Trophic transfer, bioaccumulation and translocation of microplastics in an international listed wetland on the Montreux record

Microplastics (MPs) are concerning emerging pollutants. Here, MPs in four edible aquatic species of different trophic levels (between ∼2-4), including fish species Esox lucius (Esocidae: Esocinae); Cyprinus carpio (Cyprinidae: Cyprininae); and Luciobarbus caspius (Cyprinidae: Barbinae); and the swan mussel Anodonta cygnea (Unionidae), were assessed in the Anzali freshwater ecosystem. It is a listed wetland in the Montreux record. MPs were extracted from gastrointestinal tracts (GI), gills, muscles, and skin. All the studied fish and mussels (n = 33) had MPs. MP fibres, fragments and sheets were detected in every GI examined, however, fibres were the only type of MPs in skins, muscles and gills and were the most abundant MP. The MPs found in the fish and mussels were mainly made of nylon (35% of the total MPs), polypropylene-low density polyethylene (30%), and polycarbonate (25%). The average numbers of MPs found in every fish specimen, expressed per wet body mass, had a moderate negative correlation with the condition factor (K) (MP/g - K: Pearson correlation r= -0.413, p = 0.049), and there was no significant relation with the growth factor (b) (r = -0.376; p = 0.068). Importantly, Luciobarbus caspius (with trophic level 2.7-2.8) bioaccumulated MPs and presented a strong correlation between their MP contamination and age (r = 0.916 p < 0.05). Greater gill mass (or related factors) played an important role in the accumulation of MPs, and there was a strong correlation between these factors for Esox lucius and Cyprinus carpio (r = 0.876; r = 0.846; p < 0.05 respectively). The highest MP/g gills (1.91±2.65) were in the filter feeder Anodonta cygnea inhabiting the benthic zone. Esox lucius (piscivorous, trophic level 4.1) was the most contaminated species overall (a total of 83 MPs in 8 individuals, with 0.92 MPs/g fish), and their gills where MPs mainly accumulated. Cyprinus carpio was the most contaminated specimen (MPs in specimens), while the number of MPs per mass unit increased with the trophic level. Their feeding and ecological behavior in the aquatic habitat affected the level of accumulation. This work includes evidence of translocation of MPs within the aquatic organisms.

Foraging-induced craniofacial plasticity is associated with an early, robust and dynamic transcriptional response

Phenotypic plasticity is the ability of a single genotype to vary its phenotype in response to the environment. Plasticity of the skeletal system in response to mechanical input is widely studied, but the timing of its transcriptional regulation is not well understood. Here, we used the cichlid feeding apparatus to examine the transcriptional dynamics of skeletal plasticity over time. Using three closely related species that vary in their ability to remodel bone and a panel of 11 genes, including well-studied skeletal differentiation markers and newly characterized environmentally sensitive genes, we examined plasticity at one, two, four and eight weeks following the onset of alternate foraging challenges. We found that the plastic species exhibited environment-specific bursts in gene expression beginning at one week, followed by a sharp decline in levels, while the species with more limited plasticity exhibited consistently low levels of gene expression. This trend held across nearly all genes, suggesting that it is a hallmark of the larger plasticity regulatory network. We conclude that plasticity of the cichlid feeding apparatus is not the result of slowly accumulating gene expression difference over time, but rather is stimulated by early bursts of environment-specific gene expression followed by a return to homeostatic levels.

Colonization, diversity, and seasonality of fishes at pelagic fish aggregating devices

The pelagic zone of the ocean can be a challenging environment in which to conduct research and as a result we lack the robust baseline abundance and diversity data, compared to what is available in more accessible coastal habitats, to be able to track changes or stressors to the biota in this environment. Many large-scale fisheries target pelagic fish, and much of the information available on these species is based on fisheries-dependent data that may be biased towards hotspots and commercially valuable fishes. Here, a long-term video and visual fish survey was conducted on two subsurface moored fish aggregating devices (FADs) in the pelagic waters of the central Bahamas to determine the feasibility of using moored pelagic FADs as tools for collecting fish abundance and diversity data. A wide range of species was documented, including large migratory fish that are the focus of commercial and recreational fisheries, and smaller often overlooked species on which little abundance or seasonality information exists. We found that FADs colonize quickly and reach a peak stable (albeit seasonally cyclical) abundance and diversity within the first several months after deployment. Species richness was higher in video surveys, but abundance was higher in visual surveys, except for sharks. Our results highlight the need to tailor survey methods to fit the context and study objective, and provide further evidence for the importance of fisheries-independent data in monitoring pelagic species.

Phylogenomic position of eupelagonemids, abundant, and diverse deep-ocean heterotrophs

Eupelagonemids, formerly known as Deep Sea Pelagic Diplonemids I (DSPD I), are among the most abundant and diverse heterotrophic protists in the deep ocean, but little else is known about their ecology, evolution, or biology in general. Originally recognized solely as a large clade of environmental ribosomal subunit RNA gene sequences (SSU rRNA), branching with a smaller sister group DSPD II, they were postulated to be diplonemids, a poorly studied branch of Euglenozoa. Although new diplonemids have been cultivated and studied in depth in recent years, the lack of cultured eupelagonemids has limited data to a handful of light micrographs, partial SSU rRNA gene sequences, a small number of genes from single amplified genomes, and only a single formal described species, Eupelagonema oceanica. To determine exactly where this clade goes in the tree of eukaryotes and begin to address the overall absence of biological information about this apparently ecologically important group, we conducted single-cell transcriptomics from two eupelagonemid cells. A SSU rRNA gene phylogeny shows that these two cells represent distinct subclades within eupelagonemids, each different from E. oceanica. Phylogenomic analysis based on a 125-gene matrix contrasts with the findings based on ecological survey data and shows eupelagonemids branch sister to the diplonemid subgroup Hemistasiidae.

Pelagic metagenome-assembled genomes from an estuarine salinity gradient in San Francisco Bay

San Francisco Bay (SFB) is a large and highly human-impacted estuarine system. We produced 449 metagenome-assembled genomes from SFB waters, collected along the salinity gradient, providing a rich data set to compare the metabolic potential of microorganisms from different salinity zones within SFB and to other estuarine systems.

Stepping up to genome scan allows stock differentiation in the worldwide distributed blue shark Prionace glauca

The blue shark Prionace glauca is a top predator with one of the widest geographical distributions of any shark species. It is classified as Critically Endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population. The blue shark was proposed as a possible archetype of the "grey zone of population differentiation," coined to designate cases where population structure may be too recent or too faint to be detected using a limited set of markers. Here, blue shark samples collected throughout its global range were sequenced using a specific RAD method (DArTseq), which recovered 37,655 genome-wide single nucleotide polymorphisms (SNPs). Two main groups emerged, with Mediterranean Sea and northern Atlantic samples (Northern population) differentiated significantly from the Indo-west Pacific samples (Southern population). Significant pairwise F_ST values indicated further genetic differentiation within the Atlantic Ocean, and between the Atlantic Ocean and the Mediterranean Sea. Reconstruction of recent demographic history suggested divergence between Northern and Southern populations occurred about 500 generations ago and revealed a drastic reduction in effective population size from a large ancestral population. Our results illustrate the power of genome scans to detect population structure and reconstruct demographic history in highly migratory marine species. Given that the management plans of the blue shark (targeted or bycatch) fisheries currently assume panmictic regional stocks, we strongly recommend that the results presented here be considered in future stock assessments and conservation strategies.

Quantifying Catch Rates, Shark Abundance and Depredation Rate at a Spearfishing Competition on the Great Barrier Reef, Australia

We developed and applied a method to quantify spearfisher effort and catch, shark interactions and shark depredation in a boat-based recreational spearfishing competition in the Great Barrier Reef Marine Park in Queensland. Survey questions were designed to collect targeted quantitative data whilst minimising the survey burden of spearfishers. We provide the first known scientific study of shark depredation during a recreational spearfishing competition and the first scientific study of shark depredation in the Great Barrier Reef region. During the two-day spearfishing competition, nine vessels with a total of 33 spearfishers reported a catch of 144 fish for 115 h of effort (1.25 fish per hour). A subset of the catch comprised nine eligible species under competition rules, of which 47 pelagic fish were weighed. The largest fish captured was a 34.4 kg Sailfish (Istiophorus platypterus). The most common species captured and weighed was Spanish Mackerel (Scomberomorus commerson). The total weight of eligible fish was 332 kg and the average weight of each fish was 7.1 kg. During the two-day event, spearfishers functioned as citizen scientists and counted 358 sharks (115 h effort), averaging 3.11 sharks per hour. Grey Reef Sharks (Carcharhinus amblyrhynchos) comprised 64% of sightings. Nine speared fish were fully depredated by sharks as spearfishers attempted to retrieve their catch, which equates to a depredation rate of 5.9%. The depredated fish included four pelagic fish and five reef fish. The shark species responsible were Grey Reef Shark (C. amblyrhynchos) (66%), Bull Shark (Carcharhinus leucas) (11%), Whitetip Reef Shark (Triaenodon obesus) (11%) and Great Hammerhead (Sphyrna mokarran) (11%). There were spatial differences in fish catch, shark sightings and rates of depredation. We developed a report card that compared average catch of fish, sightings of sharks per hour and depredation rate by survey area, which assists recreational fishers and marine park managers to assess spatio-temporal changes. The participating spearfishers can be regarded as experienced (average 18 days a year for average 13.4 years). Sixty percent of interviewees perceived that shark numbers have increased in the past 10 years, 33% indicated no change and 7% indicated shark numbers had decreased. Total fuel use of all vessels was 2819 L and was equivalent to 6.48 tons of greenhouse gas emissions for the competition.

Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay

Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of “Candidatus Nitrosomarinus catalina” SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB.

IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)—the largest estuary on the west coast of North America—and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.

DNA-metabarcoding reveals the importance of gelatinous zooplankton in the diet of Pandalus borealis, a keystone species in the Arctic

Information about the dietary composition of a species is crucial to understanding their position and role in the food web. Increasingly molecular approaches such as DNA-metabarcoding are used in studying trophic relations, not least because they may alleviate problems such as low taxonomic resolution or underestimation of digestible taxa in the diet. Here, we used DNA-metabarcoding with universal primers for cytochrome c oxidase I (COI), to study the diet composition of the Northern shrimp (Pandalus borealis), an Arctic keystone species with large socio-economic importance. Across locations, jellyfish and chaetognaths were the most important components in the diet of P. borealis, jointly accounting for 40-60% of the total read abundance. This dietary importance of gelatinous zooplankton contrasts sharply with published results based on SCA. At the same time, diet composition differed between fjord and shelf locations, pointing to different food webs supporting P. borealis in these two systems. Our study underscores the potential of molecular approaches to provide new insights into the diet of marine invertebrates that are difficult to obtain with traditional methods, and calls for a revision of the role of gelatinous zooplankton in the diet of the key Arctic species P. borealis, and in extension, Arctic food webs.

Autofluorescence Is a Common Trait in Different Oceanic Fungi

Natural autofluorescence is a widespread phenomenon observed in different types of tissues and organisms. Depending on the origin of the autofluorescence, its intensity can provide insights on the physiological state of an organism. Fungal autofluorescence has been reported in terrestrial and human-derived fungal samples. Yet, despite the recently reported ubiquitous presence and importance of marine fungi in the ocean, the autofluorescence of pelagic fungi has never been examined. Here, we investigated the existence and intensity of autofluorescence in five different pelagic fungal isolates. Preliminary experiments of fungal autofluorescence at different growth stages and nutrient conditions were conducted, reflecting contrasting physiological states of the fungi. In addition, we analysed the effect of natural autofluorescence on co-staining with DAPI. We found that all the marine pelagic fungi that were studied exhibited autofluorescence. The intensity of fungal autofluorescence changed depending on the species and the excitation wavelength used. Furthermore, fungal autofluorescence varied depending on the growth stage and on the concentration of available nutrients. Collectively, our results indicate that marine fungi can be auto-fluorescent, although its intensity depends on the species and growth condition. Hence, oceanic fungal autofluorescence should be considered in future studies when fungal samples are stained with fluorescent probes (i.e., fluorescence in situ hybridization) since this could lead to misinterpretation of results.

Vertically migrating Isoxys and the early Cambrian biological pump

The biological pump is crucial for transporting nutrients fixed by surface-dwelling primary producers to demersal animal communities. Indeed, the establishment of an efficient biological pump was likely a key factor enabling the diversification of animals over 500 Myr ago during the Cambrian explosion. The modern biological pump operates through two main vectors: the passive sinking of aggregates of organic matter, and the active vertical migration of animals. The coevolution of eukaryotes and sinking aggregates is well understood for the Proterozoic and Cambrian; however, little attention has been paid to the establishment of the vertical migration of animals. Here we investigate the morphological variation and hydrodynamic performance of the Cambrian euarthropod Isoxys. We combine elliptical Fourier analysis of carapace shape with computational fluid dynamics simulations to demonstrate that Isoxys species likely occupied a variety of niches in Cambrian oceans, including vertical migrants, providing the first quantitative evidence that some Cambrian animals were adapted for vertical movement in the water column. Vertical migration was one of several early Cambrian metazoan innovations that led to the biological pump taking on a modern-style architecture over 500 Myr ago.

Detection of the elusive Dwarf sperm whale (Kogia sima) using environmental DNA at Malpelo island (Eastern Pacific, Colombia)

Monitoring large marine mammals is challenging due to their low abundances in general, an ability to move over large distances and wide geographical range sizes.The distribution of the pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales is informed by relatively rare sightings, which does not permit accurate estimates of their distribution ranges. Hence, their conservation status has long remained Data Deficient (DD) in the Red list of the International Union for Conservation of Nature (IUCN), which prevent appropriate conservation measures.Environmental DNA (eDNA) metabarcoding uses DNA traces left by organisms in their environments to detect the presence of targeted taxon, and is here proved to be useful to increase our knowledge on the distribution of rare but emblematic megafauna.Retrieving eDNA from filtered surface water provides the first detection of the Dwarf sperm whale (Kogia sima) around the remote Malpelo island (Colombia).Environmental DNA collected during oceanic missions can generate better knowledge on rare but emblematic animals even in regions that are generally well sampled for other taxa.

Embryo Buoyancy and Cell Death Gene Expression During Embryogenesis of Yellow-Tail Kingfish Seriola lalandi

In pelagic fish, embryo buoyancy is a noteworthy aspect of the reproductive strategy, and is associated with overall quality, survival, and further developmental success. In captivity, the loss of buoyancy of early embryos correlates with high mortality that might be related to massive cell death. Therefore, the aim of this study was to evaluate under captivity conditions the expression of genes related to the apoptosis process during the early embryonic development of the pelagic fish Seriola lalandi, and its relationship to the buoyancy of embryos. The relative expression of bcl2, bax-like, casp9, casp8, and casp3 was evaluated by RT-qPCR and FasL/Fas protein levels by western blot in five development stages of embryos sorted as floating or low-floating. All genes examined were expressed in both floating and low-floating embryos up to 24 h of development. Expression of the pro-apoptotic factors bax, casp9, casp8, and casp3 was higher in low-floating as compared with floating embryos in a developmental stage-specific manner. In contrast, there was no difference in expression of bcl2 between floating and low-floating embryos. Fas protein was detected as a single band in floating embryos without changes in expression throughout development; however, in low-floating embryos, three higher intensity reactive bands were detected in the 24-h embryos. Interestingly, FasL was only detected at 24-h in floating embryos, whereas in low-floating samples this ligand was present at all stages, with a sharp increase as development progressed. Cell death, as evaluated by the terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay, was highly increased in low-floating embryos as compared to floating embryos throughout all developmental stages, with the highest levels observed during the gastrula stage and at 24 h. The results of this study suggest that an increase in cell death, probably associated with the intrinsic and extrinsic apoptosis pathways, is present in low-floating embryos that might explain their lower developmental potential under captivity conditions.

A new southern record of the holopelagic annelid Poeobius meseres Heath, 1930 (Flabelligeridae)

Background

The unusual holopelagic annelid Poeobiusmeseres Heath, 1930 (Flabelligeridae) was first collected from Monterey Bay, California and has been subsequently recorded across the northern Pacific from Japan to the Gulf of California. Rare occurrences in the eastern tropical Pacific have extended as far as 7° S off Peru.

New information

Using molecular phylogenetic analysis of a newly-collected specimen from the Salas y Gómez Ridge off Chile, we extend the known geographic range of P.meseres southwards by 2040 km. This subtropical specimen showed higher genetic similarity to a specimen from the type locality (< 1.5% pairwise COI distance) than to representatives from the Aleutian Islands and Japan (5-6%), establishing the first genetically-confirmed occurrence of this species in the Southern Hemisphere. The latitudinal range of P.meseres encompasses the sole collection locality, off Ecuador, of Enigmaterwielii Betrem, 1925, a pelagic annelid which has been compared to P.meseres, but is indeterminable due to an inadequate description. We therefore suggest that the earlier sole record of E.terwielii may have been an occurrence of what is known now as P.meseres.

Lifeform indicators reveal large-scale shifts in plankton across the North-West European shelf

Increasing direct human pressures on the marine environment, coupled with climate-driven changes, is a concern to marine ecosystems globally. This requires the development and monitoring of ecosystem indicators for effective management and adaptation planning. Plankton lifeforms (broad functional groups) are sensitive indicators of marine environmental change and can provide a simplified view of plankton biodiversity, building an understanding of change in lower trophic levels. Here, we visualize regional-scale multi-decadal trends in six key plankton lifeforms as well as their correlative relationships with sea surface temperature (SST). For the first time, we collate trends across multiple disparate surveys, comparing the spatially and temporally extensive Continuous Plankton Recorder (CPR) survey (offshore) with multiple long-term fixed station-based time-series (inshore) from around the UK coastline. These analyses of plankton lifeforms showed profound long-term changes, which were coherent across large spatial scales. For example, 'diatom' and 'meroplankton' lifeforms showed strong alignment between surveys and coherent regional-scale trends, with the 1998-2017 decadal average abundance of meroplankton being 2.3 times that of 1958-1967 for CPR samples in the North Sea. This major, shelf-wide increase in meroplankton correlated with increasing SSTs, and contrasted with a general decrease in holoplankton (dominated by small copepods), indicating a changing balance of benthic and pelagic fauna. Likewise, inshore-offshore gradients in dinoflagellate trends, with contemporary increases inshore contrasting with multi-decadal decreases offshore (approx. 75% lower decadal mean abundance), urgently require the identification of causal mechanisms. Our lifeform approach allows the collation of many different data types and time-series across the NW European shelf, providing a crucial evidence base for informing ecosystem-based management, and the development of regional adaptation plans.

The evolution of specialized dentition in the deep-sea lanternfishes (Myctophiformes)

The evolution of heterodonty, the possession of varied tooth morphologies on the jaws of animals, has been relatively unexplored in ray-finned fishes compared to terrestrial vertebrates, and to an even lesser degree in deep-sea fish lineages. Lanternfishes (Myctophiformes) are an abundant and species-rich group endemic to deep-sea pelagic habitats. In this study, we document the presence of heterodonty on the oral jaws of lanternfishes, identifying differing anatomical and positional variations of dentition. We survey the anatomical variation in tooth morphology on the oral jaws of 114 lanternfish species across 37 genera and integrate our findings with a hypothesis of evolutionary relationships of lanternfishes to infer the number of times heterodonty evolved in this lineage. Our results indicate that heterodonty evolved at least six separate times on the oral jaws of lanternfishes, occurring as variable tooth morphologies in combination with villiform teeth. These combinations of tooth types include villiform plus hooked teeth, villiform plus hooked and recurved teeth, villiform plus spade, tricuspid, and hooked teeth, and villiform plus caniniform teeth. The reoccurring evolution of hooked teeth on the premaxilla and dentary in lanternfishes suggests heterodonty may serve an important functional role in their pelagic deep-sea environment. Hooked teeth could aid in securing and retaining prey in the oral cavity and allow for species to specialize on differing food resources, vital attributes for organisms living in open-ocean habitats.

Pelagic occurrences of the ice amphipod Apherusa glacialis throughout the Arctic

Apherusa glacialis is a common, sea ice-associated amphipod found throughout the Arctic Ocean and has long been considered permanently associated with the sea ice habitat. However, pelagic occurrences of A. glacialis have also been reported. It was recently suggested that A. glacialis overwinters at depth within the Atlantic-water inflow near Svalbard, to avoid being exported out of the Arctic Ocean through the Fram Strait. This study collated pelagic occurrence records over a 71-year period and found that A. glacialis was consistently found away from its presumed sea ice habitat on a pan-Arctic scale, in different depths and water masses. In the Svalbard region, A. glacialis was found in Atlantic Water both in winter and summer. Additionally, we analyzed A. glacialis size distributions throughout the year, collected mostly from sea ice, in order to elucidate potential life cycle strategies. The majority of young-of-the-year A. glacialis was found in the sea ice habitat during spring, supporting previous findings. Data on size distributions and sex ratios suggest a semelparous lifestyle. A synchronous seasonal vertical migration was not evident, but our data imply a more complex life history than previously assumed. We provide evidence that A. glacialis can no longer be regarded as an autochthonous sympagic species.

PelagiCam: a novel underwater imaging system with computer vision for semi-automated monitoring of mobile marine fauna at offshore structures

Engineered structures in the open ocean are becoming more frequent with the expansion of the marine renewable energy industry and offshore marine aquaculture. Floating engineered structures function as artificial patch reefs providing novel and relatively stable habitat structure not otherwise available in the pelagic water column. The enhanced physical structure can increase local biodiversity and benefit fisheries yet can also facilitate the spread of invasive species. Clear evidence of any ecological consequences will inform the design and placement of structures to either minimise negative impacts or enhance ecosystem restoration. The development of rapid, cost-effective and reliable remote underwater monitoring methods is crucial to supporting evidence-based decision-making by planning authorities and developers when assessing environmental risks and benefits of offshore structures. A novel, un-baited midwater video system, PelagiCam, with motion-detection software (MotionMeerkat) for semi-automated monitoring of mobile marine fauna, was developed and tested on the UK's largest offshore rope-cultured mussel farm in Lyme Bay, southwest England. PelagiCam recorded Atlantic horse mackerel (Trachurus trachurus), garfish (Belone belone) and two species of jellyfish (Chrysaora hysoscella and Rhizostoma pulmo) in open water close to the floating farm structure. The software successfully distinguished video frames where fishes were present versus absent. The PelagiCam system provides a cost-effective remote monitoring tool to streamline biological data acquisition in impact assessments of offshore floating structures. With the rise of sophisticated artificial intelligence for object recognition, the integration of computer vision techniques should receive more attention in marine ecology and has great potential to revolutionise marine biological monitoring.

Dive behaviour and foraging effort of female Cape fur seals Arctocephalus pusillus pusillus

While marine top predators can play a critical role in ecosystem structure and dynamics through their effects on prey populations, how the predators function in this role is often not well understood. In the Benguela region of southern Africa, the Cape fur seal (Arctocephalus pusillus pusillus) population constitutes the largest marine top predator biomass, but little is known of its foraging ecology other than its diet and some preliminary dive records. Dive information was obtained from 32 adult females instrumented with dive recorders at the Kleinsee colony (29°34.17' S, 16°59.80' E) in South Africa during 2006-2008. Most dives were in the depth range of epipelagic prey species (less than 50 m deep) and at night, reflecting the reliance of Cape fur seals on small, vertically migrating, schooling prey. However, most females also performed benthic dives, and benthic diving was prevalent in some individuals. Benthic diving was significantly associated with the frequency with which females exceeded their aerobic dive limit. The greater putative costs of benthic diving highlight the potential detrimental effects to Cape fur seals of well-documented changes in the availability of epipelagic prey species in the Benguela.

Depth-Dependent Environmental Drivers of Microbial Plankton Community Structure in the Northern Gulf of Mexico

The Gulf of Mexico (GoM) is a dynamic marine ecosystem influenced by multiple natural and anthropogenic processes and inputs, such as the intrusion of warm oligotrophic water via the Loop Current, freshwater and nutrient input by the Mississippi River, and hydrocarbon inputs via natural seeps and industrial spills. Microbial plankton communities are important to pelagic food webs including in the GoM but understanding the drivers of the natural dynamics of these passively distributed microorganisms can be challenging in such a large and heterogeneous system. As part of the DEEPEND consortium, we applied high throughput 16S rRNA sequencing to investigate the spatial and temporal dynamics of pelagic microbial plankton related to several environmental conditions during two offshore cruises in 2015. Our results show dramatic community shifts across depths, especially between photic and aphotic zones. Though we only have two time points within a single year, observed temporal shifts in microbial plankton communities were restricted to the seasonally influenced epipelagic zone (0-200 m), and appear mainly driven by changes in temperature. Environmental selection in microbial plankton communities was depth-specific, with variables such as turbidity, salinity, and abundance of photosynthetic taxa strongly correlating with community structure in the epipelagic zone, while variables such as oxygen and specific nutrient concentrations were correlated with community structure at deeper depths.

The Palaeozoic colonization of the water column and the rise of global nekton

The colonization of the water column is among the most important transformations in the evolution of animal life and global ecosystems. The Devonian nekton revolution has been identified as a major macroevolutionary event signifying the rapid occupation of the water column by independent radiations of swimming animals. Using new data, an expanded taxonomic coverage, sample standardization and increased ecological resolution, we analysed patterns of nektonization during the Palaeozoic. We find that nekton and eunekton were well established prior to the Devonian and did not diversify dramatically during any Palaeozoic interval. Relative nektic diversity and occurrences decreased rather than increased during the Devonian. Eunektic diversity and occurrences increased throughout the Palaeozoic, but this rise was protracted and cannot be attributed to any single interval. Our new data indicate that the metazoan colonization of the water column was considerably more complex and gradual than previously understood.

Spatial distributions of Southern Ocean mesozooplankton communities have been resilient to long-term surface warming

The biogeographic response of oceanic planktonic communities to climatic change has a large influence on the future stability of marine food webs and the functioning of global biogeochemical cycles. Temperature plays a pivotal role in determining the distribution of these communities and ocean warming has the potential to cause major distributional shifts, particularly in polar regions where the thermal envelope is narrow. We considered the impact of long-term ocean warming on the spatial distribution of Southern Ocean mesozooplankton communities through examining plankton abundance in relation to sea surface temperature between two distinct periods, separated by around 60 years. Analyses considered 16 dominant mesozooplankton taxa (in terms of biomass and abundance) in the southwest Atlantic sector of the Southern Ocean, from net samples and in situ temperature records collected during the Discovery Investigations (1926-1938) and contemporary campaigns (1996-2013). Sea surface temperature was found to have increased significantly by 0.74°C between the two eras. The corresponding sea surface temperature at which community abundance peaked was also significantly higher in contemporary times, by 0.98°C. Spatial projections indicated that the geographical location of community peak abundance had remained the same between the two eras despite the poleward advance of sea surface isotherms. If the community had remained within the same thermal envelope as in the 1920s-1930s, community peak abundance would be 500 km further south in the contemporary era. Studies in the northern hemisphere have found that dominant taxa, such as calanoid copepods, have conserved their thermal niches and tracked surface isotherms polewards. The fact that this has not occurred in the Southern Ocean suggests that other selective pressures, particularly food availability and the properties of underlying water masses, place greater constraints on spatial distributions in this region. It further demonstrates that this community is thermally resilient to present levels of sea surface warming.

The shrimp superfamily Sergestoidea: a global phylogeny with definition of new families and an assessment of the pathways into principal biotopes

The phylogenetic analysis of Sergestoidea based on 253 morphological characters and encompassing all 99 valid species confirmed all previously recognized genus-level clades. Analysis retrieved five major robust clades that correspond to families Luciferidae, Sergestidae, Acetidae fam.n., Sicyonellidae fam.n. and Petalidiumidae fam.n. Synonymy, emended diagnoses and composition of revealed family-level clades are provided. Three types of morphological characters were important in the phylogeny of the Sergestoidea: general external characters, copulatory organs, and photophores. Novel metrics to quantify the contribution of these character types were tested. General external characters were significant in supporting the major clades (80% of the families and nearly half of the genera). Copulatory organ characters and photophores greatly supported the medium-level clades: Lucifer, Belzebub, Petalidium, Neosergestes, Challengerosergia (copulatory organ characters) and Lucensosergia, Challengerosergia, Gardinerosergia, Phorcosergia (photophores). An evolutionary model of the Sergestoidea showing their pathways into their principal biotopes is proposed: the major clades evolved in a vertical direction (from epi- to bathypelagic); further divergence at the genus level occurred within vertical zones in a horizontal direction, with the invasion of the benthopelagic and neritic (shelf and estuarine) habitats and speciation within these domains.

The importance of benthic-pelagic coupling for marine ecosystem functioning in a changing world

Benthic-pelagic coupling is manifested as the exchange of energy, mass, or nutrients between benthic and pelagic habitats. It plays a prominent role in aquatic ecosystems, and it is crucial to functions from nutrient cycling to energy transfer in food webs. Coastal and estuarine ecosystem structure and function are strongly affected by anthropogenic pressures; however, there are large gaps in our understanding of the responses of inorganic nutrient and organic matter fluxes between benthic habitats and the water column. We illustrate the varied nature of physical and biological benthic-pelagic coupling processes and their potential sensitivity to three anthropogenic pressures - climate change, nutrient loading, and fishing - using the Baltic Sea as a case study and summarize current knowledge on the exchange of inorganic nutrients and organic material between habitats. Traditionally measured benthic-pelagic coupling processes (e.g., nutrient exchange and sedimentation of organic material) are to some extent quantifiable, but the magnitude and variability of biological processes are rarely assessed, preventing quantitative comparisons. Changing oxygen conditions will continue to have widespread effects on the processes that govern inorganic and organic matter exchange among habitats while climate change and nutrient load reductions may have large effects on organic matter sedimentation. Many biological processes (predation, bioturbation) are expected to be sensitive to anthropogenic drivers, but the outcomes for ecosystem function are largely unknown. We emphasize how improved empirical and experimental understanding of benthic-pelagic coupling processes and their variability are necessary to inform models that can quantify the feedbacks among processes and ecosystem responses to a changing world.

Tambora and the mackerel year: Phenology and fisheries during an extreme climate event

Global warming has increased the frequency of extreme climate events, yet responses of biological and human communities are poorly understood, particularly for aquatic ecosystems and fisheries. Retrospective analysis of known outcomes may provide insights into the nature of adaptations and trajectory of subsequent conditions. We consider the 1815 eruption of the Indonesian volcano Tambora and its impact on Gulf of Maine (GoM) coastal and riparian fisheries in 1816. Applying complex adaptive systems theory with historical methods, we analyzed fish export data and contemporary climate records to disclose human and piscine responses to Tambora's extreme weather at different spatial and temporal scales while also considering sociopolitical influences. Results identified a tipping point in GoM fisheries induced by concatenating social and biological responses to extreme weather. Abnormal daily temperatures selectively affected targeted fish species-alewives, shad, herring, and mackerel-according to their migration and spawning phenologies and temperature tolerances. First to arrive, alewives suffered the worst. Crop failure and incipient famine intensified fishing pressure, especially in heavily settled regions where dams already compromised watersheds. Insufficient alewife runs led fishers to target mackerel, the next species appearing in abundance along the coast; thus, 1816 became the "mackerel year." Critically, the shift from riparian to marine fisheries persisted and expanded after temperatures moderated and alewives recovered. We conclude that contingent human adaptations to extraordinary weather permanently altered this complex system. Understanding how adaptive responses to extreme events can trigger unintended consequences may advance long-term planning for resilience in an uncertain future.

Body size-trophic position relationships among fishes of the lower Mekong basin

Body size is frequently claimed to be a major determinant of animal trophic interactions, yet few studies have explored relationships between body size and trophic interactions in rivers, especially within the tropics. We examined relationships between body size and trophic position (TP) within fish assemblages in four lowland rivers of the Lower Mekong Basin in Cambodia. Stable isotope analysis (based on δ¹⁵N) was used to estimate TP of common fish species in each river, and species were classified according to occupation of benthic versus pelagic habitats and major feeding guilds. Regression analysis yielded strong correlations between body size and TP among fishes from the Sesan and Sreprok rivers, but not those from the Mekong and Sekong rivers. The Mekong fish assemblage had higher average TP compared with those of other rivers. The relationship between body size and TP was positive and significantly correlated for piscivores and omnivores, but not for detritivores and insectivores. The body size-TP relationship did not differ between pelagic and benthic fishes. Body size significantly predicted TP within the orders Siluriformes and Perciformes, but not for Cypriniformes, the most species-rich and ecologically diverse order in the Lower Mekong River. We conclude that for species-rich, tropical fish assemblages with many detritivores and invertivores, body size would not be an appropriate surrogate for TP in food web models and other ecological applications.

Predator-guided sampling reveals biotic structure in the bathypelagic

We targeted a habitat used differentially by deep-diving, air-breathing predators to empirically sample their prey's distributions off southern California. Fine-scale measurements of the spatial variability of potential prey animals from the surface to 1,200 m were obtained using conventional fisheries echosounders aboard a surface ship and uniquely integrated into a deep-diving autonomous vehicle. Significant spatial variability in the size, composition, total biomass, and spatial organization of biota was evident over all spatial scales examined and was consistent with the general distribution patterns of foraging Cuvier's beaked whales (Ziphius cavirostris) observed in separate studies. Striking differences found in prey characteristics between regions at depth, however, did not reflect differences observed in surface layers. These differences in deep pelagic structure horizontally and relative to surface structure, absent clear physical differences, change our long-held views of this habitat as uniform. The revelation that animals deep in the water column are so spatially heterogeneous at scales from 10 m to 50 km critically affects our understanding of the processes driving predator-prey interactions, energy transfer, biogeochemical cycling, and other ecological processes in the deep sea, and the connections between the productive surface mixed layer and the deep-water column.

A PELAGIC OUTBREAK OF AVIAN CHOLERA IN NORTH AMERICAN GULLS: SCAVENGING AS A PRIMARY MECHANISM FOR TRANSMISSION?

Avian cholera, caused by the bacterium Pasteurella multocida , is an endemic disease globally, often causing annual epizootics in North American wild bird populations with thousands of mortalities. From December 2006 to March 2007, an avian cholera outbreak caused mortality in marine birds off the coast of Atlantic Canada, largely centered 300-400 km off the coast of the island of Newfoundland. Scavenging gulls ( Larus spp.) were the primary species detected; however, mortality was also identified in Black-legged Kittiwakes ( Rissa tridactyla ) and one Common Raven ( Corvus corax ), a nonmarine species. The most common gross necropsy findings in the birds with confirmed avian cholera were acute fibrinous and necrotizing lesions affecting the spleen, air sacs, and pericardium, and nonspecific hepatomegaly and splenomegaly. The etiologic agent, P. multocida serotype 1, was recovered from 77 of 136 carcasses examined, and confirmed or probable avian cholera was diagnosed in 85 cases. Mortality observed in scavenging gull species was disproportionately high relative to their abundance, particularly when compared to nonscavenging species. The presence of feather shafts in the ventricular lumen of the majority of larid carcasses diagnosed with avian cholera suggests scavenging of birds that died from avian cholera as a major mode of transmission. This documentation of an outbreak of avian cholera in a North American pelagic environment affecting primarily scavenging gulls indicates that offshore marine environments may be a component of avian cholera dynamics.

Estuarine fish communities respond to climate variability over both river and ocean basins

Estuaries are dynamic environments at the land-sea interface that are strongly affected by interannual climate variability. Ocean-atmosphere processes propagate into estuaries from the sea, and atmospheric processes over land propagate into estuaries from watersheds. We examined the effects of these two separate climate-driven processes on pelagic and demersal fish community structure along the salinity gradient in the San Francisco Estuary, California, USA. A 33-year data set (1980-2012) on pelagic and demersal fishes spanning the freshwater to marine regions of the estuary suggested the existence of five estuarine salinity fish guilds: limnetic (salinity = 0-1), oligohaline (salinity = 1-12), mesohaline (salinity = 6-19), polyhaline (salinity = 19-28), and euhaline (salinity = 29-32). Climatic effects propagating from the adjacent Pacific Ocean, indexed by the North Pacific Gyre Oscillation (NPGO), affected demersal and pelagic fish community structure in the euhaline and polyhaline guilds. Climatic effects propagating over land, indexed as freshwater outflow from the watershed (OUT), affected demersal and pelagic fish community structure in the oligohaline, mesohaline, polyhaline, and euhaline guilds. The effects of OUT propagated further down the estuary salinity gradient than the effects of NPGO that propagated up the estuary salinity gradient, exemplifying the role of variable freshwater outflow as an important driver of biotic communities in river-dominated estuaries. These results illustrate how unique sources of climate variability interact to drive biotic communities and, therefore, that climate change is likely to be an important driver in shaping the future trajectory of biotic communities in estuaries and other transitional habitats.

Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod

Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open-ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite FST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.

Assessing niche width of endothermic fish from genes to ecosystem

Endothermy in vertebrates has been postulated to confer physiological and ecological advantages. In endothermic fish, niche expansion into cooler waters is correlated with specific physiological traits and is hypothesized to lead to greater foraging success and increased fitness. Using the seasonal co-occurrence of three tuna species in the eastern Pacific Ocean as a model system, we used cardiac gene expression data (as a proxy for thermal tolerance to low temperatures), archival tag data, and diet analyses to examine the vertical niche expansion hypothesis for endothermy in situ. Yellowfin, albacore, and Pacific bluefin tuna (PBFT) in the California Current system used more surface, mesopelagic, and deep waters, respectively. Expression of cardiac genes for calcium cycling increased in PBFT and coincided with broader vertical and thermal niche utilization. However, the PBFT diet was less diverse and focused on energy-rich forage fishes but did not show the greatest energy gains. Ecosystem-based management strategies for tunas should thus consider species-specific differences in physiology and foraging specialization.

Systematically variable planktonic carbon metabolism along a land-to-lake gradient in a Great Lakes coastal zone

During the summers of 2002-2013, we measured rates of carbon metabolism in surface waters of six sites across a land-to-lake gradient from the upstream end of drowned river-mouth Muskegon Lake (ML) (freshwater estuary) to 19 km offshore in Lake Michigan (LM) (a Great Lake). Despite considerable inter-year variability, the average rates of gross production (GP), respiration (R) and net production (NP) across ML (604 ± 58, 222 ± 22 and 381 ± 52 µg C L^-1 day^-1, respectively) decreased steeply in the furthest offshore LM site (22 ± 3, 55 ± 17 and -33 ± 15 µg C L^-1day^-1, respectively). Along this land-to-lake gradient, GP decreased by 96 ± 1%, whereas R only decreased by 75 ± 9%, variably influencing the carbon balance along this coastal zone. All ML sites were consistently net autotrophic (mean GP:R = 2.7), while the furthest offshore LM site was net heterotrophic (mean GP:R = 0.4). Our study suggests that pelagic waters of this Great Lakes coastal estuary are net carbon sinks that transition into net carbon sources offshore. Reactive and dynamic estuarine coastal zones everywhere may contribute similarly to regional and global carbon cycles.

Latitudinal and photic effects on diel foraging and predation risk in freshwater pelagic ecosystems

Clark & Levy (American Naturalist, 131, 1988, 271-290) described an antipredation window for smaller planktivorous fish during crepuscular periods when light permits feeding on zooplankton, but limits visual detection by piscivores. Yet, how the window is influenced by the interaction between light regime, turbidity and cloud cover over a broad latitudinal gradient remains unexplored. We evaluated how latitudinal and seasonal shifts in diel light regimes alter the foraging-risk environment for visually feeding planktivores and piscivores across a natural range of turbidities and cloud covers. Pairing a model of aquatic visual feeding with a model of sun and moon illuminance, we estimated foraging rates of an idealized planktivore and piscivore over depth and time across factorial combinations of latitude (0-70°), turbidity (0.1-5 NTU) and cloud cover (clear to overcast skies) during the summer solstice and autumnal equinox. We evaluated the foraging-risk environment based on changes in the magnitude, duration and peak timing of the antipredation window. The model scenarios generated up to 10-fold shifts in magnitude, 24-fold shifts in duration and 5.5-h shifts in timing of the peak antipredation window. The size of the window increased with latitude. This pattern was strongest during the solstice. In clear water at low turbidity (0.1-0.5 NTU), peaks in the magnitude and duration of the window formed at 57-60° latitude, before falling to near zero as surface waters became saturated with light under a midnight sun and clear skies at latitudes near 70°. Overcast dampened the midnight sun enough to allow larger windows to form in clear water at high latitudes. Conversely, at turbidities ≥ 2 NTU, greater reductions in the visual range of piscivores than planktivores created a window for long periods at high latitudes. Latitudinal dependencies were essentially lost during the equinox, indicating a progressive compression of the window from early summer into autumn. Model results show that diel-seasonal foraging and predation risk in freshwater pelagic ecosystems changes considerably with latitude, turbidity and cloud cover. These changes alter the structure of pelagic predator-prey interactions, and in turn, the broader role of pelagic consumers in habitat coupling in lakes.

Combined climate- and prey-mediated range expansion of Humboldt squid (Dosidicus gigas), a large marine predator in the California Current System

Climate-driven range shifts are ongoing in pelagic marine environments, and ecosystems must respond to combined effects of altered species distributions and environmental drivers. Hypoxic oxygen minimum zones (OMZs) in midwater environments are shoaling globally; this can affect distributions of species both geographically and vertically along with predator-prey dynamics. Humboldt (jumbo) squid (Dosidicus gigas) are highly migratory predators adapted to hypoxic conditions that may be deleterious to their competitors and predators. Consequently, OMZ shoaling may preferentially facilitate foraging opportunities for Humboldt squid. With two separate modeling approaches using unique, long-term data based on in situ observations of predator, prey, and environmental variables, our analyses suggest that Humboldt squid are indirectly affected by OMZ shoaling through effects on a primary food source, myctophid fishes. Our results suggest that this indirect linkage between hypoxia and foraging is an important driver of the ongoing range expansion of Humboldt squid in the northeastern Pacific Ocean.

Computational visual ecology in the pelagic realm

Visual performance and visual interactions in pelagic animals are notoriously hard to investigate because of our restricted access to the habitat. The pelagic visual world is also dramatically different from benthic or terrestrial habitats, and our intuition is less helpful in understanding vision in unfamiliar environments. Here, we develop a computational approach to investigate visual ecology in the pelagic realm. Using information on eye size, key retinal properties, optical properties of the water and radiance, we develop expressions for calculating the visual range for detection of important types of pelagic targets. We also briefly apply the computations to a number of central questions in pelagic visual ecology, such as the relationship between eye size and visual performance, the maximum depth at which daylight is useful for vision, visual range relations between prey and predators, counter-illumination and the importance of various aspects of retinal physiology. We also argue that our present addition to computational visual ecology can be developed further, and that a computational approach offers plenty of unused potential for investigations of visual ecology in both aquatic and terrestrial habitats.

Global fishmeal and fish-oil supply: inputs, outputs and markets

Recent data on fishmeal and fish-oil supply are presented identifying key producer countries and raw material sources and distinguishing between whole fish and by-products. The conversion of these raw materials into marine ingredients is discussed and global volumes presented. This is followed by a summary of the main countries using these marine ingredients over recent years. Uses of fishmeal and fish-oil by market segment are then presented. From this, a global mass balance of inputs and outputs is derived which allows the calculation of the input-to-output ratios (fish in:fish out; FIFO) for the main aquaculture production types to be made. Current areas of focus by the industry include the need to demonstrate sustainable practice, more strategic use of marine ingredients, greater use of fishery and land-animal by-products as well as vegetable substitutes, and novel sources of essential omega-3 fats, notably the long-chain polyunsaturated fatty acids, eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids. Implications are drawn for future supply prospects of fishmeal and fish-oil and their future role in aquaculture, agriculture and human health.

littoral fisheries

The food webs of littoral, pelagic, and littoral-pelagic ecotone (interface) regions of a large subtropical lake were investigated using stable isotope ratio methods, expanding the focus of a previous fish-only study to include other food web components such as primary producers and invertebrates. In these food webs, delta13C increased approximately 4 per thousand and delta15N increased approximately 10 per thousand from primary producers to fish. The delta15N of fish was approximately 9 per thousand in the littoral zone, approximately 10 per thousand in the ecotone, and approximately 12 per thousand in the pelagic zone. The cross-habitat enrichment in fish 15N corresponded with both an increase in the size of fish and an increase in the d15N of primary consumers (mollusks). Despite larger body size in the pelagic zone, fish in all three habitats appear to occur at the same average trophic level (TL = 4), assuming an enrichment factor of 3.4 per thousand per trophic level, and normalizing to the delta15N of primary consumers.