ALBERT

Description: Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO 2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO 2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions. © 2013 Macmillan Publishers Limited. All rights reserved.

Description: We present a magnesium (Mg) and strontium (Sr) record from an aragonitic speleothem (Grotte de Piste, Morocco, 34‬°N; 04°W) providing a reconstruction of effective rainfall from 619 to 1962 AD. The corresponding drip site was monitored over 2 yr for drip water Mg/Ca and Sr/Ca ratios. Results show evidence for prior aragonite precipitation, which can explain negative correlations between speleothem Mg and Sr concentrations. The data shown here have important climate implications concerning the evolution of the North Atlantic Oscillation (NAO). A comparison of the stalagmite data from Grotte de Piste with an updated tree ring based drought reconstruction from Morocco and other NAO related proxy records confirms that the Medieval Warm Period (MWP) was dominated by NAO+ conditions. The stalagmite record and multiple proxy records from the Iberian Peninsula, however, suggest that considerable rainfall variability occurred during the MWP. This implies that the NAO has been more variable during the MWP than formerly suggested.

Description: Marine Protected Areas (MPAs) now form an important part of marine conservation and fisheries management; hence, there is broad interest in developing procedures that optimize their design. We used data collected over a 10-year period (2003–2012) from direct surveys and 〉100 adult male and female loggerhead sea turtles (Caretta caretta ) tracked with devices, includ ing GPS loggers and Fastloc GPSArgos, to consider the optimum design for a MPA at a globally important breeding area, where there is already an existing national marine park aiming to protect the population (Zakynthos, Greece). Turtles primarily used areas very close to shore (approx. 7 km in length by 1 km in width, within the 〈10 m isobath) for breeding and foraging activity at different times of the year. We calculated that this small nearshore coastal zone encompassed 72% of all turtle GPS locations recorded in the MPA, and is therefore important for conservation management. We developed an index to evaluate the suitabili ty of the existing and proposed conserv ation zones based on (1) home range area use by turtles in these zones versus (2) zone size, so that the benefit to turtles could be maximized while minimizing the negative impacts to other stakeholders (e.g., boat operators). With this evidence-based approach, we propose a modification to the existing MPA that might both enhance local economic tourism activities and better safeguard this key sea turtle breeding population. The approaches used here will have general application for the design of MPAs used by mobile species that can be tracked.

Description: Microbial activity is a fundamental component of oceanic nutrient cycles. Photosynthetic microbes, collectively termed phytoplankton, are responsible for the vast majority of primary production in marine waters. The availability of nutrients in the upper ocean frequently limits the activity and abundance of these organisms. Experimental data have revealed two broad regimes of phytoplankton nutrient limitation in the modern upper ocean. Nitrogen availability tends to limit productivity throughout much of the surface low-latitude ocean, where the supply of nutrients from the subsurface is relatively slow. In contrast, iron often limits productivity where subsurface nutrient supply is enhanced, including within the main oceanic upwelling regions of the Southern Ocean and the eastern equatorial Pacific. Phosphorus, vitamins and micronutrients other than iron may also (co-)limit marine phytoplankton. The spatial patterns and importance of co-limitation, however, remain unclear. Variability in the stoichiometries of nutrient supply and biological demand are key determinants of oceanic nutrient limitation. Deciphering the mechanisms that underpin this variability, and the consequences for marine microbes, will be a challenge. But such knowledge will be crucial for accurately predicting the consequences of ongoing anthropogenic perturbations to oceanic nutrient biogeochemistry.

Description: Mass coral bleaching, resulting from the breakdown of coral-algal symbiosis has been identified as the most severe threat to coral reef survival on a global scale. Regionally, nutrient enrichment of reef waters is often associated with a significant loss of coral cover and diversity. Recently, increased dissolved inorganic nitrogen concentrations have been linked to a reduction of the temperature threshold of coral bleaching, a phenomenon for which no mechanistic explanation is available. Here we show that increased levels of dissolved inorganic nitrogen in combination with limited phosphate concentrations result in an increased susceptibility of corals to temperature-and light-induced bleaching. Mass spectrometric analyses of the algal lipidome revealed a marked accumulation of sulpholipids under these conditions. Together with increased phosphatase activities, this change indicates that the imbalanced supply of dissolved inorganic nitrogen results in phosphate starvation of the symbiotic algae. Based on these findings we introduce a conceptual model that links unfavourable ratios of dissolved inorganic nutrients in the water column with established mechanisms of coral bleaching. Notably, this model improves the understanding of the detrimental effects of coastal nutrient enrichment on coral reefs, which is urgently required to support knowledge-based management strategies to mitigate the effects of climate change. © 2013 Macmillan Publishers Limited. All rights reserved.

Description: Over much of the ocean’s surface, productivity and growth are limited by a scarcity of bioavailable nitrogen. Sedimentary δ15N records spanning the last deglaciation suggest marked shifts in the nitrogen cycle during this time, but the quantification of these changes has been hindered by the complexity of nitrogen isotope cycling. Here we present a database of δ15N in sediments throughout the world’s oceans, including 2,329 modern seafloor samples, and 76 timeseries spanning the past 30,000 years. We show that the δ15N values of modern seafloor sediments are consistent with values predicted by our knowledge of nitrogen cycling in the water column. Despite many local deglacial changes, the globally averaged δ15N values of sinking organic matter were similar during the Last Glacial Maximum and Early Holocene. Considering the global isotopic mass balance, we explain these observations with the following deglacial history of nitrogen inventory processes. During the Last Glacial Maximum, the nitrogen cycle was near steady state. During the deglaciation, denitrification in the pelagic water column accelerated. The flooding of continental shelves subsequently increased denitrification at the seafloor, and denitrification reached near steady-state conditions again in the Early Holocene. We use a recent parameterization of seafloor denitrification to estimate a 30–120% increase in benthic denitrification between 15,000 and 8,000 years ago. Based on the similarity of globally averaged δ15N values during the Last Glacial Maximum and Early Holocene, we infer that pelagic denitrification must have increased by a similar amount between the two steady states.

Description: In order to use environmental models effectively for management and decision-making, it is vital to establish an appropriate level of confidence in their performance. This paper reviews techniques available across various fields for characterising the performance of environmental models with focus on numerical, graphical and qualitative methods. General classes of direct value comparison, coupling real and modelled values, preserving data patterns, indirect metrics based on parameter values, and data transformations are discussed. In practice environmental modelling requires the use and implementation of workflows that combine several methods, tailored to the model purpose and dependent upon the data and information available. A five-step procedure for performance evaluation of models is suggested, with the key elements including: (i) (re)assessment of the model's aim, scale and scope; (ii) characterisation of the data for calibration and testing; (iii) visual and other analysis to detect under- or non-modelled behaviour and to gain an overview of overall performance; (iv) selection of basic performance criteria; and (v) consideration of more advanced methods to handle problems such as systematic divergence between modelled and observed values. Highlights ► Numerical, graphical and qualitative methods for characterising performance of environmental models are reviewed. ► A structured, iterative workflow that combines several evaluation methods is suggested. ► Selection of methods must be tailored to the model scope and purpose, and quality of data and information available.

Description: Small marine decapods often associatewith other invertebrates in order to gain protection frompredators. However, the factors that influence host choice by symbionts, such as shrimps, are poorly understood but may have important implications for the distribution and abundance of these mesoconsumers. In Hong Kong, the rhynchocinetid shrimp Rhynchocinetes brucei uses two alternative hosts: an urchin (Diadema setosum) and an anemone (Entacmaea quadricolor).We examined the association between R. brucei and its anemone and urchin hosts in the field and laboratory, investigating host choice and host fidelity. Underwater surveys on shallowrocky reefs in Hong Kong revealed that shrimps were rarely found outside refuges, such as crevices and holes, unless they were associated with anemones and urchins. Shrimps were more frequently associated with urchins than with anemones, although anemones were more abundant within the survey area. Host-choice experiments in the laboratory confirmed that, when given a choice, shrimps avoided open areas and associated with anemones, urchins or artificial refuges. Shrimps overwhelmingly chose urchins over artificial refuges, but did not show any clear preference for anemones over refuges. When offered a choice, shrimps displayed fidelity for their original host species (i.e. the host with which they were associated when collected from the field), suggesting that they imprinted upon the host. Host-imprinting may allow symbionts to efficiently relocate their original host species after separation (e.g. following nocturnal foraging trips) thereby, perhaps, reducing the risk of predation. However, host preference by R. brucei was facultative because shrimps would associate with an unfamiliar host when their original host was unavailable. This flexibility may allowshrimps to respond to local variability in host abundance. Host-use patterns and factors influencing the choice between anemone and urchin hosts by a caridean shrimp. Available from: https://www.researchgate.net/publication/257882112_Host-use_patterns_and_factors_influencing_the_choice_between_anemone_and_urchin_hosts_by_a_caridean_shrimp [accessed Oct 06 2017].

Description: In bacteria, foreign nucleic acids are silenced by clustered, regularly interspaced, short palindromic repeats (CRISPR)--CRISPR-associated (Cas) systems. Bacterial type II CRISPR systems have been adapted to create guide RNAs that direct site-specific DNA cleavage by the Cas9 endonuclease in cultured cells. Here we show that the CRISPR-Cas system functions in vivo to induce targeted genetic modifications in zebrafish embryos with efficiencies similar to those obtained using zinc finger nucleases and transcription activator-like effector nucleases.

Description: The identification of areas of natural gas hydrate occurrence, defining its concentration and regional distribution, as well as understanding the processes that control gas hydrate formation is a crucial component of regional gas hydrate assessments. In this study, we incorporate an additional element into a regional assessment strategy by including the depositional environment defined through seismic facies classes. The seismic facies classification is attempted using regional 2D seismic data and a 3D seismic volume, as well as core and log-data from two gas hydrate drilling expeditions carried out in the Ulleung Basin, East Sea, to conduct a fully integrated gas hydrate assessment. The facies classification described in this study is part of a procedure to conduct an assessment including: (1) Lithologic description of the recovered core and describe the deposition character of the sediment facies identified; (2) seismic facies classification using 2D and 3D seismic data and their derived various seismic attributes; (3) Linking seismic facies classes to core-derived sedimentological descriptions to define the host-strata most favourable for gas hydrate occurrences; (4) Defining reservoir physical properties and linking these to seismic facies classes for reservoir property description; (5) Calculating regional elements of the gas hydrate petroleum system (top of gas hydrate occurrence and base of gas hydrate stability); (6) Merging seismic facies and reservoir properties, definition of the top and base of the gas hydrate stability zone, to calculate gas hydrate saturations in each seismic facies and the total volume of gas hydrate present in the study area; (7) Defining probabilistic elements of the predicted volume of gas hydrate by combining statistical information of the individual input parameters through exhaustive Monte Carlo simulations. The seismic facies classification algorithm used in this study is based on identifying clusters (classes) that show similar properties in the seismic data and derived attribute characteristics. Our classification scheme uses seven seismic attributes (amplitude, instantaneous frequency and amplitude (also referred to as envelope), sweetness, acoustic impedance, thin-bed- and parallel-bedding indicator) and incorporates the use of principle component analysis for data reduction. The achieved classifications are overall robust and yield identical facies classes for the co-located 2D and 3D data. Linking the seismic facies classes to the recovered core and sedimentological descriptions results in a sedimentological interpretation of the seismic facies. Cross-plots of individual components as well as analysing the Eigen-vectors and -values from the principle component analysis (PCA) helps understand the physical meaning of these seismic facies classes and their seismic character. The five facies classes assigned to the 3D volume and 2D seismic line after PCA represent the mass transport deposit (MTD) units (class #1), hemipelagic mud with some sandy turbidite (class #2), hemipelagic mud with many sandy turbidites (class #3), as well as water-bearing mud with few sand layers and occurring mostly at shallow depth near the seafloor or beneath the base of the gas hydrate stability zone (classes #4 and #5). Within the study area and seismic data sets used, gas hydrate occurrences are only linked to facies classes #2 and #3.