Region-wide changes in marine ecosystem dynamics: state-space models to distinguish trends from step changes

Regime shifts are sudden changes in ecosystem structure that can be detected across several ecosystem components. The concept that regime shifts are common in marine ecosystems has gained popularity in recent years. Many studies have searched for the step-like changes in ecosystem state expected under a simple interpretation of this idea. However, other kinds of change, such as pervasive trends, have often been ignored. We assembled over 300 ecological time series from seven UK marine regions, covering two to three decades. We developed state-space models for the first principal component of the time series in each region, a common measure of ecosystem state. Our models allowed both trends and step changes, possibly in combination. We found trends in three of seven regions and step changes in two of seven regions. Gradual and sudden changes are therefore important trajectories to consider in marine ecosystems.

Macro-ecology of plankton–seabird associations in the North Pacific Ocean

In conjunction with the North Pacific Continuous Plankton Recorder program, we conducted surveys of seabirds from June 2002 to June 2007. Here, we tested the hypotheses of (i) east–west variations in coupled plankton and seabird abundance, and (ii) that surface-feeding and diving seabirds vary in their relationships to primary productivity and mesozooplankton species abundance and diversity. To test these hypotheses, we developed statistical models for 20 species of seabirds and 12 zooplankton taxonomic groups. Seabird density was highly variable between seasons, but was consistently higher in the western than eastern North Pacific. Seabird diversity was greater in the east. Zooplankton abundance did not differ between regions. We found associations at the “bulk” level between seabird density and net primary productivity, but only one association between seabirds and total zooplankton abundance or diversity. However, we found many relationships between seabird species and the abundance of different zooplankton summarized at the genus or family level. Some of these taxonomic relationships reflect direct predator–prey interactions, while others may reflect zooplankton that serve as ecological indicators of other prey, such as micronekton, upon which the birds may feed. Surface or near-surface feeding, mostly piscivorous seabirds, did not differ systematically from diving, mainly planktivorous seabirds in their zooplankton associations. Seabirds apparently respond to zooplankton taxonomic groupings more so than bulk zooplankton characteristics, such as abundance or diversity. Macro-ecological studies of remote marine ecosystems using zooplankton and seabirds as ecological indicators provide a framework for understanding and assessing spatial and temporal variations in these difficult-to-study pelagic environments.

Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers to efficiently identify parental species and hybrids. Using next-generation sequencing analysis of both the genome and transcriptome from two sibling species, Calanus finmarchicus and Calanus glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species-specific amplicon length. Furthermore, most of the markers were successfully amplified in other Calanus species, allowing the molecular identification of Calanus helgolandicus, Calanus hyperboreus and Calanus marshallae.

Bridging the gap between marine biogeochemical and fisheries sciences; configuring the zooplankton link

Exploring climate and anthropogenic impacts on marine ecosystems requires an understanding of how trophic components interact. However, integrative end-to-end ecosystem studies (experimental and/or modelling) are rare. Experimental investigations often concentrate on a particular group or individual species within a trophic level, while tropho-dynamic field studies typically employ either a bottom-up approach concentrating on the phytoplankton community or a top-down approach concentrating on the fish community. Likewise the emphasis within modelling studies is usually placed upon phytoplankton-dominated biogeochemistry or on aspects of fisheries regulation. In consequence the roles of zooplankton communities (protists and metazoans) linking phytoplankton and fish communities are typically under-represented if not (especially in fisheries models) ignored. Where represented in ecosystem models, zooplankton are usually incorporated in an extremely simplistic fashion, using empirical descriptions merging various interacting physiological functions governing zooplankton growth and development, and thence ignoring physiological feedback mechanisms. Here we demonstrate, within a modelled plankton food-web system, how trophic dynamics are sensitive to small changes in parameter values describing zooplankton vital rates and thus the importance of using appropriate zooplankton descriptors. Through a comprehensive review, we reveal the mismatch between empirical understanding and modelling activities identifying important issues that warrant further experimental and modelling investigation. These include: food selectivity, kinetics of prey consumption and interactions with assimilation and growth, form of voided material, mortality rates at different age-stages relative to prior nutrient history. In particular there is a need for dynamic data series in which predator and prey of known nutrient history are studied interacting under varied pH and temperature regimes.

Live discrimination of Calanus glacialis and C. finmarchicus females: can we trust phenological differences?

Two key players in the Arctic and subarctic marine ecosystem are the calanoid copepods, Calanus finmarchicus and C. glacialis. Although morphologically very similar, these sibling species have different life cycles and roles in the Arctic pelagic marine ecosystem. Considering that the distribution of C. glacialis corresponds to Arctic water masses and C. finmarchicus to Atlantic water masses, the species are frequently used as climate indicators. Consequently, correct identification of the two species is essential if we want to understand climate-impacted changes on Calanus-dominated marine ecosystems such as the Arctic. Here, we present a novel morphological character (redness) to distinguish live females of C. glacialis and C. finmarchicus and compare it to morphological (prosome length) and genetic identification. The characters are tested on 300 live females of C. glacialis and C. finmarchicus from Disko Bay, western Greenland. Our analysis confirms that length cannot be used as a stand-alone criterion for separation. The results based on the new morphological character were verified genetically using a single mitochondrial marker (16S) and nuclear loci (six microsatellites and 12 InDels). The pigmentation criterion was also used on individuals (n = 89) from Young Sound fjord, northeast Greenland to determine whether the technique was viable in different geographical locations. Genetic markers based on mitochondrial and nuclear loci were corroborative in their identification of individuals and revealed no hybrids. Molecular identification confirmed that live females of the two species from Greenlandic waters, both East and West, can easily be separated by the red pigmentation of the antenna and somites of C. glacialis in contrast to the pale opaque antenna and somites of C. finmarchicus, confirming that the pigmentation criterion is valid for separation of the two species

Marine baseline and monitoring strategies for carbon dioxide capture and storage (CCS)

The QICS controlled release experiment demonstrates that leaks of carbon dioxide (CO2) gas can be detected by monitoring acoustic, geochemical and biological parameters within a given marine system. However the natural complexity and variability of marine system responses to (artificial) leakage strongly suggests that there are no absolute indicators of leakage or impact that can unequivocally and universally be used for all potential future storage sites. We suggest a multivariate, hierarchical approach to monitoring, escalating from anomaly detection to attribution, quantification and then impact assessment, as required. Given the spatial heterogeneity of many marine ecosystems it is essential that environmental monitoring programmes are supported by a temporally (tidal, seasonal and annual) and spatially resolved baseline of data from which changes can be accurately identified. In this paper we outline and discuss the options for monitoring methodologies and identify the components of an appropriate baseline survey.

Valuation of ecological and amenity impacts of an offshore windfarm as a factor in marine planning

Integrated marine planning, which must take into consideration environmental and social impacts, is being introduced widely in Europe, the USA, Australia and elsewhere. Installation of offshore windfarms creates impacts both on local marine ecosystems and the view of the seascape and is one of multiple activities in the marine area that must be addressed by marine planning. The impacts on people's values (and hence welfare) of changes in ecology and amenity that could arise from the installation of a windfarm in the Irish Sea were assessed using a discrete choice experiment administered through an online survey. The ecological changes investigated were: increased species diversity resulting from artificial reef effects, and the effect of electromagnetic fields from subsea cables on marine life; whilst the amenity change was the visibility of offshore turbines from land. Respondents expressed preferences for ecological improvements but had less clear preferences regarding the height and visibility of the turbines. In particular distance decay effects were observed with respondents further away from the coast being less concerned about visual impact created by offshore turbines. Understanding ecological and amenity impacts and how they are valued by people can support the decisions made within marine planning and licensing.

Energy systems and their impacts on marine ecosystem services

Global warming and its link to the burning of fossil fuels has prompted many governments around the world to set legally binding greenhouse gas reduction targets which are to be partially realised through a stronger reliance on renewable (e.g. wind) and other lower carbon (i.e. natural gas and nuclear) energy commodities. The marine environment will play a key role in hosting or supporting these new energy strategies. However, it is unclear how the construction, operation and eventual decommissioning of these energy systems, and their related infrastructure, will impact the marine environment, the ecosystem services (i.e. cultural, regulating, provisioning and supporting) and in turn the benefits it provides for human well-being. This uncertainty stems from a lack of research that has synthesised into a common currency the various effects of each energy sector on marine ecosystems and the benefits humans derive from it. To address this gap, the present study reviews existing ecosystem impact studies for offshore components of nuclear, offshore wind, offshore gas and offshore oil sectors and translates them into the common language of ecosystem service impacts that can be used to evaluate current policies. The results suggest that differences exist in the way in which energy systems impact ecosystem services, with the nuclear sector having a predominantly negative impact on cultural ecosystem services; oil and gas a predominately negative impact on cultural, provisioning, regulating and supporting ecosystem services; while wind has a mix of impacts on cultural, provisioning and supporting services and an absence of studies for regulating services. This study suggests that information is still missing with regard to the full impact of these energy sectors on specific types of benefits that humans derive from the marine environment and proposes possible areas of targeted research.

Plastic and marine turtles: a review and call for research

Plastic debris is now ubiquitous in the marine environment affecting a wide range of taxa, from microscopic zooplankton to large vertebrates. Its persistence and dispersal throughout marine ecosystems has meant that sensitivity toward the scale of threat is growing, particularly for species of conservation concern, such as marine turtles. Their use of a variety of habitats, migratory behaviour, and complex life histories leave them subject to a host of anthropogenic stressors, including exposure to marine plastic pollution. Here, we review the evidence for the effects of plastic debris on turtles and their habitats, highlight knowledge gaps, and make recommendations for future research. We found that, of the seven species, all are known to ingest or become entangled in marine debris. Ingestion can cause intestinal blockage and internal injury, dietary dilution, malnutrition, and increased buoyancy which in turn can result in poor health, reduced growth rates and reproductive output, or death. Entanglement in plastic debris (including ghost fishing gear) is known to cause lacerations, increased drag—which reduces the ability to forage effectively or escape threats—and may lead to drowning or death by starvation. In addition, plastic pollution may impact key turtle habitats. In particular, its presence on nesting beaches may alter nest properties by affecting temperature and sediment permeability. This could influence hatchling sex ratios and reproductive success, resulting in population level implications. Additionally, beach litter may entangle nesting females or emerging hatchlings. Lastly, as an omnipresent and widespread pollutant, plastic debris may cause wider ecosystem effects which result in loss of productivity and implications for trophic interactions. By compiling and presenting this evidence, we demonstrate that urgent action is required to better understand this issue and its effects on marine turtles, so that appropriate and effective mitigation policies can be developed.

Marine reserve designation, trophic cascades and altered community dynamics

Marine ecosystems and their associated populations are increasingly at risk from the cumulative impacts of many anthropogenic threats that increase the likelihood of species extinction and altered community dynamics. In response, marine reserves can be used to protect exploited species and conserve biodiversity. The increased abundance of predatory species in marine reserves may cause indirect effects along chains of multi-trophic interactions. These trophic cascades can arise through direct predation, density-mediated indirect interactions (DMIIs), or indirect behavioural effects, termed trait-mediated indirect interactions (TMIIs). The extent of algal cover and the abundance of 4 primary consumers were determined in Lough Hyne, which was designated Europe's first marine nature reserve in 1981. The primary consumers were the sea urchin Paracentrotus lividus, the topshell Gibbula cineraria, the oyster Anomia ephippium, and the scallop Chlamys varia. The abundances of 3 starfish species (Marthasterias glacialis, Asterias rubens, and Asterina gibbosa) were also determined, as were 2 potential crustacean predators, Necora puber and Carcinus maenas. These data were compared with historical data from a 1962 (prey) and a 1963 (predator) survey to determine the nature of community interactions over adjacent trophic levels. The present study reveals a breakdown in population structure of the 4 surveyed prey species. Marine reserve designation has led to an increase in predatory crabs and M. glacialis, a subsequent decrease in primary consumers, especially the herbivore P. lividus, and an increase in macroalgal cover which is indicative of a trophic cascade. The study shows that establishing a Marine Reserve does not guarantee that conservation benefits will be distributed equally.

Identifying marine pelagic ecosystem management objectives and indicators

International policy frameworks such as the Common Fisheries Policy and the European Marine Strategy Framework Directive define high-level strategic goals for marine ecosystems. Strategic goals are addressed via general and operational management objectives. To add credibility and legitimacy to the development of objectives, for this study stakeholders explored intermediate level ecological, economic and social management objectives for Northeast Atlantic pelagic ecosystems. Stakeholder workshops were undertaken with participants being free to identify objectives based on their own insights and needs. Overall 26 objectives were proposed, with 58% agreement in proposed objectives between two workshops. Based on published evidence for pressure-state links, examples of operational objectives and suitable indicators for each of the 26 objectives were then selected. It is argued that given the strong species-specific links of pelagic species with the environment and the large geographic scale of their life cycles, which contrast to demersal systems, pelagic indicators are needed at the level of species (or stocks) independent of legislative region. Pelagic community indicators may be set at regional scale in some cases. In the evidence-based approach used in this study, the selection of species or region specific operational objectives and indicators was based on demonstrated pressure-state links. Hence observed changes in indicators can reliably inform on appropriate management measures

Dynamics of production and mortality of Aurelia SP. in thau lagoon, northwerstern Mediterranean

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Impacts from aquaculture facilities on intertidal ecosystems using quadrant surveys and antibiotic tracers

Senior thesis written for Oceanography 444

Identification et caractérisation des protéines responsables de l’entrée en phase M chez Lingulodinium polyedrum

Les dinoflagellés sont des eucaryotes unicellulaires qui composent une grande partie du phytoplancton et qui jouent un rôle important au niveau de la photosynthèse, de la production primaire et de la conservation des écosystèmes marins. Les dinoflagellés se distinguent des autres eucaryotes par leur biologie et leur organisation nucléaire unique. Lors de la mitose, leur membrane nucléaire demeure intacte et la ségrégation des chromosomes se fait à partir de fuseaux mitotiques formés dans le cytoplasme et qui traversent le noyau au travers de canaux spécialisés Aussi, leurs chromosomes sont condensés en permanence et le processus utilisé pour y arriver est encore très mal compris puisque les dinoflagellés ne possèdent aucunes histones détectables. Lingulodinium polyedrum est un dinoflagellé photosynthétique marin utilisé comme organisme modèle en ce qui concerne l’étude des rythmes circadiens (bioluminescence, migration verticale, mitose et photosynthèse). La découverte et l’étude des éléments régulateurs du cycle cellulaire peuvent nous amener à comprendre le mécanisme, l’influence et la portée du contrôle circadien sur le cycle cellulaire. De plus, l’étude du cycle cellulaire pourrait permettre de révéler des indices quant aux caractéristiques singulières des dinoflagellés qui sont pour le moment énigmatiques. Par le passé, une étude chez Lingulodinium polyedrum a permis d’identifier la cycline impliquée dans la mitose, LpCyc1, le premier régulateur du cycle cellulaire a être découvert chez les dinoflagellés. La présente étude s’attarde sur la caractérisation de la LpCyc1, soit son expression, sa localisation, sa phosphorylation. Ces trois éléments concordent de façon à synchroniser l’activité de la LpCyc1 (et ainsi la mitose) de façon circadienne. Cette étude présente aussi la création et le développement d’un outil majeur pour l’étude future de Lingulodinium polyedrum, le transcriptome des ARNm à partir d’un iv séquençage Illumina. C’est d’ailleurs avec cet outil que nous avons découvert la CDK responsable du contrôle de la phase M, LpCdk1. Cette CDK possède tous les domaines d’une CDK classique, un site de liaison des substrats, un site de liaison à l’ATP, une boucle activatrice, et une interface de liaison avec la cycline. Le transcriptome de Lingulodinium polyedrum a aussi permis de recenser toutes les protéines conservées normalement retrouvées dans le contrôle du cycle cellulaire, qui nous a permis de faire une ébauche préliminaire du cycle cellulaire de L. polyedrum. Cette analyse est une première chez Lingulodinium polyedrum et peut s’étendre pour l’étude d’une multitude d’autres processus métaboliques.

Mortality of Migratory Birds from Marine Commercial Fisheries and Offshore Oil and Gas Production in Canada

There is an imminent need for conservation and best-practice management efforts in marine ecosystems where global-scale declines in the biodiversity and biomass of large vertebrate predators are increasing and marine communities are being altered. We examine two marine-based industries that incidentally take migratory birds in Canada: (1) commercial fisheries, through bycatch, and (2) offshore oil and gas exploration, development, and production. We summarize information from the scientific literature and technical reports and also present new information from recently analyzed data to assess the magnitude and scope of mortality. Fisheries bycatch was responsible for the highest levels of incidental take of migratory bird species; estimated combined take in the longline, gillnet, and bottom otter trawl fisheries within the Atlantic, including the Gulf of St. Lawrence, and Pacific regions was 2679 to 45,586 birds per year. For the offshore oil and gas sector, mortality estimates ranged from 188 to 4494 deaths per year due to the discharge of produced waters resulting in oil sheens and collisions with platforms and vessels; however these estimates for the oil and gas sector are based on many untested assumptions. In spite of the uncertainties, we feel levels of mortality from these two industries are unlikely to affect the marine bird community in Canada, but some effects on local populations from bycatch are likely. Further research and monitoring will be required to: (1) better estimate fisheries-related mortality for vulnerable species and populations that may be impacted by local fisheries, (2) determine the effects of oil sheens from produced waters, and attraction to platforms and associated mortality from collisions, sheens, and flaring, so that better estimates of mortality from the offshore oil and gas sector can be obtained, and (3) determine impacts associated with accidental spills, which are not included in our current assessment. With a better understanding of the direct mortality of marine birds from industry, appropriate mitigation and management actions can be implemented. Cooperation from industry for data collection, research to fill knowledge gaps, and implementation of mitigation approaches will all be needed to conserve marine birds in Canada.