The best of two worlds: reprojecting 2D image annotations onto 3D models.

Imagery has become one of the main data sources for investigating seascape spatial patterns. This is particularly true in deep-sea environments, which are only accessible with underwater vehicles. On the one hand, using collaborative web-based tools and machine learning algorithms, biological and geological features can now be massively annotated on 2D images with the support of experts. On the other hand, geomorphometrics such as slope or rugosity derived from 3D models built with structure from motion (sfm) methodology can then be used to answer spatial distribution questions. However, precise georeferencing of 2D annotations on 3D models has proven challenging for deep-sea images, due to a large mismatch between navigation obtained from underwater vehicles and the reprojected navigation computed in the process of building 3D models. In addition, although 3D models can be directly annotated, the process becomes challenging due to the low resolution of textures and the large size of the models. In this article, we propose a streamlined, open-access processing pipeline to reproject 2D image annotations onto 3D models using ray tracing. Using four underwater image datasets, we assessed the accuracy of annotation reprojection on 3D models and achieved successful georeferencing to centimetric accuracy. The combination of photogrammetric 3D models and accurate 2D annotations would allow the construction of a 3D representation of the landscape and could provide new insights into understanding species microdistribution and biotic interactions.

Impacts of ocean warming on fish size reductions on the world's hottest coral reefs.

The impact of ocean warming on fish and fisheries is vigorously debated. Leading theories project limited adaptive capacity of tropical fishes and 14-39% size reductions by 2050 due to mass-scaling limitations of oxygen supply in larger individuals. Using the world's hottest coral reefs in the Persian/Arabian Gulf as a natural laboratory for ocean warming - where species have survived >35.0 °C summer temperatures for over 6000 years and are 14-40% smaller at maximum size compared to cooler locations - we identified two adaptive pathways that enhance survival at elevated temperatures across 10 metabolic and swimming performance metrics. Comparing Lutjanus ehrenbergii and Scolopsis ghanam from reefs both inside and outside the Persian/Arabian Gulf across temperatures of 27.0 °C, 31.5 °C and 35.5 °C, we reveal that these species show a lower-than-expected rise in basal metabolic demands and a right-shifted thermal window, which aids in maintaining oxygen supply and aerobic performance to 35.5 °C. Importantly, our findings challenge traditional oxygen-limitation theories, suggesting a mismatch in energy acquisition and demand as the primary driver of size reductions. Our data support a modified resource-acquisition theory to explain how ocean warming leads to species-specific size reductions and why smaller individuals are evolutionarily favored under elevated temperatures.

Ocean warming and acidification adjust inter- and intra-specific variability in the functional trait expression of polar invertebrates.

Climate change is known to affect the distribution and composition of species, but concomitant alterations to functionally important aspects of behaviour and species-environment relations are poorly constrained. Here, we examine the ecosystem ramifications of changes in sediment-dwelling invertebrate bioturbation behaviour-a key process mediating nutrient cycling-associated with near-future environmental conditions (+ 1.5 °C, 550 ppm [pCO2]) for species from polar regions experiencing rapid rates of climate change. We find that responses to warming and acidification vary between species and lead to a reduction in intra-specific variability in behavioural trait expression that adjusts the magnitude and direction of nutrient concentrations. Our analyses also indicate that species behaviour is not predetermined, but can be dependent on local variations in environmental history that set population capacities for phenotypic plasticity. We provide evidence that certain, but subtle, aspects of inter- and intra-specific variation in behavioural trait expression, rather than the presence or proportional representation of species per se, is an important and under-appreciated determinant of benthic biogeochemical responses to climate change. Such changes in species behaviour may act as an early warning for impending ecological transitions associated with progressive climate forcing.

Innovative and practical tools for monitoring and assessing biodiversity status and impacts of multiple human pressures in marine systems.

Human activities at sea can produce pressures and cumulative effects on ecosystem components that need to be monitored and assessed in a cost-effective manner. Five Horizon European projects have joined forces to collaboratively increase our knowledge and skills to monitor and assess the ocean in an innovative way, assisting managers and policy-makers in taking decisions to maintain sustainable activities at sea. Here, we present and discuss the status of some methods revised during a summer school, aiming at better management of coasts and seas. We include novel methods to monitor the coastal and ocean waters (e.g. environmental DNA, drones, imaging and artificial intelligence, climate modelling and spatial planning) and innovative tools to assess the status (e.g. cumulative impacts assessment, multiple pressures, Nested Environmental status Assessment Tool (NEAT), ecosystem services assessment or a new unifying approach). As a concluding remark, some of the most important challenges ahead are assessing the pros and cons of novel methods, comparing them with benchmark technologies and integrating these into long-standing time series for data continuity. This requires transition periods and careful planning, which can be covered through an intense collaboration of current and future European projects on marine biodiversity and ecosystem health.

Unveiling a new oceanic anoxic event at the Norian/Rhaetian boundary (Late Triassic).

The latest Triassic was characterised by protracted biotic extinctions concluding in the End-Triassic Extinction (~ 200 Ma) and a global carbon cycle perturbation. The onset of declining diversity is closely related to reducing conditions that spread globally from upper Sevatian (uppermost Norian) to across the Norian-Rhaetian boundary, likely triggered by unusually high volcanic activity. We correlate significant organic carbon cycle perturbations to an increase of CO2 in the ocean-atmosphere system, likely outgassed by the Angayucham igneous province, the onset of which is indicated by the initiation of a rapid decline in 87Sr/86Sr and 188Os/187Os seawater values. A possible causal mechanism involves elevated CO2 levels causing global warming and accelerating chemical weathering, which increased nutrient discharge to the oceans and greatly increased biological productivity. Higher export production and oxidation of organic matter led to a global O2 decrease in marine water across the Norian/Rhaetian boundary (NRB). Biotic consequences of dysoxia/anoxia include worldwide extinctions in some fossil groups, such as bivalves, ammonoids, conodonts, radiolarians.

Beyond surface: Unveiling ecological and economic ramifications of microplastic pollution in the oceans.

Every year, the global production of plastic waste reaches a staggering 400 million metric tons (Mt), precipitating adverse consequences for the environment, food safety, and biodiversity as it degrades into microplastics (MPs). The multifaceted nature of MP pollution, coupled with its intricate physiological impacts, underscores the pressing need for comprehensive policies and legislative frameworks. Such measures, alongside advancements in technology, hold promise in averting ecological catastrophe in the oceans. Mandated legislation represents a pivotal step towards restoring oceanic health and securing the well-being of the planet. This work offers an overview of the policy hurdles, legislative initiatives, and prospective strategies for addressing global pollution due to MP. Additionally, this work explores innovative approaches that yield fresh insights into combating plastic pollution across various sectors. Emphasizing the importance of a global plastics treaty, the article underscores its potential to galvanize collaborative efforts in mitigating MP pollution's deleterious effects on marine ecosystems. Successful implementation of such a treaty could revolutionize the plastics economy, steering it towards a circular, less polluting model operating within planetary boundaries. Failure to act decisively risks exacerbating the scourge of MP pollution and its attendant repercussions on both humanity and the environment. Central to this endeavor are the formulation, content, and execution of the treaty itself, which demand careful consideration. While recognizing that a global plastics treaty is not a panacea, it serves as a mechanism for enhancing plastics governance and elevating global ambitions towards achieving zero plastic pollution by 2040. Adopting a life cycle approach to plastic management allows for a nuanced understanding of possible trade-offs between environmental impact and economic growth, guiding the selection of optimal solutions with socio-economic implications in mind. By embracing a comprehensive strategy that integrates legislative measures and technological innovations, we can substantially reduce the influx of marine plastic litter at its sources, safeguarding the oceans for future generations.

Temporal dynamics of climate change exposure and opportunities for global marine biodiversity.

Climate change is exposing marine species to unsuitable temperatures while also creating new thermally suitable habitats of varying persistence. However, understanding how these different dynamics will unfold over time remains limited. We use yearly sea surface temperature projections to estimate temporal dynamics of thermal exposure (when temperature exceeds realised species' thermal limits) and opportunity (when temperature at a previously unsuitable site becomes suitable) for 21,696 marine species globally until 2100. Thermal opportunities are projected to arise earlier and accumulate gradually, especially in temperate and polar regions. Thermal exposure increases later and occurs more abruptly, mainly in the tropics. Assemblages tend to show either high exposure or high opportunity, but seldom both. Strong emissions reductions reduce exposure around 100-fold whereas reductions in opportunities are halved. Globally, opportunities are projected to emerge faster than exposure until mid-century when exposure increases more rapidly under a high emissions scenario. Moreover, across emissions and dispersal scenarios, 76%-97% of opportunities are projected to persist until 2100. These results indicate thermal opportunities could be a major source of marine biodiversity change, especially in the near- and mid-term. Our work provides a framework for predicting where and when thermal changes will occur to guide monitoring efforts.

The Central Paratethys Sea-rise and demise of a Miocene European marine biodiversity hotspot.

The Miocene Climate Optimum (MCO, ~ 17-14 Ma) was a time of extraordinary marine biodiversity in the Circum-Mediterranean Region. This boom is best recorded in the deposits of the vanished Central Paratethys Sea, which covered large parts of central to southeastern Europe. This sea harbored an extraordinary tropical to subtropical biotic diversity. Here, we present a georeferenced dataset of 859 gastropod species and discuss geodynamics and climate as the main drivers to explain the changes in diversity. The tectonic reorganization around the Early/Middle Miocene boundary resulted in the formation of an archipelago-like landscape and favorable conditions of the MCO allowed the establishment of coral reefs. Both factors increased habitat heterogeneity, which boosted species richness. The subsequent cooling during the Middle Miocene Climate Transition (~ 14-13 Ma) caused a drastic decline in biodiversity of about 67%. Among the most severely hit groups were corallivorous gastropods, reflecting the loss of coral reefs. Deep-water faunas experienced a loss by 57% of the species due to changing patterns in circulation. The low sea level led to a biogeographic fragmentation reflected in higher turnover rates. The largest turnover occurred with the onset of the Sarmatian when bottom water dysoxia eradicated the deep-water fauna whilst surface waters-dwelling planktotrophic species underwent a crisis.

A climate vulnerability assessment of the fish community in the Western Baltic Sea.

Marine fisheries are increasingly impacted by climate change, affecting species distribution and productivity, and necessitating urgent adaptation efforts. Climate vulnerability assessments (CVA), integrating expert knowledge, are vital for identifying species that could thrive or suffer under changing environmental conditions. This study presents a first CVA for the Western Baltic Sea's fish community, a crucial fishing area for Denmark and Germany. Characterized by a unique mix of marine, brackish, and freshwater species, this coastal ecosystem faces significant changes due to the combined effects of overfishing, eutrophication and climate change. Our CVA involved a qualitative expert scoring of 22 fish species, assessing their sensitivity and exposure to climate change. Our study revealed a dichotomy in climate change vulnerability within the fish community of the Western Baltic Sea because traditional fishing targets cod and herring as well as other species with complex life histories are considered to face increased risks, whereas invasive or better adaptable species might thrive under changing conditions. Our findings hence demonstrate the complex interplay between life-history traits and climate change vulnerability in marine fish communities. Eventually, our study provides critical knowledge for the urgent development of tailored adaptation efforts addressing existing but especially future effects of climate change on fish and fisheries in the Western Baltic Sea, to navigate this endangered fisheries systems into a sustainable future.

Nutrient sources, phytoplankton blooms, and hypoxia along the Chinese coast in the East China Sea: Insight from 2014.

Phytoplankton blooms are common along the Chinese coast in the East China Sea, driven by various nutrient sources including river discharge, bottom water regeneration, and Kuroshio subsurface water intrusion. A notable 2014 summer bloom off the Zhejiang coast, exhibiting a Chl a concentration of 20.1 µg L-1, was significantly influenced by Changjiang River discharge, and high nutrient concentrations are often observed in the region's surface water. During blooms, primary production peaks at 1686.3 mg C m-3 d-1, indicating substantial CO2 absorption, with surface water fCO2 declining to 299.5 µatm, closely linked to plankton activities. Hypoxia often coincides with these frequent bloom occurrences, implicating marine-derived organic matter decomposition as a pivotal factor. Elevated particulate organic carbon concentrations further support this assumption, alongside increased nutrient levels, fCO2, and low pH in hypoxic waters. These findings underscore the intricate interplay between phytoplankton, nutrient cycling, and hypoxia formation, essential for effective coastal ecosystem management.

Spatiotemporal variation of sterols in sediment as markers of primary production and ocean sewage dumping in the southwestern East Sea (Japan Sea).

The sedimentation of organic carbon in the Ulleung Basin, in the southwestern East Sea (Japan Sea) was investigated using radiocarbon and sterols. The accumulation rates of organic carbon and the contents of brassicasterol and dinosterol were higher on the slope than in the central basin, reflecting the surface water productivity, whereas cholesterol showed similar or higher contents in the central basin. The coprostanol concentration in surface sediments reflected the dispersion of sewage dumped in this region. The vertical distribution showed that the coprostanol concentration was the highest in the top 5-cm layer near the Korea Strait, close to one of the two dumping sites. A high coprostanol concentration was also found near the coast further north, where the content peaked at ∼10 cm depth. The vertical distribution of coprostanol helped to estimate the sediment accumulation rate at sites where radiocarbon gradient was too small or the values were too variable.

Mixotrophic growth of a ubiquitous marine diatom.

Diatoms are major players in the global carbon cycle, and their metabolism is affected by ocean conditions. Understanding the impact of changing inorganic nutrients in the oceans on diatoms is crucial, given the changes in global carbon dioxide levels. Here, we present a genome-scale metabolic model (iMK1961) for Cylindrotheca closterium, an in silico resource to understand uncharacterized metabolic functions in this ubiquitous diatom. iMK1961 represents the largest diatom metabolic model to date, comprising 1961 open reading frames and 6718 reactions. With iMK1961, we identified the metabolic response signature to cope with drastic changes in growth conditions. Comparing model predictions with Tara Oceans transcriptomics data unraveled C. closterium's metabolism in situ. Unexpectedly, the diatom only grows photoautotrophically in 21% of the sunlit ocean samples, while the majority of the samples indicate a mixotrophic (71%) or, in some cases, even a heterotrophic (8%) lifestyle in the light. Our findings highlight C. closterium's metabolic flexibility and its potential role in global carbon cycling.

Cod otoliths document accelerating climate impacts in the Baltic Sea.

Anthropogenic deoxygenation of the Baltic Sea caused major declines in demersal and benthic habitat quality with consequent impacts on biodiversity and ecosystem services. Using Baltic cod otolith chemical proxies of hypoxia, salinity, and fish metabolic status and growth, we tracked changes from baseline conditions in the late Neolithic (4500 BP) and early twentieth century to the present, in order to understand how recent, accelerating climate change has affected this key species. Otolith hypoxia proxies (Mn:Mg) increased with expanding anoxic water volumes, but decreased with increasing salinity indexed by otolith Sr:Ca. Metabolic status proxied by otolith Mg:Ca and reconstructed growth were positively related to dissolved oxygen percent saturation, with particularly severe declines since 2010. This long-term record of otolith indicators provides further evidence of a profound state change in oxygen for the worse, in one of the world's largest inland seas. Spreading hypoxia due to climate warming will likely impair fish populations globally and evidence can be tracked with otolith chemical biomarkers.

Ecological associations distribution modelling of marine plankton at a global scale.

Marine plankton communities form intricate networks of interacting organisms at the base of the food chain, and play a central role in regulating ocean biogeochemical cycles and climate. However, predicting plankton community shifts in response to climate change remains challenging. While species distribution models are valuable tools for predicting changes in species biogeography under climate change scenarios, they generally overlook the key role of biotic interactions, which can significantly shape ecological processes and ecosystem responses. Here, we introduce a novel statistical framework, association distribution modelling (ADM), designed to model and predict ecological associations distribution in space and time. Applied on a Tara Oceans genome-resolved metagenomics dataset, the present-day biogeography of ADM-inferred marine plankton associations revealed four major biogeographic biomes organized along a latitudinal gradient. We predicted the evolution of these biome-specific communities in response to a climate change scenario, highlighting differential responses to environmental change. Finally, we explored the functional potential of impacted plankton communities, focusing on carbon fixation, outlining the predicted evolution of its geographical distribution and implications for ecosystem function.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

Spatial food webs in the Barents Sea: atlantification and the reorganization of the trophic structure.

Climate change affects ecosystems at several levels: by altering the spatial distribution of individual species, by locally rewiring interspecific interactions, and by reorganizing trophic networks at larger scales. The dynamics of marine food webs are becoming more and more sensitive to spatial processes and connections in the seascape. As a case study, we study the atlantification of the Barents Sea: we compare spatio-temporal subsystems at three levels: the identity of key organisms, critically important interactions and the entire food web. Network analysis offers quantitative measurements, including centrality indices, trophic similarity indices, a topological measure of interaction asymmetry and network-level measures. We found that atlantification alters the identity of key species (boreal demersals becoming hubs), results in strongly asymmetric interactions (dominated by haddock), changes the dominant regulation regime (from bottom-up to wasp-waist control) and makes the food web less modular. Since the results of food web analysis may be quite sensitive to network construction, the aggregation of food web data was explicitly studied to increase the robustness of food web analysis. We found that an alternative, mathematical aggregation algorithm better preserves some network properties (e.g. density) of the original, unaggregated network than the biologically inspired aggregation into functional groups. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

Global expansion of marine protected areas and the redistribution of fishing effort.

The expansion of marine protected areas (MPAs) is a core focus of global conservation efforts, with the "30x30" initiative to protect 30% of the ocean by 2030 serving as a prominent example of this trend. We consider a series of proposed MPA network expansions of various sizes, and we forecast the impact this increase in protection would have on global patterns of fishing effort. We do so by building a predictive machine learning model trained on a global dataset of satellite-based fishing vessel monitoring data, current MPA locations, and spatiotemporal environmental, geographic, political, and economic features. We then use this model to predict future fishing effort under various MPA expansion scenarios compared to a business-as-usual counterfactual scenario that includes no new MPAs. The difference between these scenarios represents the predicted change in fishing effort associated with MPA expansion. We find that regardless of the MPA network objectives or size, fishing effort would decrease inside the MPAs, though by much less than 100%. Moreover, we find that the reduction in fishing effort inside MPAs does not simply redistribute outside-rather, fishing effort outside MPAs would also decline. The overall magnitude of the predicted decrease in global fishing effort principally depends on where networks are placed in relation to existing fishing effort. MPA expansion will lead to a global redistribution of fishing effort that should be accounted for in network design, implementation, and impact evaluation.

[Profiles of Antibiotic Resistance Genes in the Coastal Aquatic Environment of Xiamen City].

The coastal areas and the adjacent islands are the hotspots of human economic and social activities, including urbanization, industrialization, and agricultural practices, which have profound impacts on the ecological environment of the coastal environment. Antibiotic resistance genes （ARGs）, as emerging contaminants, have become hot topics in water ecological security and public concern. However, the profiles of antibiotic resistome in the costal water remain largely unknown, impeding resistome risk assessment associated with coastal environments. In this study, the high-throughput quantitative PCR technique was used to investigate the abundance and distribution of ARGs in the coastal environment of Xiamen City. Combined with the 16S rDNA gene amplicon sequencing method, the structure and composition of the microbial community in a water environment were investigated, and the influencing factors and associated mechanism of ARGs in seawater were deeply explained. The results of this study showed that a total of 187 ARGs were detected in the coastal water environment, and the abundance level was up to 1.29×1010 copies·L-1. Multidrug resistance, aminoglycosides, and ß lactamase resistance genes were the three main classes of antibiotic resistance genes in the water environment of the Xiamen coastal zone. On the whole, the profile of ARGs was of high abundance, great diversity, and common co-existence, and the coastal water environment was an important hot area and reservoir for antibiotic resistance genes. Twenty-two microbes, including Nautella, Candidatus, Tenacibaculum, Rubripirellula, and Woeseia, were potential carriers of the corresponding 16 antibiotic resistance genes. The mobile genetic elements （MGEs） and microbial community structure accounted for 93.9% of the variation in environmental resistance genes in water. Therefore, microbial community and its mobile genetic elements were the most important driving forces for the occurrence and evolution of ARGs in coastal waters. Based on the results, it is implied that the environmental antibiotic resistance genes in the waters near Xiamen Island have potential risks to water ecological security and human health and highlight the necessity for comprehensive surveillance of ARGs associated with microbial contamination in the coastal aquatic environment.

Streamlining large-scale oceanic biomonitoring using passive eDNA samplers integrated into vessel's continuous pump underway seawater systems.

Passive samplers are enabling the scaling of environmental DNA (eDNA) biomonitoring in our oceans, by circumventing the time-consuming process of water filtration. Designing a novel passive sampler that does not require extensive sample handling time and can be connected to ocean-going vessels without impeding normal underway activities has potential to rapidly upscale global biomonitoring efforts onboard the world's oceanic fleet. Here, we demonstrate the utility of an artificial sponge sampler connected to the continuous pump underway seawater system as a means to enable oceanic biomonitoring. We compared the performance of this passive sampling protocol with standard water filtration at six locations during a research voyage from New Zealand to Antarctica in early 2023. Eukaryote metabarcoding of the mitochondrial COI gene revealed no significant difference in phylogenetic α-diversity between sampling methods and both methods delineated a progressive reduction in number of Zero-Radius Operational Taxonomic Units (ZOTUs) with increased latitudes. While both sampling methods revealed comparable trends in geographical community compositions, distinct clusters were identified for passive samplers and water filtration at each location. Additionally, greater variability between replicates was observed for passive samplers, resulting in an increased estimated level of replication needed to recover 90 % of the biodiversity. Furthermore, traditional water filtration failed to detect three phyla observed by passive samplers and extrapolation analysis estimated passive samplers recover a larger number of ZOTUs compared to water filtration for all six locations. Our results demonstrate the potential of this passive eDNA sampler protocol and highlight areas where this emerging technology could be improved, thereby enabling large-scale offshore marine eDNA biomonitoring by leveraging the world's oceanic fleet without interfering with onboard activities.

Anthropocene 129I Record in the Yellow Sea Sediments and Its Indication for River-Delivered Radioactive Pollution to Marginal Seas.

As the number of coastal nuclear facilities rapidly increases and the wastewater from the Fukushima Nuclear Plant has been discharged into the Pacific Ocean, the nuclear environmental safety of China's marginal seas is gaining increased attention along with the heightened potential risk of nuclear accidents. However, insufficient work limits our understanding of the impact of human nuclear activities on the Yellow Sea (YS) and the assessment of their environmental process. This study first reports the 129I and 127I records of posthuman nuclear activities in the two YS sediments. Source identification of anthropogenic 129I reveals that, in addition to the gaseous 129I release and re-emission of oceanic 129I discharged from the European Nuclear Fuel Reprocessing Plants (NFRPs), the Chinese nuclear weapons testing fallout along with the global fallout is an additional 129I input for the continental shelf of the YS. The 129I/127I atomic ratios in the North YS (NYS) sediment are significantly higher than those in the other adjacent coastal areas, attributed to the significant riverine input of particulate 129I by the Yellow River. Furthermore, we found a remarkable 129I latitudinal disparity in the sediments than those in the seawaters in the various China seas, revealing that sediments in China's marginal seas already received a huge anthropogenic 129I from terrigenous sources via rivers and thus became a significant sink of anthropogenic 129I. This study broadens an insight into the potential impacts of terrigenous anthropogenic pollution on the Chinese coastal marine radioactive ecosystem.