Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs.

BACKGROUND: Understanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained from Atlantic salmon (Salmo salar) gills by swabbing versus biopsy excision. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome. RESULTS: The microbiome was sampled using swabs and biopsies from fish gills, with identical treatment of samples for 16S next generation Illumina sequencing. Results show a clear divergence in microbial communities obtained through the different sampling strategies, with swabbing consistently isolating a more diverse microbial consortia, and suffering less from the technical issue of host DNA contamination associated with biopsy use. Sequencing results from biopsy-derived extractions, however, hint at the potential for more cryptic localisation of some community members. CONCLUSIONS: Overall, results demonstrate a divergence in the obtained microbial community when different sampling methodology is used. Swabbing appears a superior method for sampling the microbiota of mucosal surfaces for broad ecological research in fish, whilst biopsies might be best applied in exploration of communities beyond the reach of swabs, such as sub-surface and intracellular microbes, as well as in pathogen diagnosis. Most studies on the external microbial communities of aquatic organisms utilise swabbing for sample collection, likely due to convenience. Much of the ultrastructure of gill tissue in live fish is, however, potentially inaccessible to swabbing, meaning swabbing might fail to capture the full diversity of gill microbiota. This work therefore also provides valuable insight into partitioning of the gill microbiota, informing varied applications of different sampling methods in experimental design for future research.

Scaling laws of marine predator search behaviour.

Many free-ranging predators have to make foraging decisions with little, if any, knowledge of present resource distribution and availability. The optimal search strategy they should use to maximize encounter rates with prey in heterogeneous natural environments remains a largely unresolved issue in ecology. Lévy walks are specialized random walks giving rise to fractal movement trajectories that may represent an optimal solution for searching complex landscapes. However, the adaptive significance of this putative strategy in response to natural prey distributions remains untested. Here we analyse over a million movement displacements recorded from animal-attached electronic tags to show that diverse marine predators-sharks, bony fishes, sea turtles and penguins-exhibit Lévy-walk-like behaviour close to a theoretical optimum. Prey density distributions also display Lévy-like fractal patterns, suggesting response movements by predators to prey distributions. Simulations show that predators have higher encounter rates when adopting Lévy-type foraging in natural-like prey fields compared with purely random landscapes. This is consistent with the hypothesis that observed search patterns are adapted to observed statistical patterns of the landscape. This may explain why Lévy-like behaviour seems to be widespread among diverse organisms, from microbes to humans, as a 'rule' that evolved in response to patchy resource distributions.

Links between the three-dimensional movements of whale sharks (Rhincodon typus) and the bio-physical environment off a coral reef.

BACKGROUND: Measuring coastal-pelagic prey fields at scales relevant to the movements of marine predators is challenging due to the dynamic and ephemeral nature of these environments. Whale sharks (Rhincodon typus) are thought to aggregate in nearshore tropical waters due to seasonally enhanced foraging opportunities. This implies that the three-dimensional movements of these animals may be associated with bio-physical properties that enhance prey availability. To date, few studies have tested this hypothesis. METHODS: Here, we conducted ship-based acoustic surveys, net tows and water column profiling (salinity, temperature, chlorophyll fluorescence) to determine the volumetric density, distribution and community composition of mesozooplankton (predominantly euphausiids and copepods) and oceanographic properties of the water column in the vicinity of whale sharks that were tracked simultaneously using satellite-linked tags at Ningaloo Reef, Western Australia. Generalised linear mixed effect models were used to explore relationships between the 3-dimensional movement behaviours of tracked sharks and surrounding prey fields at a spatial scale of ~ 1 km. RESULTS: We identified prey density as a significant driver of horizontal space use, with sharks occupying areas along the reef edge where densities were highest. These areas were characterised by complex bathymetry such as reef gutters and pinnacles. Temperature and salinity profiles revealed a well-mixed water column above the height of the bathymetry (top 40 m of the water column). Regions of stronger stratification were associated with reef gutters and pinnacles that concentrated prey near the seabed, and entrained productivity at local scales (~ 1 km). We found no quantitative relationship between the depth use of sharks and vertical distributions of horizontally averaged prey density. Whale sharks repeatedly dove to depths where spatially averaged prey concentration was highest but did not extend the time spent at these depth layers. CONCLUSIONS: Our work reveals previously unrecognized complexity in interactions between whale sharks and their zooplankton prey.

Re-assessing thermal response of schistosomiasis transmission risk: evidence for a higher thermal optimum than previously predicted.

The geographical range of schistosomiasis is affected by the ecology of schistosome parasites and their obligate host snails, including their response to temperature. Previous models predicted schistosomiasis' thermal optimum at 21.7 °C, which is not compatible with the temperature in sub-Saharan Africa (SSA) regions where schistosomiasis is hyperendemic. We performed an extensive literature search for empirical data on the effect of temperature on physiological and epidemiological parameters regulating the free-living stages of S. mansoni and S. haematobium and their obligate host snails, i.e., Biomphalaria spp. and Bulinus spp., respectively. We derived nonlinear thermal responses fitted on these data to parameterize a mechanistic, process-based model of schistosomiasis. We then re-cast the basic reproduction number and the prevalence of schistosome infection as functions of temperature. We found that the thermal optima for transmission of S. mansoni and S. haematobium range between 23.1-27.3 °C and 23.6-27.9 °C (95 % CI) respectively. We also found that the thermal optimum shifts toward higher temperatures as the human water contact rate increases with temperature. Our findings align with an extensive dataset of schistosomiasis prevalence in SSA. The refined nonlinear thermal-response model developed here suggests a more suitable current climate and a greater risk of increased transmission with future warming for more than half of the schistosomiasis suitable regions with mean annual temperature below the thermal optimum.

Re-assessing thermal response of schistosomiasis transmission risk: Evidence for a higher thermal optimum than previously predicted.

The geographical range of schistosomiasis is affected by the ecology of schistosome parasites and their obligate host snails, including their response to temperature. Previous models predicted schistosomiasis' thermal optimum at 21.7°C, which is not compatible with the temperature in sub-Saharan Africa (SSA) regions where schistosomiasis is hyperendemic. We performed an extensive literature search for empirical data on the effect of temperature on physiological and epidemiological parameters regulating the free-living stages of S. mansoni and S. haematobium and their obligate host snails, i.e., Biomphalaria spp. and Bulinus spp., respectively. We derived nonlinear thermal responses fitted on these data to parameterize a mechanistic, process-based model of schistosomiasis. We then re-cast the basic reproduction number and the prevalence of schistosome infection as functions of temperature. We found that the thermal optima for transmission of S. mansoni and S. haematobium range between 23.1-27.3°C and 23.6-27.9°C (95% CI) respectively. We also found that the thermal optimum shifts toward higher temperatures as the human water contact rate increases with temperature. Our findings align with an extensive dataset of schistosomiasis prevalence in SSA. The refined nonlinear thermal-response model developed here suggests a more suitable current climate and a greater risk of increased transmission with future warming for more than half of the schistosomiasis suitable regions with mean annual temperature below the thermal optimum.

Changes in seasonal expression patterns of ecdysone receptor, retinoid X receptor and an A-type allatostatin in the copepod, Calanus finmarchicus, in a sea loch environment: an investigation of possible mediators of diapause.

The marine copepod, Calanus finmarchicus, is a crucial component of the pelagic food web in the North Atlantic and peripheral seas where it is a major player in biogeochemical cycles and the productivity of commercially important fisheries. A key stage in its life cycle is the emergence of the pre-adult, copepodite developmental stage five (CV) from a period of overwintering dormancy, known as diapause. As is the case in many insect species, diapause is also likely to be under endocrine control in C. finmarchicus. To investigate the hormonal regulation of diapause behaviour of stage CV C. finmarchicus, the expression of three key genes: ecdysone receptor (EcR), retinoid X receptor (RXR) and an A-type allatostatin (A-type AST), were measured in specimens collected at monthly intervals from Loch Etive, a ca. 150m deep sea loch on the west coast of Scotland, between June 2006 and May 2007. The full length RXR gene was cloned and sequenced from C. finmarchicus, and was found to share 49-53% total identity with equivalent genes encoding proteins from other crustaceans, and >80% identity in the DNA binding domain with other crustaceans, insects and vertebrates. EcR expression was least in December when the animals are expected to be in diapause, but began to increase in January, when the animals were terminating diapause. Concomittant with the rise in EcR in January was low expression of A-type AST and high expression of RXR.

Variability in prey field structure drives inter-annual differences in prey encounter by a marine predator, the little penguin.

Understanding how marine predators encounter prey across patchy landscapes remains challenging due to difficulties in measuring the three-dimensional structure of pelagic prey fields at scales relevant to animal movement. We measured at-sea behaviour of a central-place forager, the little penguin (Eudyptula minor), over 5 years (2015-2019) using GPS and dive loggers. We made contemporaneous measurements of the prey field within the penguins' foraging range via boat-based acoustic surveys. We developed a prey encounter index by comparing estimates of acoustic prey density encountered along actual penguin tracks to those encountered along simulated penguin tracks with the same characteristics as real tracks but that moved randomly through the prey field. In most years, penguin tracks encountered prey better than simulated random movements greater than 99% of the time, and penguin dive depths matched peaks in the vertical distribution of prey. However, when prey was unusually sparse and/or deep, penguins had worse than random prey encounter indices, exhibited dives that mismatched depth of maximum prey density, and females had abnormally low body mass (5.3% lower than average). Reductions in prey encounters owing to decreases in the density or accessibility of prey may ultimately lead to reduced fitness and population declines in central-place foraging marine predators.

Ecosystem approach to harvesting in the Arctic: Walking the tightrope between exploitation and conservation in the Barents Sea.

Projecting the consequences of warming and sea-ice loss for Arctic marine food web and fisheries is challenging due to the intricate relationships between biology and ice. We used StrathE2EPolar, an end-to-end (microbes-to-megafauna) food web model incorporating ice-dependencies to simulate climate-fisheries interactions in the Barents Sea. The model was driven by output from the NEMO-MEDUSA earth system model, assuming RCP 8.5 atmospheric forcing. The Barents Sea was projected to be > 95% ice-free all year-round by the 2040s compared to > 50% in the 2010s, and approximately 2 °C warmer. Fisheries management reference points (FMSY and BMSY) for demersal fish (cod, haddock) were projected to increase by around 6%, indicating higher productivity. However, planktivorous fish (capelin, herring) reference points were projected to decrease by 15%, and upper trophic levels (birds, mammals) were strongly sensitive to planktivorous fish harvesting. The results indicate difficult trade-offs ahead, between harvesting and conservation of ecosystem structure and function.

Antarctic ecosystem: are deep krill ecological outliers or portents of a paradigm shift?

Serendipitous observations of Antarctic krill feeding at abyssal depths may revolutionise our view of the ecology of this supposed surface-dwelling animal that is key to the function of the Southern Ocean ecosystem.

Bayesian Network Analysis reveals resilience of the jellyfish Aurelia aurita to an Irish Sea regime shift.

Robust time-series of direct observations of jellyfish abundance are not available for many ecosystems, leaving it difficult to determine changes in jellyfish abundance, the possible causes (e.g. climate change) or the consequences (e.g. trophic cascades). We sought an indirect ecological route to reconstruct jellyfish abundance in the Irish Sea: since zooplankton are jellyfish prey, historic variability in zooplankton communities may provide proxies for jellyfish abundance. We determined the Bayesian ecological network of jellyfish-zooplankton dependencies using jellyfish- and zooplankton-abundance data obtained using nets during a 2-week cruise to the Irish Sea in 2008. This network revealed that Aurelia aurita abundance was dependent on zooplankton groups Warm Temperate and Temperate Oceanic as defined by previous zooplankton ecology work. We then determined historic zooplankton networks across the Irish Sea from abundance data from Continuous Plankton Recorder surveys conducted between 1970 and 2000. Transposing the 2008 spatial dependencies onto the historic networks revealed that Aurelia abundance was more strongly dependent over time on sea surface temperature than on the zooplankton community. The generalist predatory abilities of Aurelia may have insulated this jellyfish over the 1985 regime shift when zooplankton composition in the Irish Sea changed abruptly, and also help explain its globally widespread distribution.

Improved bathymetry leads to >4000 new seamount predictions in the global ocean - but beware of phantom seamounts!

Seamounts are important marine habitats that are hotspots of species diversity. Relatively shallow peaks, increased productivity and offshore locations make seamounts vulnerable to human impact and difficult to protect. Present estimates of seamount numbers vary from anywhere between 10,000 to more than 60,000. Seamount locations can be estimated by extracting large, cone-like features from bathymetry grids (based on criteria of size and shape). These predicted seamounts are a useful reference for marine researchers and can help direct exploratory surveys. However, these predictions are dependent on the quality of the surveys underpinning the bathymetry. Historically, quality has been patchy, but is improving as mapping efforts step up towards the target of complete seabed coverage by 2030. This study presents an update of seamount predictions based on SRTM30 PLUS global bathymetry version 11 and examines a potential source of error in these predictions. This update was prompted by a seamount survey in the British Indian Ocean Territory in 2016, where locations of two putative seamounts were visited. These 'seamounts' were targeted based on previous predictions, but these features were not detected during echosounder surveys. An examination of UK hydrographic office navigational (Admiralty) charts for the area showed that the summits of these putative features had soundings reporting 'no bottom detected at this depth' where 'this depth' was similar to the seabed reported from the bathymetry grids: we suspect that these features likely resulted from an initial misreading of the charts. We show that 15 'phantom seamount' features, derived from a misinterpretation of no bottom sounding data, persist in current global bathymetry grids and updated seamount predictions. Overall, we predict 37,889 seamounts, an increase of 4437 from the previous predictions derived from an older global bathymetry grid (SRTM30 PLUS v6). This increase is due to greater detail in newer bathymetry grids as acoustic mapping of the seabed expands. The new seamount predictions are available at https://doi.pangaea.de/10.1594/PANGAEA.921688.

The Simrad EK60 echosounder dataset from the Malaspina circumnavigation.

We provide the raw acoustic data collected from the R/V Hesperides during the global Malaspina 2010 Spanish Circumnavigation Expedition (14th December 2010, Cádiz-14th July 2011, Cartagena) using a Simrad EK60 scientific echosounder operating at 38 and 120 kHz. The cruise was divided into seven legs: leg 1 (14th December 2010, Cádiz-13th January 2011, Rio de Janeiro), leg 2 (17th January 2011, Rio de Janeiro-6th February 2011, Cape Town), leg 3 (11th February 2011, Cape Town-13th March 2011, Perth), leg 4 (17th March 2011, Perth-30th March 2011, Sydney), leg 5 (16th April 2011, Auckland-8th May 2011, Honolulu), leg 6 (13th May 2011, Honolulu-10th June 2011, Cartagena de Indias) and leg 7 (19th June 2011, Cartagena de Indias-14th July 2011, Cartagena). The echosounder was calibrated at the start of the expedition and calibration parameters were updated in the data acquisition software (ER60) i.e., the logged raw data are calibrated. We also provide a data summary of the acoustic data in the form of post-processed products.

Krill and salp faecal pellets contribute equally to the carbon flux at the Antarctic Peninsula.

Krill and salps are important for carbon flux in the Southern Ocean, but the extent of their contribution and the consequences of shifts in dominance from krill to salps remain unclear. We present a direct comparison of the contribution of krill and salp faecal pellets (FP) to vertical carbon flux at the Antarctic Peninsula using a combination of sediment traps, FP production, carbon content, microbial degradation, and krill and salp abundances. Salps produce 4-fold more FP carbon than krill, but the FP from both species contribute equally to the carbon flux at 300 m, accounting for 75% of total carbon. Krill FP are exported to 72% to 300 m, while 80% of salp FP are retained in the mixed layer due to fragmentation. Thus, declining krill abundances could lead to decreased carbon flux, indicating that the Antarctic Peninsula could become a less efficient carbon sink for anthropogenic CO2 in future.

Gill Transcriptomic Responses to Toxin-producing Alga Prymnesium parvum in Rainbow Trout.

The gill of teleost fish is a multifunctional organ involved in many physiological processes, including protection of the mucosal gill surface against pathogens and other environmental antigens by the gill-associated lymphoid tissue (GIALT). Climate change associated phenomena, such as increasing frequency and magnitude of harmful algal blooms (HABs) put extra strain on gill function, contributing to enhanced fish mortality and fish kills. However, the molecular basis of the HAB-induced gill injury remains largely unknown due to the lack of high-throughput transcriptomic studies performed on teleost fish in laboratory conditions. We used juvenile rainbow trout (Oncorhynchus mykiss) to investigate the transcriptomic responses of the gill tissue to two (high and low) sublethal densities of the toxin-producing alga Prymnesium parvum, in relation to non-exposed control fish. The exposure time to P. parvum (4-5 h) was sufficient to identify three different phenotypic responses among the exposed fish, enabling us to focus on the common gill transcriptomic responses to P. parvum that were independent of dose and phenotype. The inspection of common differentially expressed genes (DEGs), canonical pathways, upstream regulators and downstream effects pointed towards P. parvum-induced inflammatory response and gill inflammation driven by alterations of Acute Phase Response Signalling, IL-6 Signalling, IL-10 Signalling, Role of PKR in Interferon Induction and Antiviral Response, IL-8 Signalling and IL-17 Signalling pathways. While we could not determine if the inferred gill inflammation was progressing or resolving, our study clearly suggests that P. parvum blooms may contribute to the serious gill disorders in fish. By providing insights into the gill transcriptomic responses to toxin-producing P. parvum in teleost fish, our research opens new avenues for investigating how to monitor and mitigate toxicity of HABs before they become lethal.

Oxidative stress, metabolic activity and mercury concentrations in Antarctic krill Euphausia superba and myctophid fish of the Southern Ocean.

Indicators of oxidative stress and metabolic capacity are key factors in understanding the fitness of wild populations. In the present study, these factors were evaluated in the pelagic Southern Ocean taxa Antarctic krill (Euphausia superba) and myctophid fish (Electrona antarctica, Gymnoscopelus braueri and G. nicholsi) to establish a baseline record for future studies. Mercury (Hg) concentrations were also analysed to evaluate its potential impacts on species biochemical performance. E. superba had higher metabolic activity than most of the myctophid species, which may explain the comparatively lower energy reserves found in the former. The activity of antioxidant enzymes showed, generally, a lower level in E. superba than in the myctophid species. The lack of any relationship between Hg concentrations and organisms' antioxidant and biotransformation defence mechanisms indicate that levels of Hg accumulated in the studied species were not high enough to affect their biochemical processes adversely.

Mercury biomagnification in a Southern Ocean food web.

Biomagnification of mercury (Hg) in the Scotia Sea food web of the Southern Ocean was examined using the stable isotope ratios of nitrogen (δ15N) and carbon (δ13C) as proxies for trophic level and feeding habitat, respectively. Total Hg and stable isotopes were measured in samples of particulate organic matter (POM), zooplankton, squid, myctophid fish, notothenioid fish and seabird tissues collected in two years (austral summers 2007/08 and 2016/17). Overall, there was extensive overlap in δ13C values across taxonomic groups suggesting similarities in habitats, with the exception of the seabirds, which showed some differences, possibly due to the type of tissue analysed (feathers instead of muscle). δ15N showed increasing enrichment across groups in the order POM to zooplankton to squid to myctophid fish to notothenioid fish to seabirds. There were significant differences in δ15N and δ13C values among species within taxonomic groups, reflecting inter-specific variation in diet. Hg concentrations increased with trophic level, with the lowest values in POM (0.0005 ± 0.0002 µg g-1 dw) and highest values in seabirds (3.88 ± 2.41 µg g-1 in chicks of brown skuas Stercorarius antarcticus). Hg concentrations tended to be lower in 2016/17 than in 2007/08 for mid-trophic level species (squid and fish), but the opposite was found for top predators (i.e. seabirds), which had higher levels in the 2016/17 samples. This may reflect an interannual shift in the Scotia Sea marine food web, caused by the reduced availability of a key prey species, Antarctic krill Euphausia superba. In 2016/17, seabirds would have been forced to feed on higher trophic-level prey, such as myctophids, that have higher Hg burdens. These results suggest that changes in the food web are likely to affect the pathway of mercury to Southern Ocean top predators.

Fisheries ecology: hunger for shark fin soup drives clam chowder off the menu.

Removal by fishing of large sharks has reduced predation-pressure on shark prey and, via a trophic cascade, caused clam populations to crash. This indirect response illustrates why fisheries should be managed in a whole-ecosystem context.

Microplastic study reveals the presence of natural and synthetic fibres in the diet of King Penguins (Aptenodytes patagonicus) foraging from South Georgia.

Marine ecosystems are experiencing substantial disturbances due to climate change and overfishing, and plastic pollution is an additional growing threat. Microfibres are among the most pervasive pollutants in the marine environment, including in the Southern Ocean. However, evidence for microfibre contamination in the diet of top predators in the Southern Ocean is rare. King Penguins (Aptenodytes patagonicus) feed on mesopelagic fish, which undergo diel vertical migrations towards the surface at night. Microfibres are concentrated in surface waters and sediments but can also be concentrated in fish, therefore acting as contamination vectors for diving predators feeding at depth. In this study, we investigate microfibre contamination of King Penguin faecal samples collected in February and March 2017 at South Georgia across three groups: incubating, chick-rearing and non-breeding birds. After a KOH digestion to dissolve the organic matter and a density separation step using a NaCl solution, the samples were filtered to collect microfibres. A total of 77% of the penguin faecal samples (36 of 47) contained microfibres. Fibres were measured and characterized using Fourier-Transform Infrared spectroscopy to determine their polymeric identity. Most fibres (88%) were made of natural cellulosic materials (e.g. cotton, linen), with only 12% synthetic (e.g. polyester, nylon) or semi-synthetic (e.g. rayon). An average of 21.9 ±â€¯5.8 microfibres g-1 of faeces (lab dried mass) was found, with concentrations more than twice as high in incubating penguins than in penguins rearing chicks. Incubating birds forage further north at the Antarctic Polar Front and travel longer distances from South Georgia than chick-rearing birds. This suggests that long-distance travelling penguins are probably more exposed to the risk of ingesting microfibres when feeding north of the Antarctic Polar Front, which might act as a semi-permeable barrier for microfibres. Microfibres could therefore provide a signature for foraging location in King Penguins.