Deep-water longline fishing has reduced impact on Vulnerable Marine Ecosystems

eDNA metabarcoding shows highly diverse but distinct shallow, mid-water, and deep-water eukaryotic communities within a marine biodiversity hotspot

As the impact of human activities continues to move beyond shallow coastal waters into deeper ocean layers, it is fundamental to describe how diverse and distinct the eukaryotic assemblages from the deep layers are compared to shallow ecosystems. Environmental DNA (eDNA) metabarcoding has emerged as a molecular tool that can overcome many logistical barriers in exploring remote deep ocean areas. We analyzed shallow water samples (<30 m) collected via SCUBA diving and adjacent deeper samples (mid-water 30-150 m, deep-water >200 m) obtained with Niskin samplers within 16 locations in a recognized hotspot of marine biodiversity (Gulf of California, Mexico). We sequenced an eDNA metabarcoding library targeting a fragment of the COI gene of eukaryotes. We demonstrated that the diversity of operational taxonomic units (OTUs) did not peak at shallow coastal regions and that the mid-water and deep-water benthic and pelagic samples had similar levels of biodiversity compared to shallow sites, but detected a significant vertical zonation between shallow and deeper habitats. Our results suggest that the deep refugia hypothesis, which posits that deep environments protect biodiversity during environmental changes, enabling species to survive and repopulate shallower regions, is not supported for most taxa and only applies to about a third (34.9%) of the 5,495 OTUs identified that were shared between the shallow and deeper layers. In comparison, the rest of the taxa were exclusive to either shallow (30.8%) or deeper zones (34.28%). The observation that mid-water and deep-water benthic and pelagic communities were as rich but quite distinct as shallow communities supports extending spatial management and conservation tools to deeper habitats to include a significant fraction of unique phylogenetic and functional diversity.

Tracking bottom-fishing activities in protected vulnerable marine ecosystem areas and below 800-m depth in European Union waters

Numerous studies have highlighted bottom-contact fishing gears as the primary threat to vulnerable marine ecosystems (VMEs). In November 2022, the European Commission closed 87 VME protection polygons to bottom fishing in European waters. Using public automatic identification system (AIS) data, we found an 81% decrease in bottom-contact fishing effort within these areas in the year following the closures. However, approximately 3500 hours of bottom-contact fishing persisted within the closures. We also quantified up to 17,600 hours of bottom-contact fishing in unprotected areas where VMEs are known or likely to occur. Last, our analysis revealed ongoing bottom trawling below 800 meters in European waters totaling 19,200 hours over 2 years. These findings underscore the urgent need for states to enhance surveillance and monitoring of their fleets to ensure effective fisheries management.

Assessment of seabed litter at Concepción Seamount (Canary island) using a remotely operated towed vehicle

The seafloor is recognised as a major sink for marine litter. However, studies conducted in this compartment addressing marine litter densities and its interactions with fauna are scarce, mainly due to sampling constraints. In this paper, we assess marine litter density, composition and interactions with marine communities and evaluate its relationship with fishing activities at the "Banco de la Concepción" seamount (Canary Islands, Spain). We took advantage of underwater video records taken with a Remotely Operated Towed Vehicle in the framework of the LIFE IP INTEMARES project. A total of 56 video transects were analysed covering about 9 km with 19 h of video recording. Transects were categorised as high, low, and null fishing effort based on the Vessel Monitoring System (VMS) positional data registered between 2009 and 2017. Litter items were recorded in 70% of the transects with a mean density of 2122 (±2464) items km-2. There were significant differences in litter densities over the three levels of fishing pressure, with a density decrease from stations of high to stations of null fishing pressure. Regarding categories, plastic was by far the most abundant category found (83.1%), mainly consisting of fishing lines, both monofilaments and entangled longlines. The study of the interactions of marine litter with fauna showed that less than 20% of the items presented an interaction with benthic organisms either by causing or not a visible impact. The sponge Asconema setubalense accounted for more than half (57.4%) of all interactions, but only 5% of all A. setubalense specimens showed physical damage.

Predicting the distribution and abundance of abandoned, lost or discarded fishing gear (ALDFG) in the deep sea of the Azores (North Atlantic)

Abandoned, lost, or discarded fishing gear (ALDFG), represents a significant percentage of the global plastic pollution, currently considered one of the major sources from sea-based activities. However, there is still limited understanding of the quantities of ALDFG present on the seafloor and their impacts. In this study, data on the presence of ALDFG was obtained from a large archive of seafloor video footage (351 dives) collected by different imaging platforms in the Azores region over 15 years (2006-2020). Most ALDFG items observed in the images relate to the local bottom longline fishery operating in the region, and include longlines but also anchors, weights, cables and buoys. A generalized additive mixed model (GAMM) was used to predict the distribution and abundance of ALDFG over the seafloor within the limits of the Azores Exclusive Economic Zone (EEZ) using a suite of environmental and anthropogenic variables. We estimated an average of 113 ± 310 items km-2 (597 ± 756 per km-2 above 1000 m depth), which could imply that over 20 million ALDFG items are present on the deep seafloor of the Azores EEZ. The resulting model identified potential hotspots of ALDFG along the seabed, some of them located over sensitive benthic habitats, such as specific seamounts. In addition, the interactions between ALDFG and benthic organisms were also analysed. Numerous entanglements were observed with several species of large anthozoans and sponges. The use of predictive distribution modelling for ALDFG should be regarded as a useful tool to support ecosystem-based management, which can provide indirect information about fishing pressure and allow the identification of potential high-risk areas. Additional knowledge about the sources, amounts, fates and impacts of ALDFG will be key to address the global issue of plastic pollution and the effects of fishing on marine ecosystems.

Coexistence of megabenthic assemblages and artisanal fishers: The case of Cap de Creus Marine Protected Area (North-Western Mediterranean Sea)

Artisanal fisheries, although considered less harmful, can still endanger marine ecosystems, especially in areas with long-standing tradition. In Cap de Creus, where artisanal fisheries has likely occurred for centuries, the status of benthic communities in fishing grounds was poorly understood. Through collaboration with local fishers, the benthic assemblages in three artisanal fishing grounds within Cap de Creus Marine Protected Area (MPA) were studied. Using video transects recorded by a remotely operated vehicle (ROV), the diversity and distribution of species were analysed in relation to substrate type, slope, and depth. The study also assessed the impacts on these communities by examining marine litter, lost fishing gear, and the condition of gorgonian populations. The findings identified three megabenthic assemblages and revealed higher fishing pressure and impact in the Maça d'Oros area, likely due to multiple fishing guilds converging. However, the study demonstrated lower impact in MPAs compared to unprotected Mediterranean areas, highlighting the importance of coastal management.

Towards a scientific community consensus on designating Vulnerable Marine Ecosystems from imagery

Management of deep-sea fisheries in areas beyond national jurisdiction by Regional Fisheries Management Organizations/Arrangements (RFMO/As) requires identification of areas with Vulnerable Marine Ecosystems (VMEs). Currently, fisheries data, including trawl and longline bycatch data, are used by many RFMO/As to inform the identification of VMEs. However, the collection of such data creates impacts and there is a need to collect non-invasive data for VME identification and monitoring purposes. Imagery data from scientific surveys satisfies this requirement, but there currently is no established framework for identifying VMEs from images. Thus, the goal of this study was to bring together a large international team to determine current VME assessment protocols and establish preliminary global consensus guidelines for identifying VMEs from images. An initial assessment showed a lack of consistency among RFMO/A regions regarding what is considered a VME indicator taxon, and hence variability in how VMEs might be defined. In certain cases, experts agreed that a VME could be identified from a single image, most often in areas of scleractinian reefs, dense octocoral gardens, multiple VME species' co-occurrence, and chemosynthetic ecosystems. A decision flow chart is presented that gives practical interpretation of the FAO criteria for single images. To further evaluate steps of the flow chart related to density, data were compiled to assess whether scientists perceived similar density thresholds across regions. The range of observed densities and the density values considered to be VMEs varied considerably by taxon, but in many cases, there was a statistical difference in what experts considered to be a VME compared to images not considered a VME. Further work is required to develop an areal extent index, to include a measure of confidence, and to increase our understanding of what levels of density and diversity correspond to key ecosystem functions for VME indicator taxa. Based on our results, the following recommendations are made: 1. There is a need to establish a global consensus on which taxa are VME indicators. 2. RFMO/As should consider adopting guidelines that use imagery surveys as an alternative (or complement) to using bycatch and trawl surveys for designating VMEs. 3. Imagery surveys should also be included in Impact Assessments. And 4. All industries that impact the seafloor, not just fisheries, should use imagery surveys to detect and identify VMEs.

Dense cold-water coral garden of Paragorgia johnsoni suggests the importance of the Mid-Atlantic Ridge for deep-sea biodiversity

Mid-ocean ridges generate a myriad of physical oceanographic processes that favor the supply of food and nutrients to suspension- and filter-feeding organisms, such as cold-water corals and deep-sea sponges. However, the pioneering work conducted along the Mid-Atlantic Ridge failed to report the presence of large and dense living coral reefs, coral gardens, or sponge aggregations. Here, we describe the densest, near-natural, and novel octocoral garden composed of large red and white colonies of Paragorgia johnsoni Gray, 1862 discovered at 545-595 m depth on the slopes of the Mid-Atlantic Ridge, in the Azores region. This newly discovered octocoral garden is a good candidate for protection since it fits many of the FAO criteria that define what constitutes a Vulnerable Marine Ecosystem. The observations described here corroborate the existence of a close relationship between the octocoral structure and the ambient currents on ridge-like topographies, providing new insights into the functioning of mid-ocean ridges' ecosystems. The ubiquitous presence of biogenic and geological topographies associated with mid-ocean ridges, which could act as climate refugia, suggests their global importance for deep-sea biodiversity. A better understanding of the processes involved is, therefore, required. Our observations may inspire future deep-sea research initiatives to narrow existing knowledge gaps of biophysical connections with benthic fauna at small spatial scales along mid-ocean ridges.

Seafloor litter sorting in different domains of Cap de Creus continental shelf and submarine canyon (NW Mediterranean Sea)

We analyzed litter occurrence in 68 underwater video transects performed on the middle/outer continental shelf and submarine canyon off Cap de Creus (NW Mediterranean), an area recently declared Site of Community Importance (SCI). Low densities of urban litter were registered on the shelf (7.2 items ha^-1), increasing in abundance towards the deepest part of the submarine canyon, with 188 items ha^-1 below 1000 m depth. We hypothesize that the strong bottom currents that recurrently affect this area efficiently move litter objects from the shelf towards the deep. Of all litter items, approximately 50% had a fishing-related origin, mostly longlines entangled on rocks in the canyon head and discarded trawl nets in deeper areas. Over 10% of cold-water colonies observed had longlines entangled, indicating the harmful effects of such practices over benthic habitats. These results should be considered when designing mitigation measures to reduce litter pollution in Cap de Creus SCI.

Ecological variables for developing a global deep-ocean monitoring and conservation strategy

The deep sea (>200 m depth) encompasses >95% of the world's ocean volume and represents the largest and least explored biome on Earth (<0.0001% of ocean surface), yet is increasingly under threat from multiple direct and indirect anthropogenic pressures. Our ability to preserve both benthic and pelagic deep-sea ecosystems depends upon effective ecosystem-based management strategies and monitoring based on widely agreed deep-sea ecological variables. Here, we identify a set of deep-sea essential ecological variables among five scientific areas of the deep ocean: (1) biodiversity; (2) ecosystem functions; (3) impacts and risk assessment; (4) climate change, adaptation and evolution; and (5) ecosystem conservation. Conducting an expert elicitation (1,155 deep-sea scientists consulted and 112 respondents), our analysis indicates a wide consensus amongst deep-sea experts that monitoring should prioritize large organisms (that is, macro- and megafauna) living in deep waters and in benthic habitats, whereas monitoring of ecosystem functioning should focus on trophic structure and biomass production. Habitat degradation and recovery rates are identified as crucial features for monitoring deep-sea ecosystem health, while global climate change will likely shift bathymetric distributions and cause local extinction in deep-sea species. Finally, deep-sea conservation efforts should focus primarily on vulnerable marine ecosystems and habitat-forming species. Deep-sea observation efforts that prioritize these variables will help to support the implementation of effective management strategies on a global scale.

A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem.

Fishing lines and fish hooks as neglected marine litter: first data on chemical composition, densities, and biological entrapment from a Mediterranean beach

We reported first data on the densities and chemical composition of fishing lines and fish hooks deposited on a Mediterranean beach. On a sampling area of 1.5 ha, we removed a total of 185,028 cm of fishing lines (density 12.34 cm/m²) and 33 hooks (density 22 units/ha). Totally, 637.62 g (42.5 mg/m²) of fishing lines were collected. We sampled 120 items entangled belongings to 7 animal taxa (density 6.49 items/100 m of fishing lines). We also observed a not quantifiable number of egagropiles (Posidonia oceanica spheroids), Rhodophyceae (Halymenia sp.) and segments of reeds of Phragmites communis, trapped in the fishing lines. Fourier transform infrared (FTIR) spectroscopy was used in order to identify the chemical composition of the fishing lines: 92% was made of nylon while 8.0% was determined as fluorocarbon based polymers (polyvinylidene fluoride). Because of their subtlety and reduced size, sandy beach cleaning operations should include at least two consecutive removal samplings: indeed, a part of this litter (12.14%) is not removed in the first sampling. The unexpected high density of fishing lines suggests specific management actions aimed to periodically remove this neglected anthropogenic litter.

Associations between fish and cold-water coral habitats on the Icelandic shelf

The association between fish assemblages and cold-water coral habitats was evaluated based on analysis of longline catches in the Lónsdjúp trough, SE-Iceland. In 2009 and 2010, longlines were set in locations with varying coral cover within the trough. The study site is characterised by a depression (50-100 m deep), intersected by several ridges. Colonies of the cold-water coral Lophelia pertusa and other coral species were mainly found on the ridges. Among the fifteen fish species recorded, tusk (Brosme brosme) contributed ∼80% to the total fish abundance in both surveys and their catch per unit effort was twofold greater on the ridges than in adjacent flat areas. Multivariate analyses showed differences between the structure of fish communities on and off the ridges. Constrained redundancy ordinations followed by variance partitioning revealed that the structure of the fish community varied with seabed complexity, cold-water coral coverage and geographical position. It was not possible to separate between the effects of seabed complexity and coral cover, as these were strongly correlated.

Species distribution models of two critically endangered deep-sea octocorals reveal fishing impacts on vulnerable marine ecosystems in central Mediterranean Sea

Deep-sea coral assemblages are key components of marine ecosystems that generate habitats for fish and invertebrate communities and act as marine biodiversity hot spots. Because of their life history traits, deep-sea corals are highly vulnerable to human impacts such as fishing. They are an indicator of vulnerable marine ecosystems (VMEs), therefore their conservation is essential to preserve marine biodiversity. In the Mediterranean Sea deep-sea coral habitats are associated with commercially important crustaceans, consequently their abundance has dramatically declined due to the effects of trawling. Marine spatial planning is required to ensure that the conservation of these habitats is achieved. Species distribution models were used to investigate the distribution of two critically endangered octocorals (Funiculina quadrangularis and Isidella elongata) in the central Mediterranean as a function of environmental and fisheries variables. Results show that both species exhibit species-specific habitat preferences and spatial patterns in response to environmental variables, but the impact of trawling on their distribution differed. In particular F. quadrangularis can overlap with fishing activities, whereas I. elongata occurs exclusively where fishing is low or absent. This study represents the first attempt to identify key areas for the protection of soft and compact mud VMEs in the central Mediterranean Sea.

Marine litter on the seafloor of the Faial-Pico Passage, Azores Archipelago

Plastic pollution in the marine environment attracts much attention from both researchers and the general public. Plastic items and other debris are commonly observed everywhere in the ocean, from the surface down to the deep ocean floor. In this study, we analysed 45.2km of video footage, collected during 56 transects surveying the seafloor of the Faial-Pico Passage in order to quantify the abundance of marine litter and its interactions with benthic fauna. The footage was collected by a Remotely Operated Vehicle (ROV) and a manned submersible at depths ranging between 40 and 525m. The mean litter density in the passage was 0.26±0.03 items·100m^-1 (±SE) and was significantly higher between 151 and 250m compared to other depth strata. Overall, derelict fishing gear, mostly made of plastic, were the most common objects found on the seafloor, representing 64% of all items. Although we observed few evidence of direct deleterious effects by the litter, interactions with fauna were observed in more than half of the items. This study makes an important contribution in quantifying the abundance of marine litter on the seafloor of the Azores. The location of the Faial-Pico Passage, close to shore, makes it an appropriate site for long-term monitoring of litter on the seafloor and evaluate the efficiency of upcoming public policies aimed at reducing litter input into the oceans.

Marine litter in the upper São Vicente submarine canyon (SW Portugal): Abundance, distribution, composition and fauna interactions

Marine litter has become a worldwide environmental problem, tainting all ocean habitats. The abundance, distribution and composition of litter and its interactions with fauna were evaluated in the upper S. Vicente canyon using video images from 3 remote operated vehicle exploratory dives. Litter was present in all dives and the abundance was as high as 3.31 items100m(-1). Mean abundance of litter over rock bottom was higher than on soft substrate. Mean litter abundance was slightly higher than reported for other canyons on the Portuguese margin, but lower in comparison to more urbanized coastal areas of the world. Lost fishing gear was the prevalent type of litter, indicating that the majority of litter originates from maritime sources, mainly fishing activity. Physical contact with sessile fauna and entanglement of specimens were the major impacts of lost fishing gear. Based on the importance of this region for the local fishermen, litter abundance is expected to increase.