustic and environmental data, can provide a more comprehensive monitoring of deep-sea biodiversity. Here, we describe the potential for acquiring eDNA as a core component for the expanding ecological monitoring capabilities through cabled observatories and their docked Internet Operated Vehicles (IOVs), such as crawlers. Furthermore, we provide a critical overview of four areas of development: (i) Integrating eDNA with optoacoustic imaging; (ii) Development of eDNA repositories and cross-linking with other biodiversity databases; (iii) Artificial Intelligence for eDNA analyses and integration with imaging data; and (iv) Benefits of eDNA augmented observatories for the conservation and sustainable management of deep-sea biodiversity. Finally, we discuss the technical limitations and recommendations for future eDNA monitoring of the deep-sea. It is hoped that this review will frame the future direction of an exciting journey of biodiscovery in remote and yet vulnerable areas of our planet, with the overall aim to understand deep-sea biodiversity and hence manage and protect vital marine resources.

Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies

Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large-volume eDNA sampler with in situ filtration, capable of taking up to 12 samples per deployment. We conducted three deployments of our sampler on the robotic vehicle Mesobot in the Flower Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico and collected samples from 20 to 400 m depth. We compared the large volume (~40-60 liters) samples collected by Mesobot with small volume (~2 liters) samples collected using the conventional CTD-mounted Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which detects a broad range of invertebrate taxa, and found that while both methods detected biodiversity changes associated with depth, our large volume samples detected approximately 66% more taxa than the CTD small volume samples. We found that the fraction of the eDNA signal originating from metazoans relative to the total eDNA signal decreased with sampling depth, indicating that larger volume samples may be especially important for detecting metazoans in mesopelagic and deep ocean environments. We also noted substantial variability in biological replicates from both the large volume Mesobot and small volume CTD sample sets. Both of the sample sets also identified taxa that the other did not; although the number of unique taxa associated with the Mesobot samples was almost four times larger than those from the CTD samples. Large volume eDNA sampling with in situ filtration, particularly when coupled with robotic platforms, has great potential for marine biodiversity surveys, and we discuss practical methodological and sampling considerations for future applications.

Beachrock Formation Mechanism Using Multiproxy Experimental Data from Natural and Artificial Beachrocks: Insights for a Potential Soft Engineering Method

Beachrocks are a window to the past environmental, geological, sedimentological and morphological conditions that were dominant in the coastal zone during their formation. Furthermore, beachrocks have the ability to reduce coastal erosion impact on sandy beaches. This study focuses on the beachrock formation mechanism through the comparison of cement characteristics, mineral chemistry and sedimentology of beachrock occurrences from two different geological and geographical localities: Diolkos, Corinth, Greece and Sumuide, Okinawa, Japan. In addition, in order to investigate a potential soft engineering method to protect coasts from erosion, artificial beachrock samples were created in vitro using sand samples and ureolytic bacteria from both areas under accelerating conditions. For Okinawa artificial beachrock experiments, the bacteria Pararhodobacter sp. was used, and for Diolkos, it was the bacteria Micrococcus yunnainensis sp. For the natural beachrocks, a multi-analytical approach was accomplished with the use of microscopic investigation, a scanning electron microscope, energy-dispersive X-ray spectroscopy, X-ray diffraction and X-ray fluorescence. Correlations were made between natural and artificial beachrocks. Results have shown that Diolkos beachrock was formed in the upper part of the intertidal zone, consisting of detrital material originating from the local bedrock, while Sumuide beachrock formed in the low intertidal–upper subtidal zone, consisting of coral sand and foraminifera fragments. For the artificial beachrocks, three samples were created using the microbial-induced carbonate precipitation (MICP) method, one from Diolkos (Corinth, Greece) and two from Sumuide (Okinawa, Japan). Diolkos artificial beachrock was better consolidated in comparison to Sumuide. Our investigation has shown that bacterial density was the key factor for the creation of the artificial beachrocks, while the samples’ granulometry played a secondary role in the process. The laboratory artificial beachrocks show encouraging results for a new soft engineering method to encounter beach erosion while keeping an ecofriendly character by saving energy, material resources and gas emissions. Artificial beachrocks can share the same properties of a natural beachrock and can contribute positively to marine biodiversity as a natural rocky habitat.

Quantifying Transboundary Plastic Pollution in Marine Protected Areas Across the Mediterranean Sea

Micro- and macro-plastics pollution is a growing threat for marine biodiversity, ecosystem functioning, and consequently human wellbeing. Numerical models that consider main sources of plastics and simulate their dispersal characteristics are unique tools for exploring plastic pollution in marine protected areas (MPAs). Here, we used a Lagrangian plastic drift model, taking into account various sizes/types of plastic litter, originating from major land-based sources (coastal cities and rivers), to predict plastic accumulation zones in protected areas of the Mediterranean Sea (i.e., nationally designated MPAs, Natura 2000 sites, and Cetacean Critical Habitats). The model predicted that the size of plastic litters plays a key role in their dispersion and ultimate destination (i.e., larger litter travel longer distances). Most of the studied Mediterranean countries (13 out of 15) had at least one national MPA with over 55% of macroplastics originating from sources beyond their borders. Consequently, in many cases, local efforts to reduce plastic pollution in protected areas would be insufficient, especially for macroplastics management. Transboundary collaboration among Mediterranean countries is critical for implementing successful management plans against plastic pollution in their territorial waters and specifically in MPAs.

Spatial and Short-Term Temporal Patterns of Octocoral Assemblages in the West Philippine Sea

Octocorals are relatively understudied than other coral reef organisms despite their ecological and economic values. The Philippines is known to have high marine biodiversity, but information on octocorals is lacking. This study investigated spatial and temporal variations in the assemblage of octocorals in selected reef sites in the West Philippine Sea (WPS)- the Kalayaan Island Group (i.e., Pag-asa, Sabina, Lawak, and Northeast Investigator) and Ulugan in 2017 and 2019. Results showed high octocoral taxonomic richness (at least 10 families) in the study sites. Mean percent octocoral cover in WPS was 5.35% SE ± 0.55, with Sabina having the highest octocoral cover in both years. Significant differences in octocoral cover were observed among sites in both years, but among-station differences were only observed in 2017. Octocoral assemblage also differed among sites in both years (ANOSIM: R > 0.5, p < 0.05), wherein different octocoral taxa dominated in different sites. In particular, variations were driven by high cover of holaxonians, nephtheids, and coelogorgiids in Sabina, and clavulariids, tubiporiids, and xeniids in Northeast Investigator in 2017. In 2019, significant variations were driven by high cover of helioporiids in Pag-asa, while Sabina had higher abundance of holaxonians, nephtheids, alcyoniids, and xeniids. Short-term temporal variation on octocoral cover in monitoring stations in Pag-asa was not observed (Kruskal-Wallis, p > 0.05), although the overall mean octocoral cover increased from 1.23% ± SE 0.47 in 2017 to 2.09% SE ± 0.37 in 2019. Further, there was no significant change in the octocoral assemblage in Pag-asa between years (ANOSIM, R = 0.11, p = 0.07). This study highlights high octocoral taxonomic richness in the WPS relative to other sites in the Indo-Pacific Region and provides baseline information on the octocoral assemblages, which can be useful for future ecological studies and marine biodiversity conservation efforts.

Ocean climate connectivity and the future range shifts of marine biodiversity.

Shifting distribution to track suitable climate is a potential strategy for marine species to cope with ocean warming. Yet, the ability of species to successfully reach future climate analogs largely depends on the length of the paths that connect them, and on the exposure of these paths to extreme climates during this transition. Here, we evaluate marine climate connectivity for trajectories between climatic analogs on a global scale. We find that while movement between climatic analogs is more intense in the northern seas of the planet, they require longer trajectories to reach climatic analogs, with high climatic exposure to extreme conditions. On the contrary, the southern seas host areas that have closer climatic analogs, further subjected to a lower exposure to dissimilar climates. These patterns are mirrored in the connectivity properties of the global marine protected areas, highlighting sites which might fail to facilitate connectivity to future climates. Our results suggest that potential shifts between climatic analogs might be subjected to more limitations than those suggested by previous studies, with marine connectivity offering novel insights for the establishment of climate-wise conservation future networks.

Estuarine Infauna Within Incidentally Retained Sediment in Artificial Rockpools

Artificial coastal structures (ACSs) are primarily designed to provide services for human use, such as flood defence or shipping, and are generally poor for marine biodiversity. Consequently, there has been significant research effort to enhance these hard structures to increase biodiversity and habitat availability via eco-engineering. On seawalls and breakwaters, this has included the creation of habitats for benthic species found on natural rocky shores, including the provision of cracks, crevices and water retaining features, such as artificial rockpools. When sediment retention in these features has occurred, it has often been deemed detrimental to the overarching aim of the intervention. Yet, it is soft sediment habitat that is impacted the most through coastal construction. As ecological enhancement of a flood defence scheme, nine concrete retrofit rockpools were installed at three different tidal elevations between mean high water neap tide and mean tide level on steel sheet piling on the Arun Estuary in Littlehampton Harbour, United Kingdom, which naturally filled with mud 1 year after installation. To explore how analogous the faunal assemblages and sediment profile of rockpool mud were to two local mudflats, core samples were taken and analysed for species richness, abundance, biomass, assemblage structure, median grain size, and organic matter content. More benthic species were observed in the artificial rockpool than in the local mudflats. Although the rockpools were placed at higher tidal levels than the lower shore mudflat, their assemblage structure and species richness were more similar to the lower shore mudflat at the base of the sheet piling than the upper shore mudflat. This study demonstrates that retained sediment within eco-engineered features on hard ACSs can create habitat for benthic assemblages. Providing sediment-retentive features on ACSs has the potential to provide a novel eco-engineering option that may be appropriate for some heavily modified waterbodies on sheltered, depositional coasts.