Investigations into food web structure in the Beaufort Sea

The effects of climate change on marine ecosystems are most pronounced in the Arctic, where ice free summers have been predicted to occur by mid-century. Climate-related changes to sea ice phenology, oceanographic habitat characteristics, and primary production regimes will likely have strong effects on ecosystem structure that could alter energy pathways, species distributions, food web dynamics, and secondary production. Knowledge of many offshore Arctic ecosystems remains poor, undermining the ability to predict the effects of a changing climate on food web structure and function. This thesis capitalizes on the first comprehensive offshore sampling program in the Canadian Beaufort Sea and Amundsen Gulf to address substantial knowledge gaps regarding fish and invertebrate food web structure in the region. Trophic structure and benthic-pelagic linkages for biological communities on the continental shelf and slope were examined using stable isotope values measured in 127 fish and invertebrate taxa, biomass distributions, and a database of biological functional traits compiled for 166 taxa. Four empirical studies were conducted to test hypotheses regarding the responses of trophic structure to environmental gradients of depth, organic matter input regimes, water mass structure, and benthic food supply. Understanding food web structure and its link to large-scale environmental gradients will be key to assessing and predicting the effects of climate change on offshore marine communities in the Canadian Beaufort Sea and Amundsen Gulf. In Chapter 2, benthic-pelagic coupling via active biological transport was identified as important for sustaining fish communities in the Beaufort Sea. Lower availability of benthic resources with increasing depth restricted biomass production for small size classes of fish in deep habitats. In those same fish communities, pelagic subsidies obtained by benthopelagic fishes were important for maintaining a relatively high biomass of large-bodied fish in deep habitats. When fish and invertebrates were considered together in Chapter 3, benthic-pelagic coupling weakened eastward alongshore, across three regions. Benthic-pelagic coupling was (1) highest west of the Mackenzie River where sinking flux of pelagic particulate organic matter (POM) is known to be relatively high, (2) intermediate on the Mackenzie Shelf where riverine inputs of terrestrial organic matter dominate the sediment, and (3) lowest in the Amundsen Gulf where strong pelagic grazing is known to limit POM sinking flux to the benthos. Within all regions considered, benthic-pelagic coupling was consistently weakest in slope habitats underlying the transition between Pacific- and Atlantic-origin waters, where much of the organic carbon is transformed or intercepted in the water column. Analyses in Chapter 4 indicated that the dominance of terrestrial POM discharged from the Mackenzie River in the Beaufort Sea dampened depth-related changes in the δ15N values of suspension/filter feeders, infaunal deposit feeders, and bulk sediment. In contrast, a faster rate of change in consumer and sediment δ15N with depth was observed in the Amundsen Gulf. Relatively high primary production in the Amundsen Gulf likely promoted intensified biological transformation of autochthonous POM in the pelagic zone and lower downward POM flux, causing greater change in POM δ15N. Surprisingly, when isotopic diversity was weighted by species biomasses in Chapter 5, most benthic communities in the Canadian Beaufort Sea and Amundsen Gulf were found to rely on similarly diverse ranges of sedimentary organic matter, regardless of the sources. Trait-based functional diversity indicated that shelf edge communities maintained a relatively high diversity of biological trophic traits, presumably to exploit pulsed food inputs associated with dynamic shelf break hydrography. Several lines of evidence supported a role for episodic food inputs in structuring shelf edge trait composition. However, pairwise relationships between trophic traits and indicators of benthic food supply were not significant at the regional scale. Functional redundancy was low across most of the region, suggesting benthic food web function will be sensitive to species loss. The research in this thesis presents the first comprehensive empirical studies of benthic food web structure for offshore fish and invertebrate communities in the Canadian Beaufort Sea and Amundsen Gulf. Each study proposes causal explanations for spatial patterns in food web structure based on data for habitat characteristics, species biomass distributions, and previously documented physical and biological properties of the regions. Three emergent properties are identified: (1) the Canadian Beaufort Sea and Amundsen Gulf should be considered separate but interconnected ecosystems, (2) organic matter pathways are key properties that define and determine trophic structure in the study systems, and (3) local habitat complexity interrupts linear associations between environmental gradients and trophic structure at the regional scale. The research represents a significant advancement in our knowledge of food webs in a rapidly changing, and understudied ecosystem. Several significant implications for ecosystem-based management are outlined in the General Conclusions section. Further study is needed to identify species-specific feeding relationships, understand how functional food web structure relates to indicators of ecosystem function, characterise winter ecology, and, ultimately, to develop an over-arching food web model that can be used to predict the impacts of a changing benthic food supply and species loss on community structure and function

Benthic-pelagic trophic coupling in an Arctic marine food web along vertical water mass and organic matter gradients

Source at: http://doi.org/10.3354/meps12582Understanding drivers of benthic-pelagic coupling in Arctic marine ecosystems is key to identifying benthic areas that may be sensitive to climate-driven changes in hydrography and surface production. We coupled algal biomass and sedimentary characteristics with stable isotope data for 113 fishes and invertebrates in the Canadian Beaufort Sea and Amundsen Gulf to examine how trophic structure was influenced by the vertical water mass structure and organic matter input regimes, from 20 to 1000 m depths. Indices of community-level trophic diversity (isotopic niche size, 13C enrichment relative to a pelagic baseline, and δ13C isotopic range) increased from west to east, coincident with the use of more diverse dietary carbon sources among benthic functional groups. Data suggested benthic-pelagic trophic coupling was strongest in the western study region where pelagic sinking flux is relatively high, intermediate in the central region dominated by riverine inputs of terrestrial organic matter, and weakest in the east where strong pelagic grazing is known to limit sinking flux. Differences in δ13C between pelagic and benthic functional groups (up to 5.7 ‰) increased from west to east, and from the nearshore shelf to the upper slope. On the upper slope, much of the sinking organic matter may be intercepted in the water column, and dynamic hydrography likely diversifies available food sources. In waters > 750 m, there were no clear trends in benthic-pelagic coupling or community-level trophic diversity. This study represents the first description of fish and invertebrate food web structure > 200 m in the Canadian Beaufort Sea

Multi Visualization and Dynamic Query for Effective Exploration of Semantic Data

Semantic formalisms represent content in a uniform way according to ontologies. This enables manipulation and reasoning via automated means (e.g. Semantic Web services), but limits the user’s ability to explore the semantic data from a point of view that originates from knowledge representation motivations. We show how, for user consumption, a visualization of semantic data according to some easily graspable dimensions (e.g. space and time) provides effective sense-making of data. In this paper, we look holistically at the interaction between users and semantic data, and propose multiple visualization strategies and dynamic filters to support the exploration of semantic-rich data. We discuss a user evaluation and how interaction challenges could be overcome to create an effective user-centred framework for the visualization and manipulation of semantic data. The approach has been implemented and evaluated on a real company archive

Relationships between depth and δ15N of Arctic benthos vary among regions and trophic functional groups

The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.dsr.2018.03.010 © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/Stable isotope ratios of nitrogen (δ15N) of benthic primary consumers are often significantly related to water depth. This relationship is commonly attributed to preferential uptake of 14N from sinking particulate organic matter (POM) by microbes, and suggests that relationships between δ15N and water depth may be affected by local POM sources and flux dynamics. We examined the relationships between δ15N and water depth (20–500 m) for six trophic functional groups using a mixed effects modelling approach, and compared relationships between two contiguous Arctic marine ecosystems with different POM sources and sinking export dynamics: the Canadian Beaufort Sea and Amundsen Gulf. We demonstrate for the first time in the Arctic that δ15N values of mobile epifaunal carnivores increased as a function of depth when considered separately from benthopelagic and infaunal carnivores, which contrarily did not exhibit increasing δ15N with depth. The δ15N of suspension/filter feeders, infaunal deposit feeders and bulk sediment also increased with water depth, and the slopes of the relationships were steeper in the Amundsen Gulf than in the Beaufort Sea. We propose that regional differences in slopes reflect differences in POM sources exported to the benthos. In the Beaufort Sea, terrestrial POM discharged from the Mackenzie River quantitatively dominates the sedimentary organic matter across the continental shelf and slope, dampening change in δ15N of benthic POM with depth. In the Amundsen Gulf, we attribute a faster rate of change in δ15N of POM with increasing depth to larger contributions of marine-derived POM to the benthic sedimentary pool, which had likely undergone extensive biological transformation in the productive offshore pelagic zone. Differences in POM input regimes among regions should be considered when comparing food webs using stable isotopes, as such differences may impact the rate at which consumer δ15N changes with depth.Funding was provided by the Fisheries Joint Management Committee (Inuvik, NWT), Aboriginal Affairs and Northern Development Canada (BREA), Natural Resources Canada (Environmental Research Fund, Program of Energy Research and Development), internal Fisheries, National Sciences and Engineering Research Council (NSERC) grants to MP and HS, NSERC Alexander Graham Bell CGS D and NSERC Michael Smith Foreign Study Supplement scholarships awarded to AS, and internal support from UiT – The Arctic University of Norway to B

Updated resonance photo-decay amplitudes to 2 GeV

We present the results of an energy-dependent and set of single-energy partial-wave analyses of single-pion photoproduction data. These analyses extend from threshold to 2 GeV in the laboratory photon energy, and update our previous analyses to 1.8 GeV. Photo-decay amplitudes are extracted for the baryon resonances within this energy range. We consider two photoproduction sum rules and the contributions of two additional resonance candidates found in our most recent analysis of $\pi N$ elastic scattering data. Comparisons are made with previous analyses.Comment: Revtex, 26 pages, 3 figures. Postscript figures available from ftp://clsaid.phys.vt.edu/pub/pr or indirectly from http://clsaid.phys.vt.edu/~CAPS

Generation and evaluation of a Glaesserella (Haemophilus) parasuis capsular mutant

Glaesserella (Haemophilus) parasuis is a commensal of the upper respiratory tract in pigs and also the causative agent of Glässer's disease, which causes significant morbidity and mortality in pigs worldwide. Isolates are characterized into 15 serovars by their capsular polysaccharide, which has shown a correlation to isolate pathogenicity. To investigate the role capsule plays in G. parasuis virulence and host interaction, a capsule mutant of the serovar 5 strain HS069 was generated (HS069Δcap) through allelic exchange following natural transformation. HS069Δcap was unable to cause signs of systemic disease during a pig challenge study and had increased sensitivity to complement killing and phagocytosis by alveolar macrophages. When compared to the parent strain, HS069Δcap produced more robust biofilm and adhered equivalently to 3D4/31 cells; however, it was unable to persistently colonize the nasal cavity of inoculated pigs, with all pigs clearing HS069Δcap by 5 days post-challenge. Our results indicate the importance of capsular polysaccharide to G. parasuis virulence as well as nasal colonization in pigs

Interactive metagenomic visualization in a Web browser

<p>Abstract</p> <p>Background</p> <p>A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables.</p> <p>Results</p> <p>Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools.</p> <p>Conclusions</p> <p>Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: <url>http://krona.sourceforge.net</url>.</p