Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth

Transcriptomic responses and evolutionary insights of deep-sea and shallow-water mussels under high hydrostatic pressure condition

Marine mussels inhabit a wide range of ocean depths, necessitating unique adaptations to cope with varying hydrostatic pressures. This study investigates the transcriptomic responses and evolutionary adaptations of the deep-sea mussel Gigantidas platifrons and the shallow-water mussel Mytilus galloprovincialis to high hydrostatic pressure (HHP) conditions. By exposing atmospheric pressure (AP) acclimated G. platifrons and M. galloprovincialis to HHP, we aim to simulate extreme environmental challenges and assess their adaptive mechanisms. Through comparative transcriptomic analysis, we identified both conserved and species-specific mechanisms of adaptation, with a notable change in gene expression associated with immune system, substance transport, protein ubiquitination, apoptosis, lipid metabolism and antioxidant processes in both species. G. platifrons demonstrated an augmented lipid metabolism, whereas M. galloprovincialis exhibited a dampened immune function. Additionally, the expressed pattern of deep-sea mussel G. platifrons were more consistent than shallow-water mussel M. galloprovincialis under hydrostatic pressures changed conditions which corresponding the long-term living stable deep-sea environment. Moreover, evolutionary analysis pinpointed positively selected genes in G. platifrons that are linked to transmembrane transporters, DNA repair and replication, apoptosis, ubiquitination which are important to cell structural integrity, substances transport, and cellular growth regulation. This indicates a specialized adaptation strategy in G. platifrons to cope with the persistent HHP conditions of the deep sea. These results offer significant insights into the molecular underpinnings of mussel adaptation to varied hydrostatic conditions and enhance our comprehension of the evolutionary forces driving their depth-specific adaptations.

Incorporating physiological knowledge into correlative species distribution models minimizes bias introduced by the choice of calibration area

Correlative species distribution models (SDMs) are important tools to estimate species' geographic distribution across space and time, but their reliability heavily relies on the availability and quality of occurrence data. Estimations can be biased when occurrences do not fully represent the environmental requirement of a species. We tested to what extent species' physiological knowledge might influence SDM estimations. Focusing on the Japanese sea cucumber Apostichopus japonicus within the coastal ocean of East Asia, we compiled a comprehensive dataset of occurrence records. We then explored the importance of incorporating physiological knowledge into SDMs by calibrating two types of correlative SDMs: a naïve model that solely depends on environmental correlates, and a physiologically informed model that further incorporates physiological information as priors. We further tested the models' sensitivity to calibration area choices by fitting them with different buffered areas around known presences. Compared with naïve models, the physiologically informed models successfully captured the negative influence of high temperature on A. japonicus and were less sensitive to the choice of calibration area. The naïve models resulted in more optimistic prediction of the changes of potential distributions under climate change (i.e., larger range expansion and less contraction) than the physiologically informed models. Our findings highlight benefits from incorporating physiological information into correlative SDMs, namely mitigating the uncertainties associated with the choice of calibration area. Given these promising features, we encourage future SDM studies to consider species physiological information where available.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00226-0.

Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat

BACKGROUND

The deep-sea snail Phymorhynchus buccinoides belongs to the genus Phymorhynchus (Neogastropoda: Raphitomidae), and it is a dominant specie in the cold seep habitat. As the environment of the cold seep is characterized by darkness, hypoxia and high concentrations of toxic substances such as hydrogen sulfide (H2S), exploration of the diverse fauna living around cold seeps will help to uncover the adaptive mechanisms to this unique habitat. In the present study, a chromosome-level genome of P. buccinoides was constructed and a series of genomic and transcriptomic analyses were conducted to explore its molecular adaptation mechanisms to the cold seep environments.

RESULTS

The assembled genome size of the P. buccinoides was approximately 2.1 Gb, which is larger than most of the reported snail genomes, possibly due to the high proportion of repetitive elements. About 92.0% of the assembled base pairs of contigs were anchored to 34 pseudo-chromosomes with a scaffold N50 size of 60.0 Mb. Compared with relative specie in the shallow water, the glutamate regulative and related genes were expanded in P. buccinoides, which contributes to the acclimation to hypoxia and coldness. Besides, the relatively high mRNA expression levels of the olfactory/chemosensory genes in osphradium indicate that P. buccinoides might have evolved a highly developed and sensitive olfactory organ for its orientation and predation. Moreover, the genome and transcriptome analyses demonstrate that P. buccinoides has evolved a sulfite-tolerance mechanism by performing H2S detoxification. Many genes involved in H2S detoxification were highly expressed in ctenidium and hepatopancreas, suggesting that these tissues might be critical for H2S detoxification and sulfite tolerance.

CONCLUSIONS

In summary, our report of this chromosome-level deep-sea snail genome provides a comprehensive genomic basis for the understanding of the adaptation strategy of P. buccinoides to the extreme environment at the deep-sea cold seeps.

Putative photosensitivity in internal light organs (organs of Pesta) of deep-sea sergestid shrimps

Many marine species can regulate the intensity of bioluminescence from their ventral photophores in order to counterilluminate, a camouflage technique whereby animals closely match the intensity of the downwelling illumination blocked by their bodies, thereby hiding their silhouettes. Recent studies on autogenic cuticular photophores in deep-sea shrimps indicate that the photophores themselves are light sensitive. Here, our results suggest photosensitivity in a second type of autogenic photophore, the internal organs of Pesta, found in deep-sea sergestid shrimps. Experiments were conducted onboard ship on live specimens, exposing the animals to bright light, which resulted in ultrastructural changes that matched those seen in crustacean eyes during the photoreceptor membrane turnover, a process that is crucial for the proper functioning of photosensitive components. In addition, RNA-seq studies demonstrated the expression of visual opsins and phototransduction genes in photophore tissue that are known to play a role in light detection, and electrophysiological measurements indicated that the light organs are responding to light received by the eyes. The long sought after mechanism of counterillumination remains unknown, but evidence of photosensitivity in photophores may indicate a dual functionality of light detection and emission.

A 104-Ma record of deep-sea Atelostomata (Holasterioda, Spatangoida, irregular echinoids) - a story of persistence, food availability and a big bang

Deep-sea macrobenthic body fossils are scarce due to the lack of deep-sea sedimentary archives in onshore settings. Therefore, hypothesized migrations of shallow shelf taxa into the deep-sea after phases of mass extinction (onshore-offshore pattern in the literature) due to anoxic events is not constrained by the fossil record. To resolve this conundrum, we investigated 1,475 deep-sea sediment samples from the Atlantic, Pacific and Southern oceans (water depth ranging from 200 to 4,700 m), providing 41,460 spine fragments of the crown group Atelostomata (Holasteroida, Spatangoida). We show that the scarce fossil record of deep-sea echinoids is in fact a methodological artefact because it is limited by the almost exclusive use of onshore fossil archives. Our data advocate for a continuous record of deep-sea Atelostomata back to at least 104 Ma (late early Cretaceous), and literature records suggest even an older age (115 Ma). A gradual increase of different spine tip morphologies from the Albian to the Maastrichtian is observed. A subsequent, abrupt reduction in spine size and the loss of morphological inventory in the lowermost Paleogene is interpreted to be an expression of the "Lilliput Effect", related to nourishment depletion on the sea floor in the course of the Cretaceous-Paleogene (K-Pg) Boundary Event. The recovery from this event lasted at least 5 Ma, and post-K-Pg Boundary Event assemblages progress-without any further morphological breaks-towards the assemblages observed in modern deep-sea environments. Because atelostomate spine morphology is often species-specific, the variations in spine tip morphology trough time would indicate species changes taking place in the deep-sea. This observation is, therefore, interpreted to result from in-situ evolution in the deep-sea and not from onshore-offshore migrations. The calculation of the "atelostomate spine accumulation rate" (ASAR) reveals low values in pre-Campanian times, possibly related to high remineralization rates of organic matter in the water column in the course of the mid-Cretaceous Thermal Maximum and its aftermath. A Maastrichtian cooling pulse marks the irreversible onset of fluctuating but generally higher atelostomate biomass that continues throughout the Cenozoic.

Groundfish biodiversity change in northeastern Pacific waters under projected warming and deoxygenation

In the coming decades, warming and deoxygenation of marine waters are anticipated to result in shifts in the distribution and abundance of fishes, with consequences for the diversity and composition of fish communities. Here, we combine fisheries-independent trawl survey data spanning the west coast of the USA and Canada with high-resolution regional ocean models to make projections of how 34 groundfish species will be impacted by changes in temperature and oxygen in British Columbia (BC) and Washington. In this region, species that are projected to decrease in occurrence are roughly balanced by those that are projected to increase, resulting in considerable compositional turnover. Many, but not all, species are projected to shift to deeper depths as conditions warm, but low oxygen will limit how deep they can go. Thus, biodiversity will likely decrease in the shallowest waters (less than 100 m), where warming will be greatest, increase at mid-depths (100-600 m) as shallow species shift deeper, and decrease at depths where oxygen is limited (greater than 600 m). These results highlight the critical importance of accounting for the joint role of temperature, oxygen and depth when projecting the impacts of climate change on marine biodiversity. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Sea temperature is the primary driver of recent and predicted fish community structure across Northeast Atlantic shelf seas

Climate change has strongly influenced the distribution and abundance of marine fish species, leading to concern about effects of future climate on commercially harvested stocks. Understanding the key drivers of large-scale spatial variation across present-day marine assemblages enables predictions of future change. Here we present a unique analysis of standardised abundance data for 198 marine fish species from across the Northeast Atlantic collected by 23 surveys and 31,502 sampling events between 2005 and 2018. Our analyses of the spatially comprehensive standardised data identified temperature as the key driver of fish community structure across the region, followed by salinity and depth. We employed these key environmental variables to model how climate change will affect both the distributions of individual species and local community structure for the years 2050 and 2100 under multiple emissions scenarios. Our results consistently indicate that projected climate change will lead to shifts in species communities across the entire region. Overall, the greatest community-level changes are predicted at locations with greater warming, with the most pronounced effects at higher latitudes. Based on these results, we suggest that future climate-driven warming will lead to widespread changes in opportunities for commercial fisheries across the region.

Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis

Chemosynthetic symbioses between bacteria and invertebrates occur worldwide from coastal sediments to the deep sea. Most host groups are restricted to either shallow or deep waters. In contrast, Lucinidae, the most species-rich family of chemosymbiotic invertebrates, has both shallow- and deep-sea representatives. Multiple lucinid species have independently colonized the deep sea, which provides a unique framework for understanding the role microbial symbionts play in evolutionary transitions between shallow and deep waters. Lucinids acquire their symbionts from their surroundings during early development, which may allow them to flexibly acquire symbionts that are adapted to local environments. Via metagenomic analyses of museum and other samples collected over decades, we investigated the biodiversity and metabolic capabilities of the symbionts of 22 mostly deep-water lucinid species. We aimed to test the theory that the symbiont played a role in adaptation to life in deep-sea habitats. We identified 16 symbiont species, mostly within the previously described genus Ca. Thiodiazotropha. Most genomic functions were shared by both shallow-water and deep-sea Ca. Thiodiazotropha, though nitrogen fixation was exclusive to shallow-water species. We discovered multiple cases of symbiont switching near deep-sea hydrothermal vents and cold seeps, where distantly related hosts convergently acquired novel symbionts from a different bacterial order. Finally, analyses of selection revealed consistently stronger purifying selection on symbiont genomes in two extreme habitats - hydrothermal vents and an oxygen-minimum zone. Our findings reveal that shifts in symbiont metabolic capability and, in some cases, acquisition of a novel symbiont accompanied adaptation of lucinids to challenging deep-sea habitats.

Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench

The examination of genetic structure in the deep-ocean hadal zone has focused on divergence between tectonic trenches to understand how environment and geography may drive species divergence and promote endemism. There has been little attempt to examine localized genetic structure within trenches, partly because of logistical challenges associated with sampling at an appropriate scale, and the large effective population sizes of species that can be sampled adequately may mask underlying genetic structure. Here we examine genetic structure in the superabundant amphipod Hirondellea gigas in the Mariana Trench at depths of 8126-10,545 m. RAD sequencing was used to identify 3182 loci containing 43,408 single nucleotide polymorphisms (SNPs) across individuals after stringent pruning of loci to prevent paralogous multicopy genomic regions being erroneously merged. Principal components analysis of SNP genotypes resolved no genetic structure between sampling locations, consistent with a signature of panmixia. However, discriminant analysis of principal components identified divergence between all sites driven by 301 outlier SNPs in 169 loci and significantly associated with latitude and depth. Functional annotation of loci identified differences between singleton loci used in analysis and paralogous loci pruned from the data set and also between outlier and nonoutlier loci, all consistent with hypotheses explaining the role of transposable elements driving genome dynamics. This study challenges the traditional perspective that highly abundant amphipods within a trench form a single panmictic population. We discuss the findings in relation to eco-evolutionary and ontogenetic processes operating in the deep sea, and highlight key challenges associated with population genetic analysis in nonmodel systems with inherent large effective population sizes and genomes.

A latitudinal gradient of deep-sea invasions for marine fishes

Although the tropics harbor the greatest species richness globally, recent work has demonstrated that, for many taxa, speciation rates are faster at higher latitudes. Here, we explore lability in oceanic depth as a potential mechanism for this pattern in the most biodiverse vertebrates - fishes. We demonstrate that clades with the highest speciation rates also diversify more rapidly along the depth gradient, drawing a fundamental link between evolutionary and ecological processes on a global scale. Crucially, these same clades also inhabit higher latitudes, creating a prevailing latitudinal gradient of deep-sea invasions concentrated in poleward regions. We interpret these findings in the light of classic ecological theory, unifying the latitudinal variation of oceanic features and the physiological tolerances of the species living there. This work advances the understanding of how niche lability sculpts global patterns of species distributions and underscores the vulnerability of polar ecosystems to changing environmental conditions.

High polychaete diversity in the Gulf of Guinea (West African continental margin): The influence of local and intermediate scale ecological factors on a background of regional patterns

The Tropical East Atlantic is one of the least studied areas in the world's oceans, and thus a blank spot on the map of marine studies. Shaped by dynamic currents and shifting water masses, it is a key region in discussions about marine ecology, biodiversity, and zoogeography, while facing numerous, poorly understood, and unmonitored threats associated with climate change, acidification, and pollution. Polychaete diversity was assessed along four transects along the Ghana coast, from shallow to deep bottoms and distributed along the whole upwelling marine ecoregion. Despite high sampling effort, steep species accumulation curves demonstrated the necessity of further sampling in the region. We observed zonation of fauna by depth, and a decrease in species richness from 25 m to 1000 m depth. Polychaete communities were influenced by sediment type, presence of oxygen minimum zones, and local disturbances caused by elevated barium concentrations. Similar evenness along the depth gradient reflected the importance of rare species in the community structure. Differences in phylogenetic diversity, as reflected by taxonomic distinctness, were small, which suggested high ecosystem stability. The highly variable species richness at small scale (meters) showed the importance of ecological factors giving rise to microhabitat diversity, although we also noticed intermediate scale (50-300 km) differences affecting community structure. About 44 % of the species were rare (i.e. recorded only in three or fewer samples), highlighting the level of patchiness, while one fifth was distributed on all transects, therefore along the whole upwelling ecoregion, demonstrating the influence of the regional species pool on local communities at particular stations. Our study yielded 253 species, increasing the number of polychaetes known from this region by at least 50 %. This casts doubt on previous findings regarding Atlantic bioregionalization, biodiversity estimates and endemism, which appear to have been more pronouncedly affected by sampling bias than previously thought.

The interactive effects of environmental gradient and dispersal shape spatial phylogenetic patterns

Introduction

The emergence and maintenance of biodiversity include interacting environmental conditions, organismal adaptation to such conditions, and dispersal. To understand and quantify such ecological, evolutionary, and spatial processes, observation and interpretation of phylogenetic relatedness across space (e.g., phylogenetic beta diversity) is arguably a way forward as such patterns contain signals from all the processes listed above. However, it remains challenging to extract information about complex eco-evolutionary and spatial processes from phylogenetic patterns.

Methods

We link environmental gradients and organismal dispersal with phylogenetic beta diversity using a trait-based and eco-evolutionary model of diversification along environmental gradients. The combined effect of the environment and dispersal leads to distinct phylogenetic patterns between subsets of species and across geographical distances.

Results and discussion

Steep environmental gradients combined with low dispersal lead to asymmetric phylogenies, a high phylogenetic beta diversity, and the phylogenetic diversity between communities increases linearly along the environmental gradient. High dispersal combined with a less steep environmental gradient leads to symmetric phylogenies, low phylogenetic beta diversity, and the phylogenetic diversity between communities along the gradient increases in a sigmoidal form. By disentangling the eco-evolutionary mechanisms that link such interacting environment and dispersal effects and community phylogenetic patterns, our results improve understanding of biodiversity in general and help interpretation of observed phylogenetic beta diversity.

Distribution of the Order Lampriformes in the Mediterranean Sea with Notes on Their Biology, Morphology, and Taxonomy

Lampriformes are circumglobally distributed and contain several families of strictly marine bony fishes that have a peculiar morphology. Lampriformes systematics is affected by limitations in biometric, meristic, and molecular data; for this reason, it underwent several rearrangements in the past. This review aimed to describe the biological and ecological characteristics of the order Lampriformes, summarizing the current taxonomy of the group. The main aim was to clarify what is known about the distribution of the order Lampriformes in the Mediterranean Sea, collecting all the scarce and fragmented reports and notes on their occurrence. Knowledge scarcity is due to their solitary nature, in addition to their low to absent economic value. Despite this, the order Lampriformes represents a taxon of high biological and ecological importance. The high depth range of distribution characterizes their lifestyle. In the Mediterranean Sea, four families are present-Lampridae, Lophotidae, Regalecidae, and Trachipteridae-with the following species respectively, Lampris guttatus (Brünnich, 1788), Lophotus lacepede (Giorna, 1809), Regalecus glesne (Ascanius, 1772), Trachipterus arcticus (Brünnich, 1788), T. trachypterus (Gmelin, 1789), and Zu cristatus (Bonelli, 1819). Data deficiencies affect information on this taxon; the present review, which collected all the reports of the Mediterranean Sea, creates a baseline for depicting the biogeography of these rare and important species.

Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea

Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-Ser ^AGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-Ser ^AGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.

Metabolic Tolerance to Atmospheric Pressure of Two Freshwater Endemic Amphipods Mostly Inhabiting the Deep-Water Zone of the Ancient Lake Baikal

Simple Summary

Deep-water habitats are the largest ecosystem on the planet: over half of the Earth’s surface is covered with a water layer deeper than 200 m and remains poorly explored. Lake Baikal is the only freshwater body inhabited by animals adapted to the deep-water zone independently from their marine counterparts. Comparing these convergently evolved freshwater and marine animals is invaluable for revealing the basic mechanisms of adaptation to high hydrostatic pressure. However, laboratory experiments on deep-water organisms still usually require lifting them to the water’s surface and exposing them to potentially hazardous decompression, while endemics from Lake Baikal are poorly studied in this regard. Here, we compared metabolic reactions to such pressure decreases in two Baikal deep-water amphipods (shrimp-like crustaceans) from the genus Ommatogammarus: one species is known to tolerate pressures close to atmospheric levels, while the second was only observed at the pressures from 5 atm and above. We expected that the energy metabolism of the shallower-dwelling species would function better under the atmospheric pressure but found no substantial differences. Thus, despite some difference in long-term survival at atmospheric pressure, both species are suitable for laboratory studies as freshwater model objects adapted to large pressure variations.

Abstract

Lake Baikal is the only freshwater reservoir inhabited by deep-water fauna, which originated mostly from shallow-water ancestors. Ommatogammarus flavus and O. albinus are endemic scavenger amphipods (Amphipoda, Crustacea) dwelling in wide depth ranges of the lake covering over 1300 m. O. flavus had been previously collected close to the surface, while O. albinus has never been found above the depth of 47 m. Since O. albinus is a promising model species for various research, here we tested whether O. albinus is less metabolically adapted to atmospheric pressure than O. flavus. We analyzed a number of energy-related traits (contents of glucose, glycogen and adenylates, as well as lactate dehydrogenase activity) and oxidative stress markers (activities of antioxidant enzymes and levels of lipid peroxidation products) after sampling from different depths and after both species’ acclimation to atmospheric pressure. The analyses were repeated in two independent sampling campaigns. We found no consistent signs of metabolic disturbances or oxidative stress in both species right after lifting. Despite O. flavus surviving slightly better in laboratory conditions, during long-term acclimation, both species showed comparable reactions without critical changes. Thus, the obtained data favor using O. albinus along with O. flavus for physiological research under laboratory conditions.

Genome of a giant isopod, Bathynomus jamesi, provides insights into body size evolution and adaptation to deep-sea environment

BACKGROUND

The deep-sea may be regarded as a hostile living environment, due to low temperature, high hydrostatic pressure, and limited food and light. Isopods, a species-rich group of crustaceans, are widely distributed across different environments including the deep sea and as such are a useful model for studying adaptation, migration, and speciation. Similar to other deep-sea organisms, giant isopods have larger body size than their shallow water relatives and have large stomachs and fat bodies presumably to store organic reserves. In order to shed light on the genetic basis of these large crustaceans adapting to the oligotrophic environment of deep-sea, the high-quality genome of a deep-sea giant isopod Bathynomus jamesi was sequenced and assembled.

RESULTS

B. jamesi has a large genome of 5.89 Gb, representing the largest sequenced crustacean genome to date. Its large genome size is mainly attributable to the remarkable proliferation of transposable elements (84%), which may enable high genome plasticity for adaptive evolution. Unlike its relatives with small body size, B. jamesi has expanded gene families related to pathways of thyroid and insulin hormone signaling that potentially contribute to its large body size. Transcriptomic analysis showed that some expanded gene families related to glycolysis and vesicular transport were specifically expressed in its digestive organs. In addition, comparative genomics and gene expression analyses in six tissues suggested that B. jamesi has inefficient lipid degradation, low basal metabolic rate, and bulk food storage, suggesting giant isopods adopt a more efficient mechanism of nutrient absorption, storage, and utilization to provide sustained energy supply for their large body size.

CONCLUSIONS

Taken together, the giant isopod genome may provide a valuable resource for understanding body size evolution and adaptation mechanisms of macrobenthic organisms to deep-sea environments.

Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences

Precise gene expression reflects the molecular response of deep-sea organisms to their harsh living environments. However, changes in environmental factors during lifting samples from the deep sea to a research vessel can also affect gene expression. By using the transcriptomic approach, we compared the gene expression profiles of the onboard fixed with the in situ fixed samples of the deep-sea limpet Bathyacmaea lactea. Our results revealed that the concomitant stress during conventional deep-sea sampling without RNA in situ fixation greatly influenced the gene expression. Various biological activities, such as cell and tissue structure, lysosomal activity, fluid balance, and unsaturated fatty acid metabolism, were perturbed, suggesting that the sampling stress has exerted systemic impacts on the life of the limpets. These findings clearly illustrate that deep-sea samples without RNA in situ fixation can easily lead to biased results in gene expression analysis, which requires to be appropriately addressed in future studies.

Trimethylamine N-Oxide (TMAO) and Trimethylamine (TMA) Determinations of Two Hadal Amphipods

Hadal trenches are a unique habitat with high hydrostatic pressure, low temperature and scarce food supplies. Amphipods are the dominant scavenging metazoan species in this ecosystem. Trimethylamine (TMA) and trimethylamine oxide (TMAO) have been shown to play important roles in regulating osmotic pressure in mammals, hadal dwellers and even microbes. However, the distributions of TMAO and TMA concentrations of hadal animals among different tissues have not been reported so far. Here, the TMAO and TMA contents of eight tissues of two hadal amphipods, Hirondellea gigas and Alicella gigantea from the Mariana Trench and the New Britain Trench, were detected by using the ultrahigh performance liquid chromatography–mass spectrometry (UPLC-MS/MS) method. Compared with the shallow water Decapoda, Penaeus vannamei, the hadal amphipods possessed significantly higher TMAO concentrations and a similar level of TMA in all the detected tissues. A higher level of TMAO was detected in the external organs (such as the eye and exoskeleton) for both of the two hadal amphipods, which indicated that the TMAO concentration was not evenly distributed, although the same hydrostatic pressure existed in the outer and internal organs. Moreover, a strong positive correlation was found between the concentrations of TMAO and TMA in the two hadal amphipods. In addition, evolutionary analysis regarding FMO3, the enzyme to convert TMA into TMAO, was also conducted. Three positive selected sites in the conserved region and two specific mutation sites in two conserved motifs were found in the A. gigantea FMO3 gene. Combined together, this study supports the important role of TMAO for the environmental adaptability of hadal amphipods and speculates on the molecular evolution and protein structure of FMO3 in hadal species.

Biogeography, diversity and environmental relationships of shelf and deep-sea benthic Amphipoda around Iceland

The waters around Iceland, bounding the Northern North Atlantic and the Nordic seas, are a region characterized by complex hydrography and seabed topography. This and the presence of the Greenland-Iceland-Faroe-Scotland ridge (GIFR) are likely to have a major impact on the diversity and distribution of the benthic fauna there. Biodiversity in this region is also under increasing threat from climate-induced changes, ocean warming and acidification in particular, affecting the marine realm. The aim of the present study was to investigate the biodiversity and distributional patterns of amphipod crustaceans in Icelandic waters and how it relates to environmental variables and depth. A comprehensive data set from the literature and recent expeditions was compiled constituting distributional records for 355 amphipod species across a major depth gradient (18–3,700 m). Using a 1° hexagonal grid to map amphipod distributions and a set of environmental factors (depth, pH, phytobiomass, velocity, dissolved oxygen, dissolved iron, salinity and temperature) we could identify four distinct amphipod assemblages: A Deep-North, Deep-South, and a Coastal cluster as well as one restricted to the GIFR. In addition to depth, salinity and temperature were the main parameters that determined the distribution of amphipods. Diversity differed greatly between the depth clusters and was significantly higher in coastal and GIFR assemblages compared to the deep-sea clusters north and south of the GIFR. A variety of factors and processes are likely to be responsible for the perceived biodiversity patterns, which, however, appear to vary according to region and depth. Low diversity of amphipod communities in the Nordic basins can be interpreted as a reflection of the prevailing harsh environmental conditions in combination with a barrier effect of the GIFR. By contrast, low diversity of the deep North Atlantic assemblages might be linked to the variable nature of the oceanographic environment in the region over multiple spatio-temporal scales. Overall, our study highlights the importance of amphipods as a constituent part of Icelandic benthos. The strong responses of amphipod communities to certain water mass variables raise the question of whether and how their distribution will change due to climate alteration, which should be a focus of future studies.

Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs

The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (F_ST  = 0.11-0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.

Annelids of the eastern Australian abyss collected by the 2017 RV 'Investigator' voyage

In Australia, the deep-water (bathyal and abyssal) benthic invertebrate fauna is poorly known in comparison with that of shallow (subtidal and shelf) habitats. Benthic fauna from the deep eastern Australian margin was sampled systematically for the first time during 2017 RV 'Investigator' voyage 'Sampling the Abyss'. Box core, Brenke sledge, and beam trawl samples were collected at one-degree intervals from Tasmania, 42°S, to southern Queensland, 24°S, from 900 to 4800 m depth. Annelids collected were identified by taxonomic experts on individual families around the world. A complete list of all identified species is presented, accompanied with brief morphological diagnoses, taxonomic remarks, and colour images. A total of more than 6000 annelid specimens consisting of 50 families (47 Polychaeta, one Echiura, two Sipuncula) and 214 species were recovered. Twenty-seven species were given valid names, 45 were assigned the qualifier cf., 87 the qualifier sp., and 55 species were considered new to science. Geographical ranges of 16 morphospecies extended along the eastern Australian margin to the Great Australian Bight, South Australia; however, these ranges need to be confirmed with genetic data. This work providing critical baseline biodiversity data on an important group of benthic invertebrates from a virtually unknown region of the world's ocean will act as a springboard for future taxonomic and biogeographic studies in the area.

Convergent Evolution and Structural Adaptation to the Deep Ocean in the Protein-Folding Chaperonin CCTα

The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations; however, their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including chaperonin-containing TCP-1 subunit α (CCTα), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically corrected context and found that deep-sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα displays not only structural but also functional adaptations to deep-water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as a "cold-shock" protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, is a key metabolic deep-sea adaptation.

Assessing spatio-temporal changes in marine communities along the Portuguese continental shelf and upper slope based on 25 years of bottom trawl surveys

The Portuguese continental coast is influenced by several oceanographic processes and is located near the confluence of three biogeographic realms (from the North Atlantic, South Atlantic and Mediterranean). Given these features, the topography of the Portuguese coast, possible variations in fishing effort and reported increasing sea surface temperature in the last decades, we hypothesized that changes in marine communities in space and time occurred since 1990. In this study, research survey data collected yearly along the Portuguese continental slope (20-500 m deep) from 1990 to 2016 were analysed with the objective of identifying spatio-temporal changes. Latitude and depth were found to play a major role in communities' spatial differentiation, probably associated to temperature, and three ecological areas were defined (north, southwest and south). In the studied period, Macroramphosus spp. abundance showed a marked decrease in all areas whereas Sparids increased in abundance in the south. Despite these major changes and fluctuations in species abundance over time no major trends in communities were observed. Fishing activity, environmental conditions (including climate change) and biotic factors are all drivers possibly responsible for those changes.

Urinary Dimethylamine (DMA) and Its Precursor Asymmetric Dimethylarginine (ADMA) in Clinical Medicine, in the Context of Nitric Oxide (NO) and Beyond

Asymmetric protein-arginine dimethylation is a major post-translational modification (PTM) catalyzed by protein-arginine methyltransferase (PRMT). Regular proteolysis releases asymmetric dimethylarginine (ADMA). Of the daily produced ADMA, about 10% are excreted unchanged in the urine. The remaining 90% are hydrolyzed by dimethylarginine dimethylaminohydrolase (DDAH) to L-citrulline and dimethylamine (DMA), which is readily excreted in the urine. The PRMT/DDAH pathway is almost the exclusive origin of urinary ADMA and the major source of urinary DMA. Dietary fish and seafood represent additional abundant sources of urinary DMA. The present article provides an overview of urinary ADMA and DMA reported thus far in epidemiological, clinical and pharmacological studies, in connection with the L-arginine/nitric oxide (NO) pathway and beyond, in neonates, children and adolescents, young and elderly subjects, males and females. Discussed diseases mainly include those relating to the renal and cardiovascular systems such as peripheral arterial occlusive disease, coronary artery disease, chronic kidney disease, rheumatoid arthritis, Becker muscular disease, Duchenne muscular disease (DMD), attention deficit hyperactivity disorder (ADHD), and type I diabetes. Under standardized conditions involving the abstinence of DMA-rich fresh and canned fish and seafood, urinary DMA and ADMA are useful as measures of whole-body asymmetric arginine-dimethylation in health and disease. The creatinine-corrected excretion rates of DMA range from 10 to 80 µmol/mmol in adults and up to 400 µmol/mmol in children and adolescents. The creatinine-corrected excretion rates of ADMA are on average 10 times lower. In general, diseases are associated with higher urinary DMA and ADMA excretion rates, and pharmacological treatment, such as with steroids and creatine (in DMD), decreases their excretion rates, which may be accompanied by a decreased urinary excretion of nitrate, the major metabolite of NO. In healthy subjects and in rheumatoid arthritis patients, the urinary excretion rate of DMA correlates positively with the excretion rate of dihydroxyphenylglycol (DHPG), the major urinary catecholamines metabolite, suggesting a potential interplay in the PRMT/DDAH/NO pathway.

Molecular Response to High Hydrostatic Pressure: Time-Series Transcriptomic Analysis of Shallow-Water Sea Cucumber Apostichopus japonicus

Hydrostatic pressure is a key environmental factor constraining the benthic migration of shallow-water invertebrates. Although many studies have examined the physiological effects of high hydrostatic pressure on shallow-water invertebrates, the molecular response to high pressure is not fully understood. This question has received increasing attention because ocean warming is forcing the bathymetric migrations of shallow-water invertebrates. Here, we applied time-series transcriptomic analysis to high-pressure incubated and atmospheric pressure-recovered shallow-water sea cucumber (Apostichopus japonicus) to address this question. A total of 44 samples from 15 experimental groups were sequenced. Our results showed that most genes responded to pressure stress at the beginning when pressure was changed, but significant differences of gene expression appeared after 4 to 6 h. Transcription was the most sensitive biological process responding to high-pressure exposure, which was enriched among up-regulated genes after 2 h, followed by ubiquitination (4 h), endocytosis (6 h), stress response (6 h), methylation regulation (24 h), and transmembrane transportation (24 h). After high-pressure incubation, all these biological processes remained up-regulated within 4–6 h at atmospheric pressure. Overall, our results revealed the dynamic transcriptional response of A. japonicus to high-pressure exposure. Additionally, few quantitative or functional responses related to A. japonicus on transcriptional level were introduced by hydrostatic pressure changes after 1 h, and main biological responses were introduced after 4 h, suggesting that, when hydrostatic pressure is the mainly changed environmental factor, it will be better to fix sea cucumber samples for transcriptomic analysis within 1 h, but 4 h will be also acceptable.

Drivers of beta diversity in modern and ancient reef-associated soft-bottom environments

Beta diversity, the compositional variation among communities, is often associated with environmental gradients. Other drivers of beta diversity include stochastic processes, priority effects, predation, or competitive exclusion. Temporal turnover may also explain differences in faunal composition between fossil assemblages. To assess the drivers of beta diversity in reef-associated soft-bottom environments, we investigate community patterns in a Middle to Late Triassic reef basin assemblage from the Cassian Formation in the Dolomites, Northern Italy, and compare results with a Recent reef basin assemblage from the Northern Bay of Safaga, Red Sea, Egypt. We evaluate beta diversity with regard to age, water depth, and spatial distance, and compare the results with a null model to evaluate the stochasticity of these differences. Using pairwise proportional dissimilarity, we find very high beta diversity for the Cassian Formation (0.91 ± 0.02) and slightly lower beta diversity for the Bay of Safaga (0.89 ± 0.04). Null models show that stochasticity only plays a minor role in determining faunal differences. Spatial distance is also irrelevant. Contrary to expectations, there is no tendency of beta diversity to decrease with water depth. Although water depth has frequently been found to be a key factor in determining beta diversity, we find that it is not the major driver in these reef-associated soft-bottom environments. We postulate that priority effects and the biotic structuring of the sediment may be key determinants of beta diversity.

Insights into high-pressure acclimation: comparative transcriptome analysis of sea cucumber Apostichopus japonicus at different hydrostatic pressure exposures

Background

Global climate change is predicted to force the bathymetric migrations of shallow-water marine invertebrates. Hydrostatic pressure is proposed to be one of the major environmental factors limiting the vertical distribution of extant marine invertebrates. However, the high-pressure acclimation mechanisms are not yet fully understood.

Results

In this study, the shallow-water sea cucumber Apostichopus japonicus was incubated at 15 and 25 MPa at 15 °C for 24 h, and subjected to comparative transcriptome analysis. Nine samples were sequenced and assembled into 553,507 unigenes with a N50 length of 1204 bp. Three groups of differentially expressed genes (DEGs) were identified according to their gene expression patterns, including 38 linearly related DEGs whose expression patterns were linearly correlated with hydrostatic pressure, 244 pressure-sensitive DEGs which were up-regulated at both 15 and 25 MPa, and 257 high-pressure-induced DEGs which were up-regulated at 25 MPa but not up-regulated at 15 MPa.

Conclusions

Our results indicated that the genes and biological processes involving high-pressure acclimation are similar to those related to deep-sea adaptation. In addition to representative biological processes involving deep-sea adaptation (such as antioxidation, immune response, genetic information processing, and DNA repair), two biological processes, namely, ubiquitination and endocytosis, which can collaborate with each other and regulate the elimination of misfolded proteins, also responded to high-pressure exposure in our study. The up-regulation of these two processes suggested that high hydrostatic pressure would lead to the increase of misfolded protein synthesis, and this may result in the death of shallow-water sea cucumber under high-pressure exposure.

National-scale marine bioregions for the Southwest Pacific

Existing marine bioregions covering the Pacific Ocean are conceptualised at spatial scales that are too broad for national marine spatial planning. Here, we developed the first combined oceanic and coastal marine bioregionalisation at national scales, delineating 262 deep-water and 103 reef-associated bioregions across the southwest Pacific. The deep-water bioregions were informed by thirty biophysical environmental variables. For reef-associated environments, records for 806 taxa at 7369 sites were used to predict the probability of observing taxa based on environmental variables. Both deep-water and reef-associated bioregions were defined with cluster analysis applied to the environmental variables and predicted species observation probabilities, respectively to classify areas with high taxonomic similarity. Local experts further refined the delineation of the bioregions at national scales for four countries. This work provides marine bioregions that enable the design of ecologically representative national systems of marine protected areas within offshore and inshore environments in the Pacific.

Changes in key traits versus depth and latitude suggest energy-efficient locomotion, opportunistic feeding and light lead to adaptive morphologies of marine fishes

Understanding patterns and processes governing biodiversity along broad-scale environmental gradients, such as depth or latitude, requires an assessment of not just taxonomic richness, but also morphological and functional traits of organisms. Studies of traits can help to identify major selective forces acting on morphology. Currently, little is known regarding patterns of variation in the traits of fishes at broad spatial scales. The aims of this study were (a) to identify a suite of key traits in marine fishes that would allow assessment of morphological variability across broad-scale depth (50-1200 m) and latitudinal (29.15-50.91°S) gradients, and (b) to characterize patterns in these traits across depth and latitude for 144 species of ray-finned fishes in New Zealand waters. Here, we describe three new morphological traits, namely fin-base-to-perimeter ratio, jaw-length-to-mouth-width ratio, and pectoral-fin-base-to-body-depth ratio. Four other morphological traits essential for locomotion and food acquisition that are commonly measured in fishes were also included in the study. Spatial ecological distributions of individual fish species were characterized in response to a standardized replicated sampling design, and morphological measurements were obtained for each species from preserved museum specimens. With increasing depth, fishes, on average, became larger and more elongate, with higher fin-base-to-perimeter ratio and larger jaw-length-to-mouth-width ratio, all of which translates into a more eel-like anguilliform morphology. Variation in mean trait values along the depth gradient was stronger at lower latitudes for fin-base-to-perimeter ratio, elongation and total body length. Average eye size peaked at intermediate depths (500-700 m) and increased with increasing latitude at 700 m. These findings suggest that, in increasingly extreme environments, fish morphology shifts towards a body shape that favours an energy-efficient undulatory swimming style and an increase in jaw-length vs. mouth width for opportunistic feeding. Furthermore, increases in eye size with both depth and latitude indicate that changes in both the average ambient light conditions as well as seasonal variations in day-length can act to select ecomorphological adaptations in fishes.

Comparative transcriptome analysis of Eogammarus possjeticus at different hydrostatic pressure and temperature exposures

Hydrostatic pressure is an important environmental factor affecting the vertical distribution of marine organisms. Laboratory-based studies have shown that many extant shallow-water marine benthic invertebrates can tolerate hydrostatic pressure outside their known natural distributions. However, only a few studies have focused on the molecular mechanisms of pressure acclimatisation. In the present work, we examined the pressure tolerance of the shallow-water amphipod Eogammarus possjeticus at various temperatures (5, 10, 15, and 20 °C) and hydrostatic pressures (0.1–30 MPa) for 16 h. Six of these experimental groups were used for transcriptome analysis. We found that 100% of E. possjeticus survived under 20 MPa at all temperature conditions for 16 h. Sequence assembly resulted in 138, 304 unigenes. Results of differential expression analysis revealed that 94 well-annotated genes were up-regulated under high pressure. All these findings indicated that the pressure tolerance of E. possjeticus was related to temperature. Several biological processes including energy metabolism, antioxidation, immunity, lipid metabolism, membrane-related process, genetic information processing, and DNA repair are probably involved in the acclimatisation in deep-sea environments.

Contrasting processes drive ophiuroid phylodiversity across shallow and deep seafloors

Our knowledge of the distribution and evolution of deep-sea life is limited, impeding our ability to identify priority areas for conservation¹. Here we analyse large integrated phylogenomic and distributional datasets of seafloor fauna from the sea surface to the abyss and from equator to pole of the Southern Hemisphere for an entire class of invertebrates (Ophiuroidea). We find that latitudinal diversity gradients are assembled through contrasting evolutionary processes for shallow (0-200 m) and deep (>200 m) seas. The shallow-water tropical-temperate realm broadly reflects a tropical diversification-driven process that shows exchange of lineages in both directions. Diversification rates are reversed for the realm that contains the deep sea and Antarctica; the diversification rates are highest at polar and lowest at tropical latitudes, and net exchange occurs from high to low latitudes. The tropical upper bathyal (200-700 m deep), with its rich ancient phylodiversity, is characterized by relatively low diversification and moderate immigration rates. Conversely, the young, specialized Antarctic fauna is inferred to be rebounding from regional extinctions that are associated with the rapid cooling of polar waters during the mid-Cenozoic era.

Bait-attending amphipods of the Tonga Trench and depth-stratified population structure in the scavenging amphipod Hirondellea dubia Dahl, 1959

Background

The hadal zone encompasses the deepest parts of the world’s ocean trenches from depths of ∼6,000–11,000 m. The communities observed at these depths are dominated by scavenging amphipods that rapidly intercept and consume carrion as it falls to the deepest parts of the trenches. New samples collected in the Tonga Trench provide an opportunity to compare the amphipod assemblages and the population structure of a dominant species, Hirondellea dubiaDahl, 1959, between trenches and with earlier data presented for the Tonga Trench, and other trenches in the South Pacific.

Methods

Over 3,600 individual scavenging amphipods across 10 species were collected in seven baited traps at two sites; in the Horizon Deep site, the deepest part of the Tonga Trench (10,800 m) and a site directly up-slope at the trench edge (6,250 m). The composition of the bait-attending amphipods is described and a morphometric analysis of H. dubia examines the bathymetric distribution of the different life stages encountered.

Results

The amphipod assemblage was more diverse than previously reported, seven species were recorded for the first time from the Tonga Trench. The species diversity was highest at the shallower depth, with H. dubia the only species captured at the deepest site. At the same time, the abundance of amphipods collected at 10,800 m was around sevenfold higher than at the shallower site. H. dubia showed clear ontogenetic vertical structuring, with juveniles dominant at the shallow site and adults dominant at the deep site. The amphipods of the deeper site were always larger at comparable life stage.

Discussion

The numbers of species encountered in the Tonga Trench is less than reported from the New Hebrides and Kermadec trenches, and six species encountered are shared across trenches. These findings support the previous suggestion that the fauna of the New Hebrides, Tonga and Kermadec Trenches may represent a single biogeographic province. The ontogenetic shift in H. dubia between the two Tonga Trench sites supports the hypothesis of interspecific competition at the shallower bathymetric range of the species, and the presence of competitive physiological advantages that allow the adults at the trench axis to exploit the more labile organic material that reaches the bottom of the trench.

A strategy for the conservation of biodiversity on mid-ocean ridges from deep-sea mining

Mineral exploitation has spread from land to shallow coastal waters and is now planned for the offshore, deep seabed. Large seafloor areas are being approved for exploration for seafloor mineral deposits, creating an urgent need for regional environmental management plans. Networks of areas where mining and mining impacts are prohibited are key elements of these plans. We adapt marine reserve design principles to the distinctive biophysical environment of mid-ocean ridges, offer a framework for design and evaluation of these networks to support conservation of benthic ecosystems on mid-ocean ridges, and introduce projected climate-induced changes in the deep sea to the evaluation of reserve design. We enumerate a suite of metrics to measure network performance against conservation targets and network design criteria promulgated by the Convention on Biological Diversity. We apply these metrics to network scenarios on the northern and equatorial Mid-Atlantic Ridge, where contractors are exploring for seafloor massive sulfide (SMS) deposits. A latitudinally distributed network of areas performs well at (i) capturing ecologically important areas and 30 to 50% of the spreading ridge areas, (ii) replicating representative areas, (iii) maintaining along-ridge population connectivity, and (iv) protecting areas potentially less affected by climate-related changes. Critically, the network design is adaptive, allowing for refinement based on new knowledge and the location of mining sites, provided that design principles and conservation targets are maintained. This framework can be applied along the global mid-ocean ridge system as a precautionary measure to protect biodiversity and ecosystem function from impacts of SMS mining.

Metabolic costs imposed by hydrostatic pressure constrain bathymetric range in the lithodid crab Lithodes maja

The changing climate is shifting the distributions of marine species, yet the potential for shifts in depth distributions is virtually unexplored. Hydrostatic pressure is proposed to contribute to a physiological bottleneck constraining depth range extension in shallow-water taxa. However, bathymetric limitation by hydrostatic pressure remains undemonstrated, and the mechanism limiting hyperbaric tolerance remains hypothetical. Here, we assess the effects of hydrostatic pressure in the lithodid crab Lithodes maja (bathymetric range 4-790 m depth, approximately equivalent to 0.1 to 7.9 MPa hydrostatic pressure). Heart rate decreased with increasing hydrostatic pressure, and was significantly lower at ≥10.0 MPa than at 0.1 MPa. Oxygen consumption increased with increasing hydrostatic pressure to 12.5 MPa, before decreasing as hydrostatic pressure increased to 20.0 MPa; oxygen consumption was significantly higher at 7.5-17.5 MPa than at 0.1 MPa. Increases in expression of genes associated with neurotransmission, metabolism and stress were observed between 7.5 and 12.5 MPa. We suggest that hyperbaric tolerance in Lmaja may be oxygen-limited by hyperbaric effects on heart rate and metabolic rate, but that Lmaja's bathymetric range is limited by metabolic costs imposed by the effects of high hydrostatic pressure. These results advocate including hydrostatic pressure in a complex model of environmental tolerance, where energy limitation constrains biogeographic range, and facilitate the incorporation of hydrostatic pressure into the broader metabolic framework for ecology and evolution. Such an approach is crucial for accurately projecting biogeographic responses to changing climate, and for understanding the ecology and evolution of life at depth.

Metabolic rates are significantly lower in abyssal Holothuroidea than in shallow-water Holothuroidea

Recent analyses of metabolic rates in fishes, echinoderms, crustaceans and cephalopods have concluded that bathymetric declines in temperature- and mass-normalized metabolic rate do not result from resource-limitation (e.g. oxygen or food/chemical energy), decreasing temperature or increasing hydrostatic pressure. Instead, based on contrasting bathymetric patterns reported in the metabolic rates of visual and non-visual taxa, declining metabolic rate with depth is proposed to result from relaxation of selection for high locomotory capacity in visual predators as light diminishes. Here, we present metabolic rates of Holothuroidea, a non-visual benthic and benthopelagic echinoderm class, determined in situ at abyssal depths (greater than 4000 m depth). Mean temperature- and mass-normalized metabolic rate did not differ significantly between shallow-water (less than 200 m depth) and bathyal (200-4000 m depth) holothurians, but was significantly lower in abyssal (greater than 4000 m depth) holothurians than in shallow-water holothurians. These results support the dominance of the visual interactions hypothesis at bathyal depths, but indicate that ecological or evolutionary pressures other than biotic visual interactions contribute to bathymetric variation in holothurian metabolic rates. Multiple nonlinear regression assuming power or exponential models indicates that in situ hydrostatic pressure and/or food/chemical energy availability are responsible for variation in holothurian metabolic rates. Consequently, these results have implications for modelling deep-sea energetics and processes.

Short-term toxicity of 1-methylnaphthalene to Americamysis bahia and 5 deep-sea crustaceans

There are few studies that have evaluated hydrocarbon toxicity to vertically migrating deep-sea micronekton. Crustaceans were collected alive using a 9-m² Tucker trawl with a thermally insulated cod end and returned to the laboratory in 10 °C seawater. Toxicity of the polycyclic aromatic hydrocarbon 1-methylnaphthalene to Americamysis bahia, Janicella spinacauda, Systellaspis debilis, Sergestes sp., Sergia sp., and a euphausiid species was assessed in a constant exposure toxicity test utilizing a novel passive dosing toxicity testing protocol. The endpoint of the median lethal concentration tests was mortality, and the results revealed high sensitivity of the deep-sea micronekton compared with other species for which these data are available. Threshold concentrations were also used to calculate critical target lipid body burdens using the target lipid model. Environ Toxicol Chem 2017;36:3415-3423. © 2017 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.

Hydrostatic pressure and temperature affect the tolerance of the free-living marine nematode Halomonhystera disjuncta to acute copper exposure

Potential deep-sea mineral extraction poses new challenges for ecotoxicological research since little is known about effects of abiotic conditions present in the deep sea on the toxicity of heavy metals. Due to the difficulty of collecting and maintaining deep-sea organisms alive, a first step would be to understand the effects of high hydrostatic pressure and low temperatures on heavy metal toxicity using shallow-water relatives of deep-sea species. Here, we present the results of acute copper toxicity tests on the free-living shallow-water marine nematode Halomonhystera disjuncta, which has close phylogenetic and ecological links to the bathyal species Halomonhystera hermesi. Copper toxicity was assessed using a semi-liquid gellan gum medium at two levels of hydrostatic pressure (0.1MPa and 10MPa) and temperature (10°C and 20°C) in a fully crossed design. Mortality of nematodes in each treatment was assessed at 4 time intervals (24 and 48h for all experiments and additionally 72 and 96h for experiments run at 10°C). LC₅₀ values ranged between 0.561 and 1.864mg Cu²⁺L^-1 and showed a decreasing trend with incubation time. Exposure to high hydrostatic pressure significantly increased sensitivity of nematodes to copper, whereas lower temperature resulted in an apparently increased copper tolerance, possibly as a result of a slower metabolism under low temperatures. These results indicate that hydrostatic pressure and temperature significantly affect metal toxicity and therefore need to be considered in toxicity assessments for deep-sea species. Any application of pollution limits derived from studies of shallow-water species to the deep-sea mining context must be done cautiously, with consideration of the effects of both stressors.

A comparative experimental approach to ecotoxicology in shallow-water and deep-sea holothurians suggests similar behavioural responses

Exploration of deep-sea mineral resources is burgeoning, raising concerns regarding ecotoxicological impacts on deep-sea fauna. Assessing toxicity in deep-sea species is technologically challenging, which promotes interest in establishing shallow-water ecotoxicological proxy species. However, the effects of temperature and hydrostatic pressure on toxicity, and how adaptation to deep-sea environmental conditions might moderate these effects, are unknown. To address these uncertainties we assessed behavioural and physiological (antioxidant enzyme activity) responses to exposure to copper-spiked artificial sediments in a laboratory experiment using a shallow-water holothurian (Holothuria forskali), and in an in situ experiment using a deep-sea holothurian (Amperima sp.). Both species demonstrated sustained avoidance behaviour, evading contact with contaminated artificial sediment. However, A. sp. demonstrated sustained avoidance of 5mgl^-1 copper-contaminated artificial sediment whereas H. forskali demonstrated only temporary avoidance of 5mgl^-1 copper-contaminated artificial sediment, suggesting that H. forskali may be more tolerant of metal exposure over 96h. Nonetheless, the acute behavioural response appears consistent between the shallow-water species and the deep-sea species, suggesting that H. forskali may be a suitable ecotoxicological proxy for A. sp. in acute (≤24h) exposures, which may be representative of deep-sea mining impacts. No antioxidant response was observed in either species, which was interpreted to be the consequence of avoiding copper exposure. Although these data suggest that shallow-water taxa may be suitable ecotoxicological proxies for deep-sea taxa, differences in methodological and analytical approaches, and in sex and reproductive stage of experimental subjects, require caution in assessing the suitability of H. forskali as an ecotoxicological proxy for A. sp. Nonetheless, avoidance behaviour may have bioenergetic consequences that affect growth and/or reproductive output, potentially impacting fecundity and/or offspring fitness, and thus influencing source-sink dynamics and persistence of wider deep-sea populations.

The Effects of Temperature and Hydrostatic Pressure on Metal Toxicity: Insights into Toxicity in the Deep Sea

Mineral prospecting in the deep sea is increasing, promoting concern regarding potential ecotoxicological impacts on deep-sea fauna. Technological difficulties in assessing toxicity in deep-sea species has promoted interest in developing shallow-water ecotoxicological proxy species. However, it is unclear how the low temperature and high hydrostatic pressure prevalent in the deep sea affect toxicity, and whether adaptation to deep-sea environmental conditions moderates any effects of these factors. To address these uncertainties we assessed the effects of temperature and hydrostatic pressure on lethal and sublethal (respiration rate, antioxidant enzyme activity) toxicity in acute (96 h) copper and cadmium exposures, using the shallow-water ecophysiological model organism Palaemon varians. Low temperature reduced toxicity in both metals, but reduced cadmium toxicity significantly more. In contrast, elevated hydrostatic pressure increased copper toxicity, but did not affect cadmium toxicity. The synergistic interaction between copper and cadmium was not affected by low temperature, but high hydrostatic pressure significantly enhanced the synergism. Differential environmental effects on toxicity suggest different mechanisms of action for copper and cadmium, and highlight that mechanistic understanding of toxicity is fundamental to predicting environmental effects on toxicity. Although results infer that sensitivity to toxicants differs across biogeographic ranges, shallow-water species may be suitable ecotoxicological proxies for deep-sea species, dependent on adaptation to habitats with similar environmental variability.

Genome size variation in deep-sea amphipods

Genome size varies considerably across taxa, and extensive research effort has gone into understanding whether variation can be explained by differences in key ecological and life-history traits among species. The extreme environmental conditions that characterize the deep sea have been hypothesized to promote large genome sizes in eukaryotes. Here we test this supposition by examining genome sizes among 13 species of deep-sea amphipods from the Mariana, Kermadec and New Hebrides trenches. Genome sizes were estimated using flow cytometry and found to vary nine-fold, ranging from 4.06 pg (4.04 Gb) in Paralicella caperesca to 34.79 pg (34.02 Gb) in Alicella gigantea. Phylogenetic independent contrast analysis identified a relationship between genome size and maximum body size, though this was largely driven by those species that display size gigantism. There was a distinct shift in the genome size trait diversification rate in the supergiant amphipod A. gigantea relative to the rest of the group. The variation in genome size observed is striking and argues against genome size being driven by a common evolutionary history, ecological niche and life-history strategy in deep-sea amphipods.

The genomic basis of cichlid fish adaptation within the deepwater "twilight zone" of Lake Malawi

Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 50 m. We use population‐level RAD‐seq data to investigate whether four endemic deepwater species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology, and haemoglobin, many not previously implicated in cichlid adaptive radiations. Colocalization of functionally linked genes suggests coadapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions and signatures of positive selection in candidate genes. Our data provide unique insights into genomic adaptation within deepwater habitats, and suggest genome‐level specialization for life at depth as an important process in cichlid radiation.

The importance of offshore origination revealed through ophiuroid phylogenomics

Our knowledge of macro-evolutionary processes in the deep sea is poor, leading to much speculation about whether the deep sea is a source or sink of evolutionary adaptation. Here, we use a phylogenetic approach, on large molecular (688 species, 275 kbp) and distributional datasets (104 513 records) across an entire class of marine invertebrates (Ophiuroidea), to infer rates of bathymetric range shift over time between shallow and deep water biomes. Biome conservation is evident through the phylogeny, with the majority of species in most clades distributed within the same bathome. Despite this, bathymetric shifts have occurred. We inferred from ancestral reconstructions that eurybathic or intermediate distributions across both biomes were a transitional state and direct changes between shallow and deep sea did not occur. The macro-evolutionary pattern of bathome shift appeared to reflect micro-evolutionary processes of bathymetric speciation. Results suggest that most of the oldest clades have a deep-sea origin, but multiple colonization events indicate that the evolution of this group conforms neither to a simple onshore-offshore hypothesis, nor the opposite pattern. Both shallow and deep bathomes have played an important role in generating the current diversity of this major benthic class.

Thermal Preference Ranges Correlate with Stable Signals of Universal Stress Markers in Lake Baikal Endemic and Holarctic Amphipods

Temperature is the most pervasive abiotic environmental factor for aquatic organisms. Fluctuations in temperature range lead to changes in metabolic performance. Here, we aimed to identify whether surpassing the thermal preference zones is correlated with shifts in universal cellular stress markers of protein integrity, responses to oxidative stress and lactate content, as indicators of anaerobic metabolism. Exposure of the Lake Baikal endemic amphipod species Eulimnogammarus verrucosus (Gerstfeldt, 1858), Ommatogammarus flavus (Dybowski, 1874) and of the Holarctic amphipod Gammarus lacustris Sars 1863 (Amphipoda, Crustacea) to increasing temperatures resulted in elevated heat shock protein 70 (Hsp70) and lactate content, elevated antioxidant enzyme activities (i.e., catalase and peroxidase), and reduced lactate dehydrogenase and glutathione S-transferase activities. Thus, the zone of stability (absence of any significant changes) of the studied molecular and biochemical markers correlated with the behaviorally preferred temperatures. We conclude that the thermal behavioral responses of the studied amphipods are directly related to metabolic processes at the cellular level. Thus, the determined thermal ranges may possibly correspond to the thermal optima. This relationship between species-specific behavioral reactions and stress response metabolism may have significant ecological consequences that result in a thermal zone-specific distribution (i.e., depths, feed spectrum, etc.) of species. As a consequence, by separating species with different temperature preferences, interspecific competition is reduced, which, in turn, increases a species' Darwinian fitness in its environment.

Functional, size and taxonomic diversity of fish along a depth gradient in the deep sea

Biodiversity is well studied in ecology and the concept has been developed to include traits of species, rather than solely taxonomy, to better reflect the functional diversity of a system. The deep sea provides a natural environmental gradient within which to study changes in different diversity metrics, but traits of deep-sea fish are not widely known, hampering the application of functional diversity to this globally important system. We used morphological traits to determine the functional richness and functional divergence of demersal fish assemblages along the continental slope in the Northeast Atlantic, at depths of 300-2,000 m. We compared these metrics to size diversity based on individual body size and species richness. Functional richness and size diversity showed similar patterns, with the highest diversity at intermediate depths; functional divergence showed the opposite pattern, with the highest values at the shallowest and deepest parts of the study site. Species richness increased with depth. The functional implications of these patterns were deduced by examining depth-related changes in morphological traits and the dominance of feeding guilds as illustrated by stable isotope analyses. The patterns in diversity and the variation in certain morphological traits can potentially be explained by changes in the relative dominance of pelagic and benthic feeding guilds. All measures of diversity examined here suggest that the deep areas of the continental slope may be equally or more diverse than assemblages just beyond the continental shelf.

Contrasted phylogeographic patterns on mitochondrial DNA of shallow and deep brittle stars across the Atlantic-Mediterranean area

Previous studies on Ophiothrix in European waters demonstrated the existence of two distinct species, Ophiothrix fragilis and Ophiothrix sp. II. Using phylogenetic and species delimitation techniques based on two mitochondrial genes (cytochrome c oxidase I and 16S rRNA) we prove the existence of a new congeneric species (Ophiothrix sp. III), occurring in the deep Atlantic coast of the Iberian Peninsula and the Alboran Sea. We compared phylogeographic patterns of these three Ophiothrix species to test whether closely related species are differentially affected by past demographic events and current oceanographic barriers. We used 432 sequences (137 of O. fragilis, 215 of Ophiothrix sp. II, and 80 of Ophiothrix sp. III) of the 16S rRNA from 23 Atlantic-Mediterranean locations for the analyses. We observed different geographic and bathymetric distributions, and contrasted phylogeography among species. Ophiothrix fragilis appeared genetically isolated between the Atlantic and Mediterranean basins, attributed to past vicariance during Pleistocene glaciations and a secondary contact associated to demographic expansion. This contrasts with the panmixia observed in Ophiothrix sp. II across the Atlantic-Mediterranean area. Results were not conclusive for Ophiothrix sp. III due to the lack of a more complete sampling within the Mediterranean Sea.