Purine catabolic pathway revealed by transcriptomics in the model marine bacteriumRuegeria pomeroyiDSS-3

Purines are nitrogen-rich compounds that are widely distributed in the marine environment and are an important component of the dissolved organic nitrogen (DON) pool. Even though purines have been shown to be degraded by bacterioplankton, the identities of marine bacteria capable of purine degradation and their underlying catabolic mechanisms are currently unknown. This study shows that Ruegeria pomeroyi, a model marine bacterium and Marine Roseobacter Clade (MRC) representative, utilizes xanthine as a source of carbon and nitrogen. The R. pomeroyi genome contains putative genes that encode xanthine dehydrogenase (XDH), which is expressed during growth with xanthine. RNAseq-based analysis of the R. pomeroyi transcriptome revealed that the transcription of an XDH-initiated catabolic pathway is up-regulated during growth with xanthine, with transcription greatest when xanthine was the only available carbon source. The RNAseq-deduced pathway indicates that glyoxylate and ammonia are the key intermediates from xanthine degradation. Utilising a laboratory model, this study has identified the potential genes and catabolic pathway active during xanthine degradation. The ability of R. pomeroyi to utilize xanthine provides novel insights into the capabilities of the MRC that may contribute to their success in marine ecosystems and the potential biogeochemical importance of the group in processing DON.

Climate change and marine plankton

Understanding how climate change will affect the planet is a key issue worldwide. Questions concerning the pace and impacts of climate change are thus central to many ecological and biogeochemical studies, and addressing the consequences of climate change is now high on the list of priorities for funding agencies. Here, we review the interactions between climate change and plankton communities, focusing on systematic changes in plankton community structure, abundance, distribution and phenology over recent decades. We examine the potential socioeconomic impacts of these plankton changes, such as the effects of bottom-up forcing on commercially exploited fish stocks (i.e. plankton as food for fish). We also consider the crucial roles that plankton might have in dictating the future pace of climate change via feedback mechanisms responding to elevated atmospheric CO sub(2) levels. An important message emerges from this review: ongoing plankton monitoring programmes worldwide will act as sentinels to identify future changes in marine ecosystems.

Impacts of fisheries on plankton community structure

There has been much debate on the extent to which resource availability (bottom-up) versus predation pressure from fish (top-down) modulates the dynamics of plankton in marine systems. Physico/chemical bottom-up forcing has been considered to be the main mechanism structuring marine ecosystems, although some field observations and empirical correlations support top-down modulation. Models have indicated possible feedback loops to the plankton and other studies have interpreted a grazing impact from long-term changes in fish stocks. In freshwater systems, evidence for top-down forcing by fish and trophic cascading is well documented. First, evidence for equivalent top-down effects in the marine environment is presented, with an overview of relevant publications. In the second part, time series, averaged for the North Sea (when possible from 1948 to 1997), of fish catch, recruitment, and spawning stock biomass are related to the abundance of species or larger groupings of zooplankton and phytoplankton from the Continuous Plankton Recorder survey and selected environmental parameters. Preliminary analysis suggests that there is strong interaction between different fish species and the plankton and that the fishery, through top-down control, may at times be an important contributor to changes in the North Sea ecosystem.

The evaluation of time series: their scientific value and contribution to policy needs. Occasional Publication of the Marine Biological Association 22

In 2000 a Review of Current Marine Observations in relation to present and future needs was undertaken by the Inter-Agency Committee for Marine Science and Technology (IACMST). The Marine Environmental Change Network (MECN) was initiated in 2002 as a direct response to the recommendations of the report. A key part of the current phase of the MECN is to ensure that information from the network is provided to policy makers and other end-users to enable them to produce more accurate assessments of ecosystem state and gain a clearer understanding of factors influencing change in marine ecosystems. The MECN holds workshops on an annual basis, bringing together partners maintaining time-series and long-term datasets as well as end-users interested in outputs from the network. It was decided that the first workshop of the MECN continuation phase should consist of an evaluation of the time series and data sets maintained by partners in the MECN with regard to their ‘fit for purpose’ for answering key science questions and informing policy development. This report is based on the outcomes of the workshop. Section one of the report contains a brief introduction to monitoring, time series and long-term datasets. The various terms are defined and the need for MECN type data to complement compliance monitoring programmes is discussed. Outlines are also given of initiatives such as the United Kingdom Marine Monitoring and Assessment Strategy (UKMMAS) and Oceans 2025. Section two contains detailed information for each of the MECN time series / long-term datasets including information on scientific outputs and current objectives. This information is mainly based on the presentations given at the workshop and therefore follows a format whereby the following headings are addressed: Origin of time series including original objectives; current objectives; policy relevance; products (advice, publications, science and society). Section three consists of comments made by the review panel concerning all the time series and the network. Needs or issues highlighted by the panel with regard to the future of long-term datasets and time-series in the UK are shown along with advice and potential solutions where offered. The recommendations are divided into 4 categories; ‘The MECN and end-user requirements’; ‘Procedures & protocols’; ‘Securing data series’ and ‘Future developments’. Ever since marine environmental protection issues really came to the fore in the 1960s, it has been recognised that there is a requirement for a suitable evidence base on environmental change in order to support policy and management for UK waters. Section four gives a brief summary of the development of marine policy in the UK along with comments on the availability and necessity of long-term marine observations for the implementation of this policy. Policy relating to three main areas is discussed; Marine Conservation (protecting biodiversity and marine ecosystems); Marine Pollution and Fisheries. The conclusion of this section is that there has always been a specific requirement for information on long-term change in marine ecosystems around the UK in order to address concerns over pollution, fishing and general conservation. It is now imperative that this need is addressed in order for the UK to be able to fulfil its policy commitments and manage marine ecosystems in the light of climate change and other factors.

From plankton to top predators: bottom-up control of a marine food web across four trophic levels

1. Abundant mid-trophic pelagic fish often play a central role in marine ecosystems, both as links between zooplankton and top predators and as important fishery targets. In the North Sea, the lesser sandeel occupies this position, being the main prey of many bird, mammal and fish predators and the target of a major industrial fishery. However, since 2003, sandeel landings have decreased by > 50%, and many sandeel-dependent seabirds experienced breeding failures in 2004. 2. Despite the major economic implications, current understanding of the regulation of key constituents of this ecosystem is poor. Sandeel abundance may be regulated 'bottom-up' by food abundance, often thought to be under climatic control, or 'top-down' by natural or fishery predation. We tested predictions from these two hypotheses by combining unique long-term data sets (1973–2003) on seabird breeding productivity from the Isle of May, SE Scotland, and plankton and fish larvae from the Continuous Plankton Recorder survey. We also tested whether seabird breeding productivity was more tightly linked to sandeel biomass or quality (size) of individual fish. 3. The biomass of larval sandeels increased two- to threefold over the study period and was positively associated with proxies of the abundance of their plankton prey. Breeding productivity of four seabirds bringing multiple prey items to their offspring was positively related to sandeel larval biomass with a 1-year lag, indicating dependence on 1-year-old fish, but in one species bringing individual fish it was strongly associated with the size of adult sandeels. 4. These links are consistent with bottom-up ecosystem regulation and, with evidence from previous studies, indicate how climate-driven changes in plankton communities can affect top predators and potentially human fisheries through the dynamics of key mid-trophic fish. However, the failing recruitment to adult sandeel stocks and the exceptionally low seabird breeding productivity in 2004 were not associated with low sandeel larval biomass in 2003, so other mechanisms (e.g. predation, lack of suitable food after metamorphosis) must have been important in this case. Understanding ecosystem regulation is extremely important for predicting the fate of keystone species, such as sandeels, and their predators.

Review of climate change impacts on marine fisheries in the UK and Ireland

1.Commercial fishing is an important socio-economic activity in coastal regions of the UK and Ireland. Ocean–atmospheric changes caused by greenhouse gas emissions are likely to affect future fish and shellfish production, and lead to increasing challenges in ensuring long-term sustainable fisheries management. 2.The paper reviews existing knowledge and understanding of the exposure of marine ecosystems to ocean-atmospheric changes, the consequences of these changes for marine fisheries in the UK and Ireland, and the adaptability of the UK and Irish fisheries sector. 3.Ocean warming is resulting in shifts in the distribution of exploited species and is affecting the productivity of fish stocks and underlying marine ecosystems. In addition, some studies suggest that ocean acidification may have large potential impacts on fisheries resources, in particular shell-forming invertebrates. 4.These changes may lead to loss of productivity, but also the opening of new fishing opportunities, depending on the interactions between climate impacts, fishing grounds and fleet types. They will also affect fishing regulations, the price of fish products and operating costs, which in turn will affect the economic performance of the UK and Irish fleets. 5.Key knowledge gaps exist in our understanding of the implications of climate and ocean chemistry changes for marine fisheries in the UK and Ireland, particularly on the social and economic responses of the fishing sectors to climate change. However, these gaps should not delay climate change mitigation and adaptation policy actions, particularly those measures that clearly have other ‘co-benefits’.

Projected impacts of climate change on marine fish and fisheries

This paper reviews current literature on the projected effects of climate change on marine fish and shellfish, their fisheries, and fishery-dependent communities throughout the northern hemisphere. The review addresses the following issues: (i) expected impacts on ecosystem productivity and habitat quantity and quality; (ii) impacts of changes in production and habitat on marine fish and shellfish species including effects on the community species composition, spatial distributions, interactions, and vital rates of fish and shellfish; (iii) impacts on fisheries and their associatedcommunities; (iv) implications for food security and associated changes; and (v) uncertainty andmodelling skill assessment. Climate change will impact fish and shellfish, their fisheries, and fishery-dependent communities through a complex suite of linked processes. Integrated interdisciplinary research teams are forming in many regions to project these complex responses. National and international marine research organizations serve a key role in the coordination and integration of research to accelerate the production of projections of the effects of climate change on marine ecosystems and to move towards a future where relative impacts by region could be compared on a hemispheric or global level. Eight research foci were identified that will improve the projections of climate impacts on fish, fisheries, and fishery-dependent communities.

Modeling marine ecosystem responses to global climate change: Where are we now and where should we be going?

Modeling of global climate change is moving from global circulation model (GCM)-type projections with coupled biogeochemical models to projections of ecological responses, including food web and upper trophic levels. Marine and coastal ecosystems are highly susceptible to the impacts of global climate change and also produce significant ecosystem services. The effects of global climate change on coastal and marine ecosystems involve a much wider array of effects than the usual temperature, sea level rise, and precipitation. This paper is an overview for a collection of 12 papers that examined various aspects of global climate change on marine ecosystems and comprise this special issue. We summarized the major features of the models and analyses in the papers to determine general patterns. A wide range of ecosystems were simulated using a diverse set of modeling approaches. Models were either 3-dimensional or used a few spatial boxes, and responses to global climate change were mostly expressed as changes from a baseline condition. Three issues were identified from the across-model comparison: (a) lack of standardization of climate change scenarios, (b) the prevalence of site-specific and even unique models for upper trophic levels, and (c) emphasis on hypothesis evaluation versus forecasting. We discuss why these issues are important as global climate change assessment continues to progress up the food chain, and, when possible, offer some initial steps for going forward.

Rapid biogeographical plankton shifts in the North Atlantic Ocean

Large-scale biogeographical changes in the biodiversity of a key zooplankton group (calanoid copepods) were detected in the north-eastern part of the North Atlantic Ocean and its adjacent seas over the period 1960–1999. These findings provided key empirical evidence for climate change impacts on marine ecosystems at the regional to oceanic scale. Since 1999, global temperatures have continued to rise in the region. Here, we extend the analysis to the period 1958–2005 using all calanoid copepod species assemblages (nine species assemblages based on an analysis including a total of 108 calanoid species or taxa) and show that this phenomenon has been reinforced in all regions. Our study reveals that the biodiversity of calanoid copepods are responding quickly to sea surface temperature (SST) rise by moving geographically northward at a rapid rate up to about 23.16 km yr−1. Our analysis suggests that nearly half of the increase in sea temperature in the northeast Atlantic and adjacent seas is related to global temperature rises (46.35% of the total variance of temperature) while changes in both natural modes of atmospheric and oceanic circulation explain 26.45% of the total variance of temperature. Although some SST isotherms have moved northwards by an average rate of up to 21.75 km yr−1 (e.g. the North Sea), their movement cannot fully quantify all species assemblage shifts. Furthermore, the observed rates of biogeographical movements are far greater than those observed in the terrestrial realm. Here, we discuss the processes that may explain such a discrepancy and suggest that the differences are mainly explained by the fluid nature of the pelagic domain, the life cycle of the zooplankton and the lesser anthropogenic influence (e.g. exploitation, habitat fragmentation) on these organisms. We also hypothesize that despite changes in the path and intensity of the oceanic currents that may modify quickly and greatly pelagic zooplankton species, these organisms may reflect better the current impact of climate warming on ecosystems as terrestrial organisms are likely to significantly lag the current impact of climate change.

Decadal changes in climate and ecosystems in the North Atlantic Ocean and adjacent seas

Climate change is unambiguous and its effects are clearly detected in all functional units of the Earth system. This study presents new analyses of sea-surface temperature changes and show that climate change is affecting ecosystems of the North Atlantic. Changes are seen from phytoplankton to zooplankton to fish and are modifying the dominance of species and the structure, the diversity and the functioning of marine ecosystems. Changes also range from phenological to biogeographical shifts and have involved in some regions of the Atlantic abrupt ecosystem shifts. These alterations reflect a response of pelagic ecosystems to a warmer temperature regime. Mechanisms are complex because they are nonlinear exhibiting tipping points and varying in space and time. Sensitivity of organisms to temperature changes is high, implicating that a small temperature modification can have sustained ecosystem effects. Implications of these changes for biogeochemical cycles are discussed. Two observed changes detected in the North Sea that could have opposite effects on carbon cycle are discussed. Increase in phytoplankton, as inferred from the phytoplankton colour index derived from the Continuous Plankton Recorder (CPR) survey, has been detected in the North Sea. This pattern has been accompanied by a reduction in the abundance of the herbivorous species Calanus finmarchicus. This might have reduced the grazing pressure and increase diatomaceous ‘fluff’, therefore carbon export in the North Sea. Therefore, it could be argued that the biological carbon pump might increase in this region with sea warming. In the meantime, however, the mean size of organisms (calanoid copepods) has dropped. Such changes have implications for the turnover time of biogenic carbon in plankton organisms and the mean residence time of particulate carbon they produce. The system characterising the warmer period is more based on recycling and less on export. The increase in the minimum turnover time indicates an increase in the ecosystem metabolism, which can be considered as a response of the pelagic ecosystems to climate warming. This phenomenon could reduce carbon export. These two opposite patterns of change are examples of the diversity of mechanisms and pathways the ecosystems may exhibit with climate change. Oversimplification of current biogeochemical models, often due to lack of data and biological understanding, could lead to wrong projection on the direction ecosystems and therefore some biogeochemical cycles might take in a warmer world.

Marine biodiversity, ecosystem functioning and carbon cycles

Although recent studies suggest that climate change may substantially accelerate the rate of species loss in the biosphere, only a few studies have focused on the potential consequences of a spatial reorganization of biodiversity with global warming. Here, we show a pronounced latitudinal increase in phytoplanktonic and zooplanktonic biodiversity in the extratropical North Atlantic Ocean in recent decades. We also show that this rise in biodiversity paralleled a decrease in the mean size of zooplanktonic copepods and that the reorganization of the planktonic ecosystem toward dominance by smaller organisms may influence the networks in which carbon flows, with negative effects on the downward biological carbon pump and demersal Atlantic cod (Gadus morhua). Our study suggests that, contrary to the usual interpretation of increasing biodiversity being a positive emergent property promoting the stability/resilience of ecosystems, the parallel decrease in sizes of planktonic organisms could be viewed in the North Atlantic as reducing some of the services provided by marine ecosystems to humans.

Spatial variability of marine climate change impacts in the North Atlantic

There is an accumulating body of evidence to suggest that many marine ecosystems in the North Atlantic, both physically and biologically are responding to changes in regional climate caused predominately by the warming of air and sea surface temperatures (SST) and to a varying degree by the modification of oceanic currents, precipitation regimes and wind patterns. The biological manifestations of rising SST and oceanographic changes have variously taken the form of biogeographical, phenological, physiological and community changes. For example, during the last 40 years there has been a northerly movement of warmer water plankton by 10 degree latitude in the north-east Atlantic and a similar retreat of colder water plankton to the north. This geographical movement is much more pronounced than any documented terrestrial study, presumably due to advective processes playing an important role. Other research has shown that the plankton community in the North Sea has responded to changes in SST by adjusting their seasonality (in some cases a shift in seasonal cycles of over six weeks has been detected), but more importantly the response to climate warming varied between different functional groups and trophic levels, leading to mismatch. Therefore, while it has been documented that marine ecosystems in certain regions of the Atlantic have undergone some conspicuous changes over the last few decades it is not known whether this is a pan-oceanic homogenous response. Using these two most prominent responses and/or indicative signals of pelagic ecosystems to hydro-climatic change, changes in species phenology and the biogeographical movement of populations, we attempt to identify vulnerable regional areas in terms of particularly rapid and marked change.

Marine ecosystem response to the Atlantic Multidecadal Oscillation

Against the backdrop of warming of the Northern Hemisphere it has recently been acknowledged that North Atlantic temperature changes undergo considerable variability over multidecadal periods. The leading component of natural low-frequency temperature variability has been termed the Atlantic Multidecadal Oscillation (AMO). Presently, correlative studies on the biological impact of the AMO on marine ecosystems over the duration of a whole AMO cycle (~60 years) is largely unknown due to the rarity of continuously sustained biological observations at the same time period. To test whether there is multidecadal cyclic behaviour in biological time-series in the North Atlantic we used one of the world's longest continuously sustained marine biological time-series in oceanic waters, long-term fisheries data and historical records over the last century and beyond. Our findings suggest that the AMO is far from a trivial presence against the backdrop of continued temperature warming in the North Atlantic and accounts for the second most important macro-trend in North Atlantic plankton records; responsible for habitat switching (abrupt ecosystem/regime shifts) over multidecadal scales and influences the fortunes of various fisheries over many centuries.

Regional and annual variation in black-legged kittiwake breeding productivity is related to sea surface temperature

Spatiotemporal variation in seabird demographic parameters is often pronounced and may be an important source of information on the state of marine ecosystems. Black-legged kittiwakes Rissa tridactyla in Britain and Ireland show strong regional structure in breeding productivity, and both temporal and spatial variation are probably related to abundance of the principal prey of breeding kittiwakes, the lesser sandeel Ammodytes marinus. Annual regional estimates of sandeel abundance do not exist, prohibiting direct tests of this hypothesis. We examined relationships between kittiwake breeding productivity and 2 potential proxies of sandeel abundance, winter sea surface temperature (SST) and abundance of Calanus copepods, within and among 6 regions in Britain and Ireland from 1986 to 2004. Means and trends in winter SST differed among regions, with higher means and less pronounced increasing trends in western (Atlantic) regions than in eastern (North Sea) regions. A negative relationship between breeding productivity and winter SST in the previous year was found within 2 regions (East Scotland and Orkney), as well as in a cross-regional analysis. Results were inconclusive for Calanus abundance, with a positive relationship in East Scotland and negative in Orkney. These results demonstrate that although a single environmental driver (SST) is related to both within- and between-region variation in a key demographic parameter, regional heterogeneity in SST trends as well as the importance of other factors may lead to highly variable responses. Understanding this heterogeneity is critical for predicting long-term effects of climate change or other anthropogenic drivers on marine ecosystems.