The diet of toothfish species Dissostichus eleginoides and Dissostichus mawsoni with overlapping distributions

De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome

BACKGROUND

Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited.

RESULTS

A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome.

CONCLUSIONS

We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.

Trophodynamics of the Antarctic toothfish (Dissostichus mawsoni) in the Antarctic Peninsula: Ontogenetic changes in diet composition and prey fatty acid profiles

The Antarctic toothfish (Dissostichus mawsoni) is the largest notothenioid species in the Southern Ocean, playing a keystone role in the trophic web as a food source for marine mammals and a top predator in deep-sea ecosystems. Most ecological knowledge on this species relies on samples from areas where direct fishing is allowed, whereas in areas closed to fishing, such as the Antarctic Peninsula (AP), there are still key ecological gaps to ensure effective conservation, especially regarding our understanding of its trophic relationships within the ecosystem. Here, we present the first comprehensive study of the feeding behavior of Antarctic toothfish caught in the northern tip of the AP, during two consecutive fishing seasons (2019/20 and 2020/21). Stomach content was analyzed according to size-classes, sex and season. Macroscopic morphological analysis was used to identify prey, whereas DNA analysis was used in highly digested prey items. Fatty acid analysis was conducted to determine the prey's nutritional composition. The diet mainly consisted of Macrouridae, Cephalopoda, Anotopteridae, and Channichthyidae. Other prey items found were crustaceans and penguin remains; however, these were rare in terms of their presence in stomach samples. Sex had no effect on diet, whereas size-class and fishing season influenced prey composition. From 27 fatty acid profiles identified, we observed two different prey groups of fishes (integrated by families Anotopteridae, Macrouridae and Channichthyidae) and cephalopods. Our results revealed a narrow range of prey items typical of a generalist predator, which probably consumes the most abundant prey. Understanding the diet and trophic relationships of Antarctic toothfish is critical for a better comprehension of its role in the benthic-demersal ecosystem of the AP, key for ecosystemic fisheries management, and relevant for understanding and predicting the effect of climate change on this species.

Antarctic toothfish Dissostichus mawsoni as a bioindicator of trace and rare earth elements in the Southern Ocean

The Antarctic toothfish Dissostichus mawsoni is a Southern Ocean long-lived top predator which is regularly captured on an annual fishery operating in the region. By its biological and ecological characteristics, it is a potential bioindicator for the concentrations of trace and rare earth elements in the Antarctic. As these elements are mainly transferred through the diet and a deficiency or excess of these elements can lead to diverse health problems, it is important to measure their concentrations on the organisms. This study provides, for the first time, the concentration of 27 trace (major essential, minor essential and non-essential) and rare earth elements in the muscle of D. mawsoni captured in three areas of the Amundsen and Dumont D'Urville Seas (Antarctica). Major essential elements had the highest concentrations, with potassium (K) as the most concentrated, and rare earth elements the lowest. Significant differences between areas were found for most of the studied elements. No bioaccumulation nor biomagnification potential was found for the studied elements, with several elements decreasing concentrations towards larger individuals. Decreasing trends are related with the different habitats occupied by D. mawsoni through their life, suggesting that elements' concentrations in the water is determinant for the concentrations in this top predator, and/or there is a dilution effect as the fish grows. Our results also support that Se presents a detoxification potential for Hg in D. mawsoni, but only when Hg concentrations are higher to unhealthy levels. This study supports D. mawsoni as a potential bioindicator for the concentrations of the different trace and rare earth elements in the Southern Ocean, though only when comparing individuals of similar size/age, but also to evaluate annual changes on their concentrations. Furthermore, D. mawsoni can be a good source of major essential elements to humans with concentrations of major essential elements above some of other marine fish worldwide.

Ice matters: Life-history strategies of two Antarctic seals dictate climate change eventualities in the Weddell Sea

The impacts of climate change in Antarctica and the Southern Ocean are not uniform and ice-obligate species with dissimilar life-history characteristics will likely respond differently to their changing ecosystems. We use a unique data set of Weddell Leptonychotes weddellii and crabeater seals' (CESs) Lobodon carcinophaga breeding season distribution in the Weddell Sea, determined from satellite imagery. We contrast the theoretical climate impacts on both ice-obligate predators who differ in life-history characteristics: CESs are highly specialized Antarctic krill Euphausia superba predators and breed in the seasonal pack ice; Weddell seals (WESs) are generalist predators and breed on comparatively stable fast ice. We used presence-absence data and a suite of remotely sensed environmental variables to build habitat models. Each of the environmental predictors is multiplied by a 'climate change score' based on known responses to climate change to create a 'change importance product'. Results show CESs are more sensitive to climate change than WESs. Crabeater seals prefer to breed close to krill, and the compounding effects of changing sea ice concentrations and sea surface temperatures, the proximity to krill and abundance of stable breeding ice, can influence their post-breeding foraging success and ultimately their future breeding success. But in contrast to the Ross Sea, here WESs prefer to breed closer to larger colonies of emperor penguins (Aptenodytes forsteri). This suggests that the Weddell Sea may currently be prey-abundant, allowing the only two air-breathing Antarctic silverfish predators (Pleuragramma antarctica) (WESs and emperor penguins) to breed closer to each other. This is the first basin-scale, region-specific comparison of breeding season habitat in these two key Antarctic predators based on real-world data to compare climate change responses. This work shows that broad-brush, basin-scale approaches to understanding species-specific responses to climate change are not always appropriate, and regional models are needed-especially when designing marine protected areas.

Productivity and Change in Fish and Squid in the Southern Ocean

Southern Ocean ecosystems are globally important and vulnerable to global drivers of change, yet they remain challenging to study. Fish and squid make up a significant portion of the biomass within the Southern Ocean, filling key roles in food webs from forage to mid-trophic species and top predators. They comprise a diverse array of species uniquely adapted to the extreme habitats of the region. Adaptations such as antifreeze glycoproteins, lipid-retention, extended larval phases, delayed senescence, and energy-conserving life strategies equip Antarctic fish and squid to withstand the dark winters and yearlong subzero temperatures experienced in much of the Southern Ocean. In addition to krill exploitation, the comparatively high commercial value of Antarctic fish, particularly the lucrative toothfish, drives fisheries interests, which has included illegal fishing. Uncertainty about the population dynamics of target species and ecosystem structure and function more broadly has necessitated a precautionary, ecosystem approach to managing these stocks and enabling the recovery of depleted species. Fisheries currently remain the major local driver of change in Southern Ocean fish productivity, but global climate change presents an even greater challenge to assessing future changes. Parts of the Southern Ocean are experiencing ocean-warming, such as the West Antarctic Peninsula, while other areas, such as the Ross Sea shelf, have undergone cooling in recent years. These trends are expected to result in a redistribution of species based on their tolerances to different temperature regimes. Climate variability may impair the migratory response of these species to environmental change, while imposing increased pressures on recruitment. Fisheries and climate change, coupled with related local and global drivers such as pollution and sea ice change, have the potential to produce synergistic impacts that compound the risks to Antarctic fish and squid species. The uncertainty surrounding how different species will respond to these challenges, given their varying life histories, environmental dependencies, and resiliencies, necessitates regular assessment to inform conservation and management decisions. Urgent attention is needed to determine whether the current management strategies are suitably precautionary to achieve conservation objectives in light of the impending changes to the ecosystem.

Cephalopod beak sections used to trace mercury levels throughout the life of cephalopods: The giant warty squid Moroteuthopsis longimana as a case study

Cephalopods represent an important pathway for mercury transfer through food webs. Due to the general difficulties in capturing oceanic squid, beaks found in the diet of top predators can be used to study their life-cycles and ecological role. Using upper beaks of the giant warty squid Moroteuthopsis longimana (major prey in the Southern Ocean), we describe a method to assess mercury concentrations along the life of cephalopods through the segmentary analysis of beak sections (i.e. tip of the rostrum and subsections along the hood). Distinct total mercury concentrations in the different subsections support that beaks can be used to study mercury levels in different periods of cephalopods' life-cycle. Mercury values in the anterior (1.3-7.9 μg kg^-1 dw) and posterior (7.8-12.5 μg kg^-1 dw) subsections of the hood reflect juvenile and adult stages, respectively. Furthermore, these results confirm that mercury bioaccumulates continuously throughout the individuals' life, with adults doubling their mercury concentrations to juveniles.

Modelling spatiotemporal trends in range shifts of marine commercial fish species driven by climate change surrounding the Antarctic Peninsula

In recent decades, the relationships between species distributional shifts and climate change have been investigated at various geographic scales, yet there is still a gap in understanding the impacts of climate change on marine commercial fish species surrounding the Antarctic Peninsula. The dynamic bioclimate envelope model (DBEM) is a mechanistic model that encompass species distribution model and population dynamic model approaches to project the spatiotemporal change of marine commercial fish species driven by various climate change scenarios in the Southern Ocean. This paper focuses on the spatiotemporal changes of marine commercial fish species surrounding the Antarctic Peninsula under a high emissions scenario (RCP8.5) and a low emissions scenario (RCP2.6) from 1970 to 2060 following three different Earth System Models (ESMs), namely, the GFDL-ESM 2G, IPSL-CM5A-MR and MPI-ESM-MR. Results reveal that: i) The general latitudinal gradient patterns in species richness shifts poleward associated with a global abundance decrease ii) The Spp. richness in Eastern Antarctic Peninsula (EAP) is higher than in the Western Antarctic Peninsula (WAP) at the same latitude (>65°S latitude). iii) The reasons are that the krill-dependent predators in WAP could face a higher risk of depletion than that in EAP due to ocean warming and anthropogenic activities.

Metabarcoding analysis of the stomach contents of the Antarctic Toothfish (Dissostichus mawsoni) collected in the Antarctic Ocean

Stomach contents of the Antarctic toothfish, Dissostichus mawsoni, collected from subareas 58.4 and 88.3, were analyzed using next generation sequencing (NGS) technology. After processing the raw reads generated by the MiSeq platform, a total of 131,233 contigs (130 operational taxonomic units [OTUs]) were obtained from 163 individuals in subarea 58.4, and 75,961 contigs (105 OTUs) from 164 fish in subarea 88.3. At 98% sequence identity, species names were assigned to most OTUs in this study, indicating the quality of the DNA barcode database for the Antarctic Ocean was sufficient for molecular analysis, especially for fish species. A total of 19 species was identified from the stomach of D. mawsoni in this study, which included 14 fish species and five mollusks. More than 90% of contigs belonged to fish species, supporting the postulate that the major prey of D. mawsoni are fish. Two fish species, Macrourus whitsoni and Chionobathyscus dewitti, were the most important prey items (a finding similar to that of previous studies). We also obtained genotypes of prey items by NGS analysis, identifying an additional 17 representative haplotypes in this study. Comparison with three previous morphological studies and the NGS-based molecular identification in this study extended our knowledge regarding the prey of D. mawsoni, which previously was not possible. These results suggested that NGS-based diet studies are possible, if several current technical limitations, including the quality of the barcode database or the development of precise molecular quantification techniques to link them with morphological values, are overcome. To achieve this, additional studies should be conducted on various marine organisms.

Functional roles of an engineer species for coastal benthic invertebrates and demersal fish

Through their tissues or activities, engineer species create, modify, or maintain habitats and alter the distribution and abundance of many plants and animals. This study investigates key ecological functions performed by an engineer species that colonizes coastal ecosystems. The gregarious tubiculous amphipod Haploops nirae is used as a biological model. According to previous studies, the habitat engineered by H. nirae (i.e., Haploops habitat) could provide food and natural shelter for several benthic species such as benthic diatoms belonging to the gender Navicula, the micrograzer Geitodoris planata, or the bivalve Polititapes virgineus. Using data from scientific surveys conducted in two bays, this study explored whether (1) the Haploops sandy‐mud community modifies invertebrate and ichthyologic community structure (diversity and biomass); (2) H. nirae creates a preferential feeding ground; and (3) this habitat serves as a refuge for juvenile fish. Available Benthic Energy Coefficients, coupled with more traditional diversity indices, indicated higher energy available in Haploops habitat than in two nearby habitats (i.e., Sternaspis scutata and Amphiura filiformis/Owenia fusiformis habitats). The use of isotopic functional indices (IFIs) indicated (1) a higher functional richness in the Haploops habitat, related to greater diversity in food sources and longer food chains; and (2) a higher functional divergence, associated with greater consumption of a secondary food source. At the invertebrate‐prey level, IFIs indicated little specialization and little trophic redundancy in the engineered habitat, as expected for homogenous habitats. Our results partly support empirical knowledge about engineered versus nonengineered habitats and also add new perspectives on habitat use by fish and invertebrate species. Our analyses validated the refuge‐area hypothesis for a few fish species. Although unique benthic prey assemblages are associated with Haploops habitat, the hypothesis that it is a preferential feeding area was not verified. However, specialist feeding behavior was observed for predators, which calls for further investigation.

Hexabromocyclododecane flame retardant in Antarctica: Research stations as sources

Historical persistent organic pollutants (POPs) are banned from Antarctica under international treaty; but contemporary-use POPs can enter as additives within polymer and textile products. Over their useful lives these products may release additives in-situ. Indeed, we observed 226 and 109 ng/g dry weight (dw) of the total concentrations of α-, β- and γ-hexabromocyclododecane (HBCD) in indoor dust from McMurdo Station (U.S.) and Scott Station (New Zealand), respectively. Sewage sludge collected from wastewater treatment facilities at these stations exhibited ∑HBCD of 45 and 69 ng/g dw, respectively. Contaminants originally within the bases may exit to the local outdoor environment via wastewaters. Near McMurdo, maximum ∑HBCD levels in surficial marine sediments and aquatic biota (invertebrates and fish) were 2350 ng/g (total organic carbon basis) and 554 ng/g lipid weight, respectively. Levels declined with distance from McMurdo. Our results illustrate that Antarctic research stations serve as local HBCD sources to the pristine Antarctic environment.

Climate change and Southern Ocean ecosystems I: how changes in physical habitats directly affect marine biota

Antarctic and Southern Ocean (ASO) marine ecosystems have been changing for at least the last 30 years, including in response to increasing ocean temperatures and changes in the extent and seasonality of sea ice; the magnitude and direction of these changes differ between regions around Antarctica that could see populations of the same species changing differently in different regions. This article reviews current and expected changes in ASO physical habitats in response to climate change. It then reviews how these changes may impact the autecology of marine biota of this polar region: microbes, zooplankton, salps, Antarctic krill, fish, cephalopods, marine mammals, seabirds, and benthos. The general prognosis for ASO marine habitats is for an overall warming and freshening, strengthening of westerly winds, with a potential pole-ward movement of those winds and the frontal systems, and an increase in ocean eddy activity. Many habitat parameters will have regionally specific changes, particularly relating to sea ice characteristics and seasonal dynamics. Lower trophic levels are expected to move south as the ocean conditions in which they are currently found move pole-ward. For Antarctic krill and finfish, the latitudinal breadth of their range will depend on their tolerance of warming oceans and changes to productivity. Ocean acidification is a concern not only for calcifying organisms but also for crustaceans such as Antarctic krill; it is also likely to be the most important change in benthic habitats over the coming century. For marine mammals and birds, the expected changes primarily relate to their flexibility in moving to alternative locations for food and the energetic cost of longer or more complex foraging trips for those that are bound to breeding colonies. Few species are sufficiently well studied to make comprehensive species-specific vulnerability assessments possible. Priorities for future work are discussed.