Barriers to gene flow in the deepest ocean ecosystems: Evidence from global population genomics of a cosmopolitan amphipod.

The deepest marine ecosystem, the hadal zone, hosts endemic biodiversity resulting from geographic isolation and environmental selection pressures. However, the pan-ocean distribution of some fauna challenges the concept that the hadal zone is a series of isolated island-like habitats. Whether this remains true at the population genomic level is untested. We investigated phylogeographic patterns of the amphipod, Bathycallisoma schellenbergi, from 12 hadal features across the Pacific, Atlantic, Indian, and Southern oceans and analyzed genome-wide single-nucleotide polymorphism markers and two mitochondrial regions. Despite a cosmopolitan distribution, populations were highly restricted to individual features with only limited gene flow between topographically connected features. This lack of connectivity suggests that populations are on separate evolutionary trajectories, with evidence of potential cryptic speciation at the Atacama Trench. Together, this global study demonstrates that the shallower ocean floor separating hadal features poses strong barriers to dispersal, driving genetic isolation and creating pockets of diversity to conserve.

Novel coexisting mangrove-coral habitats: Extensive coral communities located deep within mangrove canopies of Panama, a global classification system and predicted distributions.

Marine ecosystems are structured by coexisting species occurring in adjacent or nested assemblages. Mangroves and corals are typically observed in adjacent assemblages (i.e., mangrove forests and coral reefs) but are increasingly reported in nested mangrove-coral assemblages with corals living within mangrove habitats. Here we define these nested assemblages as "coexisting mangrove-coral" (CMC) habitats and review the scientific literature to date to formalize a baseline understanding of these ecosystems and create a foundation for future studies. We identify 130 species of corals living within mangrove habitats across 12 locations spanning the Caribbean Sea, Red Sea, Indian Ocean, and South Pacific. We then provide the first description, to our knowledge, of a canopy CMC habitat type located in Bocas del Toro, Panama. This canopy CMC habitat is one of the most coral rich CMC habitats reported in the world, with 34 species of corals growing on and/or among submerged red mangrove aerial roots. Based on our literature review and field data, we identify biotic and abiotic characteristics common to CMC systems to create a classification framework of CMC habitat categories: (1) Lagoon, (2) Inlet, (3) Edge, and (4) Canopy. We then use the compiled data to create a GIS model to suggest where additional CMC habitats may occur globally. In a time where many ecosystems are at risk of disappearing, discovery and description of alternative habitats for species of critical concern are of utmost importance for their conservation and management.

Exploration of the Puerto Rico Trench in the mid-twentieth century: Today's significance and relevance.

The Puerto Rico Trench is a deep oceanic subduction zone that runs parallel with the northern coasts of Puerto Rico and the Dominican Republic. It is the deepest place in the Atlantic Ocean with a maximum depth of approximately 8400 m. Discovered by the HMS Challenger Expedition in 1875, the depth of the trench increased multiple times in the ensuing 100 years with the onset of sonar usage. It is perhaps unique among the world's deep trenches in that a series of unrelated but equally pioneering expeditions captured the true biological and geological characteristics of one of the deepest places in the world, observations that are still highly relevant today. Multiple deep water trawling campaigns and surveys using drop cameras and exploratory dives in a deep diving submersible provided great insight into the morphology of the trench, the types of habitat within the trench, the substrate, the food supply, and the diversity of species that inhabit these extraordinary depths. Many of these accounts are obscure and disparate, yet combined bear a remarkable similarity to recent work in other trenches. These unique and insightful accounts are collated and retold here alongside recent and comparable findings to contextualise these discoveries, prevent them from being forgotten, and keep the efforts of those involved to remain relevant as we continue to explore the deepest places of the world's oceans.

Whole genome sequencing of four bacterial strains from South Shetland Trench revealing biosynthetic and environmental adaptation gene clusters.

Whole genome sequences of four bacterial strains Dietzia maris SST1, Pseudomonas zhaodongensis SST2, Pseudomonas sp. SST3 and Halomonas sulfidaeris SST4, recovered from the South Shetland Trench sediment in Antarctica were analyzed using Ion Torrent sequencing technology. The respective sizes of their genomes (3.88, 4.99, 5.60 and 4.25 Mb) and GC contents (70.0, 60.3, 59.9 and 53.8%) are in agreement with these values of other strains of the species. The bacterial strains displayed promising antimicrobial activity against a number of pathogenic bacterial and fungal species. Whole genomes have been assembled and biosynthetic gene clusters (BGCs) have been identified using the antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) web platform. Comparative analysis of the genome sequences revealed that the strains host abundant BGCs encoding for terpenes, siderophores, arylpolyene, bacteriocins, and lassopeptides. Furthermore, the key stress-related genes were identified and their distribution provided an insight into how these isolates adapt to key marine environmental conditions. This comprehensive study is a contribution to understanding the nature of life on the deep-sea environments.

Depression chains in seafloor of contrasting morphology, Atacama Trench margin: a comment on Marsh et al. (2018).

This comment presents acoustic and visual data showing deep seafloor depression chains similar to those reported in Marsh et al. (R. Soc. open sci. 5: 180286), though from a different deep-sea setting. Marsh et al. present data collected during cruise JC120 from polymetallic nodule rich sites within the Clarion-Clipperton Fracture Zone (CCFZ), at water depths of between 3999 and 4258 m. Within this comment, we present data collected with equivalent acoustic and imaging devices on-board the RV Sonne (SO261-March/April 2018) from the Atacama Trench, approximately 4000 m depth, which shows comparable depression chains in the seafloor. In contrast with the CCFZ observations, our study area was wholly free of polymetallic nodules, an observation therefore weakening the 'ballast collection' by deep-sea diving mammals formation hypothesis discussed in their paper. We support their alternate hypothesis that if these features are indeed generated by deep-diving megafauna, then they are more likely the resultant traces of infauna feeding or marks made during opportunistic capture of benthic fish/cephalopods. We observed these potential prey fauna with lander and towed camera systems during the cruise, with example images of these presented here. Both the SO261 and JC120 cruises employed high-resolution sidescan systems at deployment altitudes seldom used routinely until the last few years during scientific deep-sea surveys. Given that both cruises found these depression chains in contrasting physical regions of the East Pacific, they may have a more ubiquitous distribution than at just these sites. Thus, the impacts of cetacean foraging behaviour on deep seafloor communities, and the potential relevance of these prey sources to deep-diving species, should be considered.

Fin healing and regeneration in sturgeon.

Pectoral fin healing in fin spines and rays were examined in juvenile Atlantic sturgeon Acipenser oxyrinchus oxyrinchus following three different sampling techniques (n = 8-9 fish per treatment): entire leading fin spine removed, a 1-2 cm portion removed near the point of articulation, or a 1-2 cm portion removed from a secondary fin ray. Also, to determine whether antibiotic treatment influences healing, an additional group of fish (n = 8) was not given an injection of an oxytetracycline (OTC)-based antibiotic following removal of the entire leading fin spine. Following fin sampling, fish from different treatments were mixed equally between three large (4,000 I) recirculating systems and fin-ray healing and mortality were monitored over a 12 month period. To assess healing, blood samples were collected at 4 months to measure immune system responses, radiographs were taken at 4, 8 and 12 months to assess the degree of calcification in regions of damaged fins and fins were analyzed histologically at 12 months. Fish grew from a mean weight of 1.8 to 3.2 kg during the experiment and survival was near 100% in all treatments, with only one fish dying of unknown causes. Leukocyte counts, an indication of health status and survival were similar among treatments and in groups with or without antibiotic injection. Radiographs revealed mineralization took longer in fish with the entire leading fin spine removed and was the slowest near the point of articulation, presumably due to the greater structural support for the pectoral fin at this location. Histological sampling indicated spines and rays had similar healing patterns. Following injury, an orderly matrix of collagen bundles and many evenly spaced scleroblasts were present, transitioning to Sharpey fibres, with concentric layers forming lamellar bone. Healing and mineralization were characterized as periosteal osteogenesis and included embedded osteocytes surrounded by an osteoid seam. Chondroid formation was apparent in a few fractures not associated with treatments. The duration of time for external wound healing and internal mineralization of spines and rays depended on the fin treatment, with the slowest healing observed in fish with the most tissue removed, the entire leading fin spine.

Egg size and emergence timing affect morphology and behavior in juvenile Chinook Salmon, Oncorhynchus tshawytscha.

Variation in early life history traits often leads to differentially expressed morphological and behavioral phenotypes. We investigated whether variation in egg size and emergence timing influence subsequent morphology associated with migration timing in juvenile spring Chinook Salmon, Oncorhynchus tshawytscha. Based on evidence for a positive relationship between growth rate and migration timing, we predicted that fish from small eggs and fish that emerged earlier would have similar morphology to fall migrants, while fish from large eggs and individuals that emerged later would be more similar to older spring yearling migrants. We sorted eyed embryos within females into two size categories: small and large. We collected early and late-emerging juveniles from each egg size category. We used landmark-based geometric morphometrics and found that egg size appears to drive morphological differences. Egg size shows evidence for an absolute rather than relative effect on body morphology. Fish from small eggs were morphologically more similar to fall migrants, while fish from large eggs were morphologically more similar to older spring yearling migrants. Previous research has shown that the body morphology of fish that prefer the surface or bottom location in a tank soon after emergence also correlates with the morphological variations between wild fall and spring migrants, respectively. We found that late-emerging fish spent more time near the surface. Our study shows that subtle differences in early life history characteristics may correlate with a diversity of future phenotypes.

Dual substrate limitation modeling and implications for mainstream deammonification.

Substrate limitation occurs frequently in wastewater treatment and knowledge about microbial behavior at limiting conditions is essential for the use of biokinetic models in system design and optimization. Monod kinetics are well-accepted for modeling growth rates when a single substrate is limiting, but several models exist for treating two or more limiting substrates simultaneously. In this study three dual limitation models (multiplicative, minimum, and Bertolazzi) were compared based on experiments using nitrite-oxidizing bacteria (limited by dissolved oxygen and nitrite) and ANaerobic AMMonia-OXidizing bacteria or Aanammox (limited by ammonium and nitrite) within mixed liquor from deammonification pilots. A deterministic likelihood-based parameter estimation followed by Bayesian inference was used to estimate model-specific parameters. The minimum model outperformed the other two by a slight margin in three separate analyses. 1) Parameters estimated using the minimum model were closest to parameters estimated from single limitation batch tests. 2) Among simulations based on each model's own estimated parameters, the minimum model best described the experimental observations. 3) Among simulations based on parameters estimated from single limitation, the minimum model best described the experimental observations. The dual substrate model selected among the three studied can effect a 75% process performance variation based on simulations of a full-scale mainstream deammonification system.

Salinity effects on plasma ion levels, cortisol, and osmolality in Chinook salmon following lethal sampling.

Studies on hydromineral balance in fishes frequently employ measurements of electrolytes following euthanasia. We tested the effects of fresh- or salt-water euthanasia baths of tricaine mesylate (MS-222) on plasma magnesium (Mg(2+)) and sodium (Na(+)) ions, cortisol and osmolality in fish exposed to saltwater challenges, and the ion and steroid hormone fluctuations over time following euthanasia in juvenile spring Chinook salmon (Oncorhynchus tshawytscha). Salinity of the euthanasia bath affected plasma Mg(2+) and Na(+) concentrations as well as osmolality, with higher concentrations in fish euthanized in saltwater. Time spent in the bath positively affected plasma Mg(2+) and osmolality, negatively affected cortisol, and had no effect on Na(+) concentrations. The difference of temporal trends in plasma Mg(2+) and Na(+) suggests that Mg(2+) may be more sensitive to physiological changes and responds more rapidly than Na(+). When electrolytes and cortisol are measured as endpoints after euthanasia, care needs to be taken relative to time after death and the salinity of the euthanasia bath.

The Influence of Data Resolution on Predicted Distribution and Estimates of Extent of Current Protection of Three 'Listed' Deep-Sea Habitats.

Modelling approaches have the potential to significantly contribute to the spatial management of the deep-sea ecosystem in a cost effective manner. However, we currently have little understanding of the accuracy of such models, developed using limited data, of varying resolution. The aim of this study was to investigate the performance of predictive models constructed using non-simulated (real world) data of different resolution. Predicted distribution maps for three deep-sea habitats were constructed using MaxEnt modelling methods using high resolution multibeam bathymetric data and associated terrain derived variables as predictors. Model performance was evaluated using repeated 75/25 training/test data partitions using AUC and threshold-dependent assessment methods. The overall extent and distribution of each habitat, and the percentage contained within an existing MPA network were quantified and compared to results from low resolution GEBCO models. Predicted spatial extent for scleractinian coral reef and Syringammina fragilissima aggregations decreased with an increase in model resolution, whereas Pheronema carpenteri total suitable area increased. Distinct differences in predicted habitat distribution were observed for all three habitats. Estimates of habitat extent contained within the MPA network all increased when modelled at fine scale. High resolution models performed better than low resolution models according to threshold-dependent evaluation. We recommend the use of high resolution multibeam bathymetry data over low resolution bathymetry data for use in modelling approaches. We do not recommend the use of predictive models to produce absolute values of habitat extent, but likely areas of suitable habitat. Assessments of MPA network effectiveness based on calculations of percentage area protection (policy driven conservation targets) from low resolution models are likely to be fit for purpose.

Benthic Assemblages of the Anton Dohrn Seamount (NE Atlantic): Defining Deep-Sea Biotopes to Support Habitat Mapping and Management Efforts with a Focus on Vulnerable Marine Ecosystems.

In 2009 the NW and SE flanks of Anton Dohrn Seamount were surveyed using multibeam echosounder and video ground-truthing to characterise megabenthic biological assemblages (biotopes) and assess those which clearly adhere to the definition of Vulnerable Marine Ecosystems, for use in habitat mapping. A combination of multivariate analysis of still imagery and video ground-truthing defined 13 comprehensive descriptions of biotopes that function as mapping units in an applied context. The data reveals that the NW and SE sides of Anton Dohrn Seamount (ADS) are topographically complex and harbour diverse biological assemblages, some of which agree with current definitions of 'listed' habitats of conservation concern. Ten of these biotopes could easily be considered Vulnerable Marine Ecosystems; three coral gardens, four cold-water coral reefs, two xenophyophore communities and one sponge dominated community, with remaining biotopes requiring more detailed assessment. Coral gardens were only found on positive geomorphic features, namely parasitic cones and radial ridges, found both sides of the seamount over a depth of 1311-1740 m. Two cold-water coral reefs (equivalent to summit reef) were mapped on the NW side of the seamount; Lophelia pertusa reef associated with the cliff top mounds at a depth of 747-791 m and Solenosmilia variabilis reef on a radial ridge at a depth of 1318-1351 m. Xenophyophore communities were mapped from both sides of the seamount at a depth of 1099-1770 m and were either associated with geomorphic features or were in close proximity (< 100 m) to them. The sponge dominated community was found on the steep escarpment either side of the seamount over at a depth of 854-1345 m. Multivariate diversity revealed the xenophyophore biotopes to be the least diverse, and a hard substratum biotope characterised by serpulids and the sessile holothurian, Psolus squamatus, as the most diverse.

Seasonal blood chemistry response of sub-tropical nearshore fishes to climate change.

Climate change due to anthropogenic activity will continue to alter the chemistry of the oceans. Future climate scenarios indicate that sub-tropical oceans will become more acidic, and the temperature and salinity will increase relative to current conditions. A large portion of previous work has focused on how future climate scenarios may impact shell-forming organisms and coral reef fish, with little attention given to fish that inhabit nearshore habitats; few studies have examined multiple challenges concurrently. The purpose of this study was to quantify the blood-based physiological response of nearshore fishes to a suite of seawater conditions associated with future climate change. Fish were exposed to an acute (30 min) increase in salinity (50 ppt), acidity (decrease in pH by 0.5 units) or temperature (7-10°C), or temperature and acidity combined, and held in these conditions for 6 h. Their physiological responses were compared across seasons (i.e. summer vs. winter). Bonefish (Albula vulpes) exposed to environmental challenges in the summer experienced a suite of blood-based osmotic and ionic disturbances relative to fish held in ambient conditions, with thermal challenges (particularly in the summer) being the most challenging. Conversely, no significant treatment effects were observed for yellowfin mojarra (Gerres cinereus) or checkered puffer (Sphoeroides testudineus) in either season. Together, results from this study demonstrate that acute climate-induced changes to thermal habitat will be the most challenging for sub-tropical fishes (particularly in the summer) relative to salinity and pH stressors, but significant variation across species exists.