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: 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 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 climatic changes of the glacial cycles are thought to have been a major driver of population declines and species extinctions. However, studies to date have focused on terrestrial fauna and there is little understanding of how marine species responded to past climate change. Here we show that a true Arctic species, the bowhead whale (Balaena mysticetus), shifted its range and tracked its core suitable habitat northwards during the rapid climate change of the Pleistocene–Holocene transition. Late Pleistocene lineages survived into the Holocene and effective female population size increased rapidly, concurrent with a threefold increase in core suitable habitat. This study highlights that responses to climate change are likely to be species specific and difficult to predict. We estimate that the core suitable habitat of bowhead whales will be almost halved by the end of this century, potentially influencing future population dynamics.

Description: At the present, the geochemical influence of the Galápagos hotspot (offshore South America) can be seen only along the Galápagos spreading center, north of the hotspot. It is possible, however, that Galápagos plume material also reached the East Pacific Rise in the past. Detecting such influence would be of particular importance for the interpretation of geochemical data from oceanic crust at Ocean Drilling Program (ODP) Site 1256, which formed ∼15 m.y. ago at the East Pacific Rise during a Miocene period of superfast spreading, and is considered to be a reference site for oceanic crust produced at fast-spreading ridges. Here we present geochemical data from Miocene basaltic crust (23–7 Ma) drilled at several Deep Sea Drilling Project (DSDP), ODP, and Integrated Ocean Drilling Program (IODP) sites that formed along the East Pacific Rise between 3°S and 7°N. Lavas formed between ca. 22.5 and ca. 11 Ma show enriched, Galápagos plume–like Pb and Nd isotope ratios (with a peak in enrichment between ≥18 and 12 Ma) compared to lavas created shortly before or after this time interval. Despite their enriched isotope composition, these samples generally show depletion in more-incompatible, relative to less-incompatible, trace elements. Derivation from an enriched Galápagos plume source that had experienced recent melt extraction before it melted further beneath the East Pacific Rise can explain the combined incompatible-trace-element depletion and isotopic enrichment of the 22.5–11 Ma lavas. The influence of plume material correlates with the interval of superfast spreading along the equatorial East Pacific Rise, suggesting a causal relationship. Enhanced ridge-plume interaction ("ridge suction") due to superfast spreading could have facilitated the flow of Galápagos plume material to the ridge. On the other hand, the arrival of Galápagos-type signatures took place immediately after formation of the Galápagos spreading center, which could have provided a pathway for hot plume material to spread into the main ridge network.

Description: The concentration of sulphate in today’s oceans—approximately 28,000 μmol l−1—is maintained by a balance between removal by pyrite burial and evaporite deposition and supply by oxidative weathering and the erosion of sulphate minerals from evaporites1. Oceanic sulphate concentrations were much lower before the rise of atmospheric oxygen about 2.4 Gyr ago2. The limited spread of δ34S values in sedimentary sulphides from 3.85 to 2.5 Gyr ago suggests that microbial sulphate reduction, if it played an important role in the Archaean marine sulphur cycle, must have occurred at sulphate concentrations of 200 μmol l−1 or less3. Here we use sulphur isotope systematics of the 2.7 Gyr old volcanogenic massive sulphide ore deposits from Kidd Creek, Ontario, to provide constraints on seawater sulphate concentrations independent of biological considerations. By comparing these values with metal and sulphur budgets from modern hydrothermal settings, we estimate that seawater sulphate concentrations 2.7 Gyr ago were roughly 80 μmol l−1. At these levels, the residence time of sulphate was on the order of 200,000 years, sufficiently long to make sulphate a conservative compound in the open ocean, but still short enough to suggest that hydrothermal sulphur fluxes were accompanied by a globally significant sink associated with microbial sulphate reduction.

Description: Half of the microbial cells in the Earth’s oceans are found in sediments1. Many of these cells are members of the Archaea2, single-celled prokaryotes in a domain of life separate from Bacteria and Eukaryota. However, most of these archaea lack cultured representatives, leaving their physiologies and placement on the tree of life uncertain. Here we show that the uncultured miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in the marine sub-sea floor. Single-cell genomic sequencing of one cell of MCG and three cells of MBG-D indicated that they form new branches basal to the archaeal phyla Thaumarchaeota3 and Aigarchaeota4, for MCG, and the order Thermoplasmatales, for MBG-D. All four cells encoded extracellular protein-degrading enzymes such as gingipain and clostripain that are known to be effective in environments chemically similar to marine sediments. Furthermore, we found these two types of peptidase to be abundant and active in marine sediments, indicating that uncultured archaea may have a previously undiscovered role in protein remineralization in anoxic marine sediments.

Description: Eight consecutive swath bathymetry data sets were obtained to monitor the submarine eruption that occurred from 10 October 2011 to 5 March 2012 south of El Hierro Island in the Canary Islands. An increase in seismic activity since July 2011 preceded the onset of the eruption, which was marked by seismic tremor and stained waters. The first bathymetry, 15 d after the eruption started, depicts a cone topping at 205 m depth, growing on a preexisting valley. Recurrent mapping shows changes in the morphology and depth of the cone, allowing us to identify collapses and calculate eruptive volumes and rates, which peaked at 12.7 × 106 m3 d−1 of non–dense rock equivalent (NDRE) on 29–30 October. The final cone consists of at least four vents along a north-northwest–south-southeast lineation, with the shallowest summit at 89 m depth. The total accumulated volume was 329 × 106 NDRE m3, of which one-third formed the cone. Similar cones have been identified on the submerged flanks of the island, with volumes ranging from 〈50 × 106 to 〉1000 × 106 NDRE m3. As in many other volcanic islands, large-scale landslides play an important role in the evolution of El Hierro. A giant flank landslide (El Golfo, 13–134 ka, 150–180 km3) mobilized, in a single event, a volume equivalent to 450–550 eruptions of the size of the reported one, showing striking differences in the construction and destruction rates of the island. This study is relevant for future monitoring programs and geohazard assessment of new submarine eruptions.