Distribution and Feeding Ecology of Bathylagus euryops (Teleostei: Microstomatidae) along the Northern Mid-Atlantic Ridge from Iceland to the Azores

The northern Mid-Atlantic Ridge, from Iceland to the Azores (MAR), ranges in depth from 800 – 4500 m and extends over an area of 3.7 million km2. Recent evidence from MAR-ECO, a Census of Marine Life field project, reported increased abundance and biomass of deep-pelagic fishes below 1000 m on the MAR. Among the fishes sampled, Bathylagus euryops was found to be the biomass-dominant species and ranked third in total abundance. In this thesis, we characterize the distribution and feeding ecology of B. euryops as a function of physical, biological, and life history parameters along a mid-ocean ridge system. Multiple biologically plausible general linear models were fitted to B. euryops catch-per-unit-effort (CPUE) data to investigate the role of various combinations of explanatory variables on the distribution of this species. Results indicated that a model containing categorical depth and geographic location variables provided the most parsimonious description of B. euryops CPUE data. Vertical migration analyses were also conducted to investigate the vertical distribution of B. euryops along the MAR and results indicated that time of day had little influence, whereas ontogeny likely influenced the vertical distribution of B. euryops. To describe the feeding ecology of B. euryops, a general diet composition was determined. Multivariate analyses, including a cluster analysis and a canonical correspondence analysis, were utilized to investigate factors that cause variability within the diet of B. euryops. Results revealed that fish size and geographic location significantly influenced the diet of B. euryops. Furthermore, daily rations were estimated to better understand the role of B. euryops in the food webs of the North Atlantic and results were consistently estimated to be less than 1% of the average wet weight along the MAR. The general trend observed was a southward increase in daily ration estimates along the MAR

Selenium Supplementation in Fish : A Combined Chemical and Biomolecular Study to Understand Sel-Plex Assimilation and Impact on Selenoproteome Expression in Rainbow Trout (Oncorhynchus mykiss)

Correction Published: February 10, 2016 Acknowledgements This study was supported by Alltech (ZY002 RGF0258) and the Principal’s Interdisciplinary Fund at the University of Aberdeen (award BL900.ROQ0061). Thanks go to the Hellenic Centre for Marine Research, which synthesized all the diets used in this experiment. D.P. carried out the experiment and performed all the molecular biology analysis, interpreted the results and drafted the manuscript. C.J.S and S.A.M.M. supervised the experiment, participating in the experimental design and revision of the manuscript. M.M.L. participated in the sampling and performed all the chemical analysis under the supervision of J.F. Pacitti D, Lawan MM, Sweetman J, Martin SAM, Feldmann J, Secombes CJ (2016) Correction: Selenium Supplementation in Fish: A Combined Chemical and Biomolecular Study to Understand Sel-Plex Assimilation and Impact on Selenoproteome Expression in Rainbow Trout (Oncorhynchus mykiss). PLoS ONE 11(2): e0144681. doi:10.1371/journal.pone.0144681 The unit used to indicate Selenium concentration appears incorrectly throughout the manuscript. The correct unit is mg Kg-1. The values for Selenium concentrations provided as 0.5, 4, and 8 mg Kg-1 throughout the article are incorrect. The correct Selenium concentrations are 0.25, 2, and 4 mg Kg-1 respectively.Peer reviewedPublisher PD

Four selenoprotein P genes exist in salmonids : Analysis of their origin and expression following Se supplementation and bacterial infection

Acknowledgements: This research was funded by Alltech. We thank Dr. Jun Zou (Shanghai Ocean University) for the provision of the recombinant proteins and PAMPS used in this study. Data Availability: All cloned sequences as reported in this study were submitted to the GenBank database at https://www.ncbi.nlm.nih.gov/genbank/ (accession number(s) MH085053-MH085057). Funding: M.A.N.P. received funding of his PhD studies by Alltech (https://www.alltech.com/) under the grant code rg13398-10. The research yielded this manuscript. The authors can confirm the funder provided support in the form of a studentship for author M.A.N.P. and salaries for JS but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

A “Rosetta Stone” for Metazoan Zooplankton: DNA Barcode Analysis of Species Diversity of the Sargasso Sea (Northwest Atlantic Ocean)

Species diversity of the metazoan holozooplankton assemblage of the Sargasso Sea, Northwest Atlantic Ocean, was examined through coordinated morphological taxonomic identification of species and DNA sequencing of a ∼650 base-pair region of mitochondrial cytochrome oxidase I (mtCOI) as a DNA barcode (i.e., short sequence for species recognition and discrimination). Zooplankton collections were made from the surface to 5,000 meters during April, 2006 on the R/V R.H. Brown. Samples were examined by a ship-board team of morphological taxonomists; DNA barcoding was carried out in both ship-board and land-based DNA sequencing laboratories. DNA barcodes were determined for a total of 297 individuals of 175 holozooplankton species in four phyla, including: Cnidaria (Hydromedusae, 4 species; Siphonophora, 47); Arthropoda (Amphipoda, 10; Copepoda, 34; Decapoda, 9; Euphausiacea, 10; Mysidacea, 1; Ostracoda, 27); and Mollusca (Cephalopoda, 8; Heteropoda, 6; Pteropoda, 15); and Chaetognatha (4). Thirty species of fish (Teleostei) were also barcoded. For all seven zooplankton groups for which sufficient data were available, Kimura-2-Parameter genetic distances were significantly lower between individuals of the same species (mean=0.0114; S.D. 0.0117) than between individuals of different species within the same group (mean=0.3166; S.D. 0.0378). This difference, known as the barcode gap, ensures that mtCOI sequences are reliable characters for species identification for the oceanic holozooplankton assemblage. In addition, DNA barcodes allow recognition of new or undescribed species, reveal cryptic species within known taxa, and inform phylogeographic and population genetic studies of geographic variation. The growing database of “gold standard” DNA barcodes serves as a Rosetta Stone for marine zooplankton, providing the key for decoding species diversity by linking species names, morphology, and DNA sequence variation. In light of the pivotal position of zooplankton in ocean food webs, their usefulness as rapid responders to environmental change, and the increasing scarcity of taxonomists, the use of DNA barcodes is an important and useful approach for rapid analysis of species diversity and distribution in the pelagic community

Active ecological restoration of cold-water corals: techniques, challenges, costs and future directions

Cold-water coral (CWC) habitats dwell on continental shelves, slopes, seamounts, and ridge systems around the world's oceans from 50 to 4000 m depth, providing heterogeneous habitats which support a myriad of associated fauna. These highly diverse ecosystems are threatened by human stressors such as fishing activities, gas and oil exploitation, and climate change. Since their life-history traits such as long lifespan and slow growth rates make CWCs very vulnerable to potential threats, it is a foremost challenge to explore the viability of restoration actions to enhance and speed up their recovery. In contrast to terrestrial and shallow-water marine ecosystems, ecological restoration in deep marine environments has received minimal attention. This review, by means of a systematic literature search, aims to identify CWC restoration challenges, assess the most suitable techniques to restore them, and discuss future perspectives. Outcomes from the few restoration actions performed to date on CWCs, which have lasted between 1 to 4 years, provide evidence of the feasibility of coral transplantation and artificial reef deployments. Scientific efforts should focus on testing novel and creative restoration techniques, especially to scale up to the spatial and temporal scales of impacts. There is still a general lack of knowledge about the biological, ecological and habitat characteristics of CWC species exploration of which would aid the development of effective restoration measures. To ensure the long-term viability and success of any restoration action it is essential to include holistic and long-term monitoring programs, and to ideally combine active restoration with natural spontaneous regeneration (i.e., passive restoration) strategies such as the implementation of deep-sea marine protected areas (MPAs). We conclude that a combination of passive and active restoration approaches with involvement of local society would be the best optimal option to achieve and ensure CWC restoration success

Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

Distribution and Trophic Ecology of Bathylagus euryops (Teleostei: Microstomatidae) Along the Northern Mid-Atlantic Ridge

The assemblage structure and ecology of meso- and bathypelagic fishes are poorly known in general, particularly over mid-ocean ridges. In June 2004, the month-long MAR-ECO (Census of Marine Life) research expedition aboard the R/V G.O. Sars sampled the deep-pelagic fauna over the northern Mid-Atlantic Ridge with the objective of quantitatively assessing the nekton associated with the ridge from Iceland to the Azores. A total of 115 discrete-depth trawl samples were taken from the surface to depths of 3000+ meters using two different double-warp midwater trawls, one of commercial fishing size (a large ‘Akra\u27 trawl) and one of oceanographic research size (‘Macroplankton\u27 or ‘Krill\u27 trawl). Catch data revealed the deep-sea smelt Bathylagus euryops to be the biomass dominant species, accounting for over 28% of total biomass, as well as being the 3rd most abundant species along the MAR. Further distributional analyses elucidated a trend in decreasing biomass from north to south with a biomass maximum around 1500-2000 meters. Understanding the food-web structure and organic cycling of deep-pelagic ecosystems is critical for increasing our knowledge of the distributional patterns of deep-sea fishes. Preliminary results indicate that gelatinous zooplankton represents a significant component of the diet of B. euryops. Molecular probes are currently being developed to identify these prey items in this, and other fishes that consume gelatinous zooplankton

Diet Composition of Bathylagus euryops (Osmeriformes: Bathylagidae) Along the Northern Mid-Atlantic Ridge

The northern Mid-Atlantic Ridge, from Iceland to the Azores (MAR), is the largest topographical feature in the Atlantic Ocean. Despite its size, few studies have described dietary patterns of pelagic fishes along the MAR. MAR-ECO, a Census of Marine Life field project, aimed to describe the food web structure of abundant fish species along the ridge through a series of research expeditions to the MAR. Among the midwater fishes sampled during the MAR-ECO project, Bathylagus euryops (Osmeriformes: Bathylagidae) was the biomass-dominant pelagic species and ranked third in total abundance. In this paper, we describe the dietary composition of B. euryops along the MAR. Overall, copepods represented the dominant prey group consumed by B. euryops. Multivariate analyses, including a cluster analysis and a canonical correspondence analysis, revealed that fish size significantly influenced the diet of B. euryops with ostracods representing the most important prey group at small sizes (\u3c95 mm) and decapod shrimp and calanoid copepods becoming more important with increasing fish size. Due to the high abundance and biomass observed along the MAR combined with its role as a link for energy transfer between zooplankton and higher trophic level predators, B. euryops appears to be an ecologically important species in the oceanic food web of the North Atlantic Ocean

Distribution of the Biomass-Dominant Pelagic Fish, Bathylagus euryops (Argentiniformes: Microstomatidae), Along the Northern Mid-Atlantic Ridge

The northern Mid-Atlantic Ridge (MAR), from Iceland to the Azores, ranges in depth from 800–4500 m and extends over an area of 3.7 million km2. Despite its size, few studies have described the distribution of pelagic fishes along the MAR. Recent evidence from MAR-ECO, a Census of Marine Life field project, reported increased abundance and biomass of deep-pelagic fishes below 1000 m on the ridge, which stands in stark contrast to the traditional view that abundance and biomass decline exponentially with increasing depth in ‘typical’ open ocean ecosystems. Among the midwater fishes sampled during the MAR-ECO campaign, Bathylagus euryops (Argentiniformes: Microstomatidae) was the biomass-dominant pelagic species and ranked third in total abundance. In this paper, we characterize the distribution of B. euryops in relation to physical and biological variables along the MAR. Average catch of B. euryops over the MAR varied between 0.68 individuals/100,000 m3±0.70 individuals at the Azorean Zone and 5.82 individuals/100,000 m3±2.08 individuals at the Reykjanes Ridge. Generalized linear models applied to B. euryops catch data indicated that ridge section, depth zone, and prey abundance were important explanatory variables in structuring the distribution along the MAR. Analyses of vertical distribution patterns, relative to time of day and fish size, showed that larger fish were found deeper in the water column, likely due to an ontogenetic migration to depth. Mean fish size increased from 58.9 mm standard length in the epipelagic zone and continually increased to 155.7 mm standard length between 2300–3000 m. Due to the high abundance and biomass observed along the MAR, B. euryops appears to be an important species in the oceanic food web of the North Atlantic Ocean