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Cold seep ecosystems are highly productive, fragmented ecosystems of the deep-sea floor. They form worldwide where methane reaches the surface seafloor, and are characterized by rich chemosynthetic communities fueled by the microbial utilization of hydrocarbons. Here we investigated with in situ (benthic chamber, microprofiler) and ex situ (pore water constituents, turnover rates of sulfate and methane, prokaryote abundance) techniques reduced sites from three different seep ecosystems in the Eastern Mediterranean deep-sea. At all three cold seep systems, the Amon Mud Volcano, Amsterdam Mud Volcano and the Nile Deep Sea Fan Pockmark area, we observed and sampled patches of highly reduced, methane-seeping sulfidic sediments which were separated by tens to hundreds of (kilo)meters with non-reduced oxygenated seafloor areas. All investigated seep sites were characterized by gassy, sulfidic sediments of blackish color, of which some were overgrown with thiotrophic bacterial mats. Fluxes of methane and oxygen, as well as sulfate reduction rates varied between the different sites. Supplement to: Pop Ristova, Petra; Wenzhöfer, Frank; Ramette, Alban; Felden, Janine; Boetius, Antje (2014): Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea). The ISME Journal, 1-13

Abstract Background Arthropod eyes have diversified during evolution to serve multiple needs, such as finding mates, hunting prey and navigating in complex surroundings under varying light conditions. This diversity is reflected in the optical apparatus, photoreceptors and neural circuits that underpin vision. Yet our ability to genetically manipulate the visual system to investigate its function is largely limited to a single species, the fruit fly Drosophila melanogaster. Here, we describe the visual system of Parhyale hawaiensis, an amphipod crustacean for which we have established tailored genetic tools. Results Adult Parhyale have apposition-type compound eyes made up of ~â 50 ommatidia. Each ommatidium contains four photoreceptor cells with large rhabdomeres (R1â 4), expected to be sensitive to the polarisation of light, and one photoreceptor cell with a smaller rhabdomere (R5). The two types of photoreceptors express different opsins, belonging to families with distinct wavelength sensitivities. Using the cis-regulatory regions of opsin genes, we established transgenic reporters expressed in each photoreceptor cell type. Based on these reporters, we show that R1â 4 and R5 photoreceptors extend axons to the first optic lobe neuropil, revealing striking differences compared with the photoreceptor projections found in related crustaceans and insects. Investigating visual function, we show that Parhyale have a positive phototactic response and are capable of adapting their eyes to different levels of light intensity. Conclusions We propose that the visual system of Parhyale serves low-resolution visual tasks, such as orientation and navigation, based on broad gradients of light intensity and polarisation. Optic lobe structure and photoreceptor projections point to significant divergence from the typical organisation found in other malacostracan crustaceans and insects, which could be associated with a shift to low-resolution vision. Our study provides the foundation for research in the visual system of this genetically tractable species.

This paper proposes a hierarchical Bayesian framework for modeling the life cycle of marine exploited fish with a spatial perspective. The application was developed for a nursery-dependent fish species, the common sole (Solea solea), on the Eastern Channel population (Western Europe). The approach combined processes of different natures and various sources of observations within an integrated framework for life-cycle modeling: (1) outputs of an individual-based model for larval drift and survival that provided yearly estimates of the dispersion and mortality of eggs and larvae, from spawning grounds to settlement in several coastal nurseries; (2) a habitat suitability model, based on juvenile trawl surveys coupled with a geographic information system, to estimate juvenile densities and surface areas of suitable juvenile habitat in each nursery sector; (3) a statistical catch-at-age model for the estimation of the numbers-at-age and the fishing mortality on subadults and adults. The approach provided estimates of hidden variables and parameters of key biological significance. A simulation approach provided insight to the robustness of the approach when only weak data are available. Estimates of spawning biomass, fishing mortality, and recruitment were close to the estimations derived from stock-assessment working groups. In addition, the model quantified mortality along the life cycle, and estimated site-specific density-dependent mortalities between settled larvae and age-0 juveniles in each nursery ground. This provided a better understanding of the productivity and the specific contribution of each nursery ground toward recruitment and population renewal. Perspectives include further development of the modeling framework on the common sole and applications to other fish species to disentangle the effects of multiple interacting stress factors (e.g., estuarine and coastal nursery habitat degradation, fishing pressure) on population renewal and to develop risk analysis in the context of marine spatial planning for sustainable management of fish resources.

This dataset contains hydrochemistry and absorption measurements from surface water bodies (standing and flowing water) from Herschel Island, Yukon, Canada collected in 2016 and Cape Bounty Arctic Watershed Observatory, Nunavut, Canada collected in 2017.The detailed methods will be found in the accompanying manuscript. Supplement to: Coch, Caroline; Juhls, Bennet; Lamoureux, Scott F; Lafrenière, Melissa J; Fritz, Michael; Heim, Birgit; Lantuit, Hugues (2019): Comparisons of dissolved organic matter and its optical characteristics in small low and high Arctic catchments. Biogeosciences, Biogeosciences, 16(23), 4535-4553

Abstract Background Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. Results We traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets. Conclusions We report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks.

Diatom assemblages from Holsteinsborg Dyb on the West Greenland shelf were analysed with high temporal resolution for the last 1200 years. A high degree of consistency between changes in frequency of selected diatom species and instrumental data from the same area during the last 70 years confirms the reliability of diatoms (particularly sea-ice species and warm-water species) for the study of palaeoceanographic changes in this area. A general cooling trend with some fluctuations is marked by an increase in sea-ice species throughout the last 1200 years. A relatively warm period with increased influence of Atlantic water masses of the Irminger Current (IC) is found at AD 750-1330, although with some oceanographic variability after AD 1000. A pronounced oceanographic shift occurred at AD 1330, corresponding in time to the transition from the so-called 'Medieval Warm Period' (MWP) to the 'Little Ice Age' (LIA). The LIA cold episode is characterized by three intervals with particularly cold sea-surface conditions at AD 1330-1350, AD 1400-1575 and AD 1660-1710 as a result of variable influence of Polar waters in the area. During the last 70 years, two relatively warm periods and one cold period (the early 1960s to mid-1990s) are indicated by changes in the diatom components. Our study demonstrates that sedimentary records on the West Greenland shelf provide valuable palaeoenvironment data that confirm a linkage between local and large-scale North Atlantic oceanographic and atmospheric oscillations. Supplement to: Sha, Longbin; Jiang, Hui; Knudsen, Karen Luise (2012): Diatom evidence of climatic change in Holsteinsborg Dyb, west of Greenland, during the last 1200 years. The Holocene, 22(3), 347-358

One of the goals of EU BASIN is to understand variability in production across the Atlantic and the impact of this variability on higher trophic levels. One aspect of these investigations is to examine the biomes defined by Longhurst (2007). These biomes are largely based on productivity measured with remote sensing. During MSM 26, mesopelagic fish and size-spectrum data were collected to test the biome classifications of the north Atlantic. In most marine systems, the size-spectrum is a decay function with more, smaller organisms and fewer larger organisms. The intercept of the size-spectrum has been linked to overall productivity while the slope represents the "rate of decay" of this productivity (Zhou 2006, doi:10.1093/plankt/fbi119). A Laser In-Situ Scattering Transmissometer was used to collect size-spectrum data and net collections were made to capture mesopelagic fish. The relationship among the mesopelagic fish size and abundance distributions will be compared to the estimates of production from the size-spectrum data to evaluate the biomes of the stations occupied during MSM 26.

Astronomical tuning of sediment sequences requires both unambiguous cycle-pattern recognition in climate proxy records and astronomical solutions, and independent information about the phase relationship between these two. Here we present two different astronomically tuned age models for the Oligocene-Miocene Transition (OMT) from Integrated Ocean Drilling Program Site U1334 (equatorial Pacific Ocean) to assess the effect tuning has on astronomically calibrated ages and the geologic time scale. These alternative age models (from ~22 to ~24 Ma) are based on different tunings between proxy records and eccentricity: the first age model is based on an aligning CaCO3 weight (wt%) to Earth's orbital eccentricity, the second age model is based on a direct age calibration of benthic foraminiferal stable carbon isotope ratios (d13C) to eccentricity. To independently test which tuned age model and associated tuning assumptions is in best agreement with independent ages based on tectonic plate-pair spreading rates, we assign our tuned ages to the magnetostratigraphic reversals identified in deep-marine magnetic anomaly profiles. Subsequently, we compute tectonic plate-pair spreading rates based on the tuned ages. The resultant, alternative spreading rate histories indicate that the CaCO3 tuned age model is most consistent with a conservative assumption of constant, or linearly changing, spreading rates. The CaCO3 tuned age model thus provides robust ages and durations for polarity chrons C6Bn.1n-C6Cn.1r, which are not based on astronomical tuning in the latest iteration of the Geologic Time Scale. Furthermore, it provides independent evidence that the relatively large (several 10,000 years) time lags documented in the benthic foraminiferal isotope records relative to orbital eccentricity, constitute a real feature of the Oligocene-Miocene climate system and carbon cycle. The age constraints from Site U1334 thus provide independent evidence that the delayed responses of the Oligocene-Miocene climate-cryosphere system and carbon cycle resulted from highly nonlinear feedbacks to astronomical forcing. Supplement to: Beddow, Helen M; Liebrand, Diederik; Wilson, Douglas S; Hilgen, Frederik J; Sluijs, Appy; Wade, Bridget S; Lourens, Lucas Joost (2018): Astronomical tunings of the Oligocene-Miocene transition from Pacific Ocean Site U1334 and implications for the carbon cycle. Climate of the Past, 14(3), 255-270