ALBERT

Description: Climate change and urban development threaten health, undermine coping and deepen existing social and environmental inequities. A changing global environment requires transformative social responses: new partnerships, deep engagement with local communities, and innovations to strengthen individual and collective assets. The chapters of this proposed edited volume will be contributed mainly by established and emerging scholars from individuals, representing social work, sociology, development studies, law, government, social anthropology, urbanism, The chapters of this proposed edited volume will be contributed mainly by established and emerging scholars from individuals representing social work, sociology, development studies, public policy, and other social sciences This book is to be used for academics, policy makers, social work students, lecturers and other stakeholders to promote advocacy for vulnerable client groups affected by Climate Change. It gives some measure of hope and make the invisible visible to change.

Description: Seeps are the expression of the migration of hydrocarbons from subsurface accumulations to the surface in sedimentary basins. They may represent an important indication of the presence of petroleum (gas and oil) reservoirs and faults, and are a natural source of greenhouse gas (methane) and atmospheric pollutants (ethane, propane) to the atmosphere. Romania is one of the countries with the largest number of seeps in the world, due to the high petroleum potential and active tectonics. Based on a review of the available literature, and on the field surveys performed by the authors during the last 17 years, we report the first comprehensive GIS-based inventory of 470 seeps in Romania (HYSED-RO), including gas seeps (10.4% of the total), oil seeps (11.7%), mud volcanoes (50.4%), gas-rich springs (12.6%), asphalt (solid) seeps (4.3%), unclassified manifestations (4.0%), and uncertain seeps (6.6%). Seeps are typically located in correspondence with major faults and vertical and fractured stratigraphic contacts associated to petroleum reservoirs (anticlines) in low heat flow areas, and their gas-geochemistry reflects that of the subsurface reservoirs. The largest and most active seeps occur in the Carpathian Foredeep, where they release thermogenic gas, and subordinately in the Transylvanian Basin, where gas is mainly microbial. HYSED-RO may represent a key reference for baseline characterization prior to subsurface petroleum extraction, for environmental studies, and atmospheric greenhouse gas emission estimates in Romania.

Description: Published

Description: 39

Description: 6A. Geochimica per l'ambiente

Description: JCR Journal

Description: Phytoplankton in the ocean are extremely diverse. The abundance of various intracellular pigments are often used to study phytoplankton physiology and ecology, and identify and quantify different phytoplankton groups. In this study, phytoplankton absorption spectra (aph(λ)) derived from underway flow-through AC-S measurements in the Fram Strait are combined with phytoplankton pigment measurements analyzed by high-performance liquid chromatography (HPLC) to evaluate the retrieval of various pigment concentrations at high spatial resolution. The performances of two approaches, Gaussian decomposition and the matrix inversion technique are investigated and compared. Our study is the first to apply the matrix inversion technique to underway spectrophotometry data. We find that Gaussian decomposition provides good estimates (median absolute percentage error, MPE 21–34%) of total chlorophyll-a (TChl-a), total chlorophyll-b (TChl-b), the combination of chlorophyll-c1 and -c2 (Chl-c1/2), photoprotective (PPC) and photosynthetic carotenoids (PSC). This method outperformed one of the matrix inversion algorithms, i.e., singular value decomposition combined with non-negative least squares (SVD-NNLS), in retrieving TChl-b, Chl-c1/2, PSC, and PPC. However, SVD-NNLS enables robust retrievals of specific carotenoids (MPE 37–65%), i.e., fucoxanthin, diadinoxanthin and 19′-hexanoyloxyfucoxanthin, which is currently not accomplished by Gaussian decomposition. More robust predictions are obtained using the Gaussian decomposition method when the observed aph(λ) is normalized by the package effect index at 675 nm. The latter is determined as a function of “packaged” aph(675) and TChl-a concentration, which shows potential for improving pigment retrieval accuracy by the combined use of aph(λ) and TChl-a concentration data. To generate robust estimation statistics for the matrix inversion technique, we combine leave-one-out cross-validation with data perturbations. We find that both approaches provide useful information on pigment distributions, and hence, phytoplankton community composition indicators, at a spatial resolution much finer than that can be achieved with discrete samples.

Description: Exposed stones in sandy sublittoral environments are hotspots for marine biodiversity, especially for benthic communities. The detection of single stones is principally possible using sidescan-sonar (SSS) backscatter data. The data resolution has to be high to visualize the acoustic shadows of the stones. Otherwise, stony substrates will not be differentiable from other high backscatter substrates (e.g., gravel). Acquiring adequate sonar data and identifying stones in backscatter images is time consuming because it usually requires visual-manual procedures. To develop a more efficient identification and demarcation procedure of stone fields, sidescan sonar and parametric echo sound data were recorded within the marine protected area of “Sylt Outer Reef” (German Bight, North Sea). The investigated area (~5.900 km2) is characterized by dispersed heterogeneous moraine and marine deposits. Data from parametric sediment echo sounder indicate hyperbolas at the sediment surface in stony areas, which can easily be exported. By combining simultaneous recorded low backscatter data and parametric single beam data, stony grounds were demarcated faster, less complex and reproducible from gravelly substrates indicating similar high backscatter in the SSS data.

Description: Backscatter mosaics based on a multi-frequency multibeam echosounder survey in the continental shelf setting of the North Sea were compared. The uncalibrated backscatter data were recorded with frequencies of 200, 400 and 600 kHz. The results showed that the seafloor appears mostly featureless in acoustic backscatter mosaics derived from 600 kHz data. The same area surveyed with 200 kHz reveals numerous backscatter anomalies with diameters of 10–70 m deviating between −2 dB and +4 dB from the background sediment. Backscatter anomalies were further subdivided based on their frequency-specific texture and were attributed to bioturbation within the sediment and the presence of polychaetes on the seafloor. While low frequencies show the highest overall contrast between different seafloor types, a consideration of all frequencies permits an improved interpretation of subtle seafloor features.

Description: The study presented here is focused on the assessment of surface elevations derived from CryoSat-2 SARIn level 1b data over the Austfonna ice cap, Svalbard, in 2016. The processing chain that must be applied to the CryoSat-2 waveforms to derive heights is non-trivial, and consists of multiple steps, all requiring subjective choices of methods such as the choice of retracker, geo-relocation, and outlier rejection. Here, we compare six CryoSat-2 level-2 type data sets of surface elevations derived using different SARIn processing chains. These data sets are validated against surface elevation data collected from an airborne laser scanner, during a dedicated CryoSat validation experiment field campaign carried out in April 2016. The flight pattern of the airborne campaign was designed so that elevations were measured in a grid pattern rather than along single lines, as has previously been the standard procedure. The flight grid pattern was chosen to optimize the comparison with the CryoSat-2 SARIn elevation data, the location of which can deviate from nadir by several kilometers due to topography within the satellite footprint. The processing chains behind the six data sets include different outlier/error rejection approaches, and do not produce the same number of data points in our region of interest. To make a consistent analysis, we provide statistics from the validation of both the full data sets from each processing chain, and on only those data that all the six data sets provide a geo-located elevation estimate for. We find that the CryoSat-2 data sets that agree best with the validation data are those derived from dedicated land ice processing schemes. This study may serve as a benchmark for future CryoSat-2 retracker developments, and the evaluation software and data set are made publicly available.

Description: The timing of snowmelt is an important turning point in the seasonal cycle of small Arctic catchments. The TerraSAR-X (TSX) satellite mission is a synthetic aperture radar system (SAR) with high potential to measure the high spatiotemporal variability of snow cover extent (SCE) and fractional snow cover (FSC) on the small catchment scale. We investigate the performance of multi-polarized and multi-pass TSX X-Band SAR data in monitoring SCE and FSC in small Arctic tundra catchments of Qikiqtaruk (Herschel Island) off the Yukon Coast in the Western Canadian Arctic. We applied a threshold based segmentation on ratio images between TSX images with wet snow and a dry snow reference, and tested the performance of two different thresholds. We quantitatively compared TSX- and Landsat 8-derived SCE maps using confusion matrices and analyzed the spatiotemporal dynamics of snowmelt from 2015 to 2017 using TSX, Landsat 8 and in situ time lapse data. Our data showed that the quality of SCE maps from TSX X-Band data is strongly influenced by polarization and to a lesser degree by incidence angle. VH polarized TSX data performed best in deriving SCE when compared to Landsat 8. TSX derived SCE maps from VH polarization detected late lying snow patches that were not detected by Landsat 8. Results of a local assessment of TSX FSC against the in situ data showed that TSX FSC accurately captured the temporal dynamics of different snow melt regimes that were related to topographic characteristics of the studied catchments. Both in situ and TSX FSC showed a longer snowmelt period in a catchment with higher contributions of steep valleys and a shorter snowmelt period in a catchment with higher contributions of upland terrain. Landsat 8 had fundamental data gaps during the snowmelt period in all 3 years due to cloud cover. The results also revealed that by choosing a positive threshold of 1 dB, detection of ice layers due to diurnal temperature variations resulted in a more accurate estimation of snow cover than a negative threshold that detects wet snow alone. We find that TSX X-Band data in VH polarization performs at a comparable quality to Landsat 8 in deriving SCE maps when a positive threshold is used. We conclude that TSX data polarization can be used to accurately monitor snowmelt events at high temporal and spatial resolution, overcoming limitations of Landsat 8, which due to cloud related data gaps generally only indicated the onset and end of snowmelt.

Description: Yedoma—extremely ice-rich permafrost with massive ice wedges formed during the Late Pleistocene—is vulnerable to thawing and degradation under climate warming. Thawing of ice-rich Yedoma results in lowering of surface elevations. Quantitative knowledge about surface elevation changes helps us to understand the freeze-thaw processes of the active layer and the potential degradation of Yedoma deposits. In this study, we use C-band Sentinel-1 InSAR measurements to map the elevation changes over ice-rich Yedoma uplands on Sobo-Sise Island, Lena Delta with frequent revisit observations (as short as six or 12 days). We observe significant seasonal thaw subsidence during summer months and heterogeneous inter-annual elevation changes from 2016–17. We also observe interesting patterns of stronger seasonal thaw subsidence on elevated flat Yedoma uplands by comparing to the surrounding Yedoma slopes. Inter-annual analyses from 2016–17 suggest that our observed positive surface elevation changes are likely caused by the delayed progression of the thaw season in 2017, associated with mean annual air temperature fluctuations.

Description: Arctic and subarctic regions are sensitive to climate change and, reversely, provide dramatic feedbacks to the global climate. With a focus on discovering paleoclimate and paleoceanographic evolution in the Arctic and Northwest Pacific Oceans during the last 20,000 years, we proposed this German–Sino cooperation program according to the announcement “Federal Ministry of Education and Research (BMBF) of the Federal Republic of Germany for a German–Sino cooperation program in the marine and polar research”. Our proposed program integrates the advantages of the Arctic and Subarctic marine sediment studies in AWI (Alfred Wegener Institute) and FIO (First Institute of Oceanography). For the first time, the collection of sediment cores can cover all climatological key regions in the Arctic and Northwest Pacific Oceans. Furthermore, the climate modeling work at AWI enables a “Data-Model Syntheses”, which are crucial for exploring the underlying mechanisms of observed changes in proxy records.

Description: An intercomparison of radiance and irradiance ocean color radiometers (the second laboratory comparison exercise—LCE-2) was organized within the frame of the European Space Agency funded project Fiducial Reference Measurements for Satellite Ocean Color (FRM4SOC) May 8–13, 2017 at Tartu Observatory, Estonia. LCE-2 consisted of three sub-tasks: (1) SI-traceable radiometric calibration of all the participating radiance and irradiance radiometers at the Tartu Observatory just before the comparisons; (2) indoor, laboratory intercomparison using stable radiance and irradiance sources in a controlled environment; (3) outdoor, field intercomparison of natural radiation sources over a natural water surface. The aim of the experiment was to provide a link in the chain of traceability from field measurements of water reflectance to the uniform SI-traceable calibration, and after calibration to verify whether di�erent instruments measuring the same object provide results consistent within the expected uncertainty limits. This paper describes the third phase of LCE-2: The results of the field experiment. The calibration of radiometers and laboratory comparison experiment are presented in a related paper of the same journal issue. Compared to the laboratory comparison, the field intercomparison has demonstrated substantially larger variability between freshly calibrated sensors, because the targets and environmental conditions during radiometric calibration were di�erent, both spectrally and spatially. Major di�erences were found for radiance sensors measuring a sunlit water target at viewing zenith angle of 139� because of the di�erent fields of view. Major di�erences were found for irradiance sensors because of imperfect cosine response of di�users. Variability between individual radiometers did depend significantly also on the type of the sensor and on the specific measurement target. Uniform SI traceable radiometric calibration ensuring fairly good consistency for indoor, laboratory measurements is insu�cient for outdoor, field measurements, mainly due to the di�erent angular variability of illumination. More stringent specifications and individual testing of radiometers for all relevant systematic e�ects (temperature, nonlinearity, spectral stray light, etc.) are needed to reduce biases between instruments and better quantify measurement uncertainties.

Description: An intercomparison of radiance and irradiance ocean color radiometers (The Second Laboratory Comparison Exercise—LCE-2) was organized within the frame of the European Space Agency funded project Fiducial Reference Measurements for Satellite Ocean Color (FRM4SOC) May 8–13, 2017 at Tartu Observatory, Estonia. LCE-2 consisted of three sub-tasks: 1) SI-traceable radiometric calibration of all the participating radiance and irradiance radiometers at the Tartu Observatory just before the comparisons; 2) Indoor intercomparison using stable radiance and irradiance sources in controlled environment; and 3) Outdoor intercomparison of natural radiation sources over terrestrial water surface. The aim of the experiment was to provide one link in the chain of traceability from field measurements of water reflectance to the uniform SI-traceable calibration, and after calibration to verify whether di�erent instruments measuring the same object provide results consistent within the expected uncertainty limits. This paper describes the activities and results of the first two phases of LCE-2: the SI-traceable radiometric calibration and indoor intercomparison, the results of outdoor experiment are presented in a related paper of the same journal issue. The indoor experiment of the LCE-2 has proven that uniform calibration just before the use of radiometers is highly e�ective. Distinct radiometers from di�erent manufacturers operated by di�erent scientists can yield quite close radiance and irradiance results (standard deviation s 〈 1%) under defined conditions. This holds when measuring stable lamp-based targets under stationary laboratory conditions with all the radiometers uniformly calibrated against the same standards just prior to the experiment. In addition, some unification of measurement and data processing must be settled. Uncertaint of radiance and irradiance measurement under these conditions largely consists of the sensor’s calibration uncertainty and of the spread of results obtained by individual sensors measuring the same object.

Description: Real-time quality-controlled surface current data derived from X-Band marine radar (MR) measurements were evaluated to estimate their operational reliability. The presented data were acquired by the standard commercial o�-the-shelf MR-based sigma s6 WaMoS® II (WaMoS® II) deployed onboard the German Research vessel Polarstern. The measurement reliability is specified by an IQ value obtained by the WaMoS® II real-time quality control (rtQC). Data which pass the rtQC without objection are assumed to be reliable. For these data sets accuracy and correlation with corresponding vessel-mounted acoustic Doppler current profiler (ADCP) measurements are determined. To reduce potential misinterpretation due to short-term oceanic variability/turbulences, the evaluation of the WaMoS® II accuracy was carried out based on sliding means over 20 min of the reliable data only. The associated standard deviation �WaMoS = 0.02 m/s of the meanWaMoS® II measurements reflect a high precision of the measurement and the successful rtQC during di�erent wave, current and weather conditions. The direct comparison of 7272 WaMoS® II/ADCP northward and eastward velocity data pairs yield a correlation of r � 0.94, with jbiasDj � 0.06 m/s and �S = 0.05 m/s. This confirms that the MR-based surface current measurements are accurate and reliable.

Description: Coring sediments in subglacial aquatic environments offers unique opportunities for research on paleo-environments and paleo-climates because it can provide data from periods even earlier than ice cores, as well as the overlying ice histories, interactions between ice and the water system, life forms in extreme habitats, sedimentology, and stratigraphy. However, retrieving sediment cores from a subglacial environment faces more difficulties than sediment coring in oceans and lakes, resulting in low yields from the most current subglacial sediment coring methods. The coring tools should pass through a hot water-drilled access borehole, then the water column, to reach the sediment layers. The access boreholes are size-limited by the hot water drilling tools and techniques. These holes are drilled through ice up to 3000–4000 m thick, with diameters ranging from 10–60 cm, and with a refreezing closure rate of up to 6 mm/h after being drilled. Several purpose-built streamline corers have been developed to pass through access boreholes and collect the sediment core. The main coring objectives are as follows: (i) To obtain undisturbed water–sediment cores, either singly or as multi-cores and (ii) to obtain long cores with minimal stratigraphic deformation. Subglacial sediment coring methods use similar tools to those used in lake and ocean coring. These methods include the following: Gravity coring, push coring, piston coring, hammer or percussion coring, vibrocoring, and composite methods. Several core length records have been attained by different coring methods, including a 290 cm percussion core from the sub-ice-shelf seafloor, a 400 cm piston core from the sub-ice-stream, and a 170 cm gravity core from a subglacial lake. There are also several undisturbed water–sediment cores that have been obtained by gravity corers or hammer corers. Most current coring tools are deployed by winch and cable facilities on the ice surface. There are three main limitations for obtaining long sediment cores which determines coring tool development, as follows: Hot-water borehole radial size restriction, the sedimentary structure, and the coring techniques. In this paper, we provide a general view on current developments in coring tools, including the working principles, corer characteristics, operational methods, coring site locations, field conditions, coring results, and possible technical improvements. Future prospects in corer design and development are also discussed.

Description: Air temperatures in the Arctic have increased substantially over the last decades, which has extensively altered the properties of the land surface. Capturing the state and dynamics of Land Surface Temperatures (LSTs) at high spatial detail is of high interest as LST is dependent on a variety of surficial properties and characterizes the land–atmosphere exchange of energy. Accordingly, this study analyses the influence of different physical surface properties on the long-term mean of the summer LST in the Arctic Mackenzie Delta Region (MDR) using Landsat 30 m-resolution imagery between 1985 and 2018 by taking advantage of the cloud computing capabilities of the Google Earth Engine. Multispectral indices, including the Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI) and Tasseled Cap greenness (TCG), brightness (TCB), and wetness (TCW) as well as topographic features derived from the TanDEM-X digital elevation model are used in correlation and multiple linear regression analyses to reveal their influence on the LST. Furthermore, surface alteration trends of the LST, NDVI, and NDWI are revealed using the Theil-Sen (T-S) regression method. The results indicate that the mean summer LST appears to be mostly influenced by the topographic exposition as well as the prevalent moisture regime where higher evapotranspiration rates increase the latent heat flux and cause a cooling of the surface, as the variance is best explained by the TCW and northness of the terrain. However, fairly diverse model outcomes for different regions of the MDR (R2 from 0.31 to 0.74 and RMSE from 0.51 °C to 1.73 °C) highlight the heterogeneity of the landscape in terms of influential factors and suggests accounting for a broad spectrum of different factors when modeling mean LSTs. The T-S analysis revealed large-scale wetting and greening trends with a mean decadal increase of the NDVI/NDWI of approximately +0.03 between 1985 and 2018, which was mostly accompanied by a cooling of the land surface given the inverse relationship between mean LSTs and vegetation and moisture conditions. Disturbance through wildfires intensifies the surface alterations locally and lead to significantly cooler LSTs in the long-term compared to the undisturbed surroundings.

Description: In this work, laboratory tests with live bivalves as well as the conceptual design of additively manufactured surrogate models are presented. The overall task of this work is to develop a surrogate best fitting to the live mussels tested in accordance to the identified surface descriptor, i.e., the Abbott–Firestone Curve, and to the hydrodynamic behaviour by means of drag and inertia coefficients. To date, very few investigations have focused on loads from currents as well as waves. Therefore, tests with a towing carriage were carried out in a wave flume. A custom-made rack using mounting clamps was built to facilitate carriage-run tests with minimal delays. Blue mussels (Mytilus edulis) extracted from a site in Germany, which were kept in aerated seawater to ensure their survival for the test duration, were used. A set of preliminary results showed drag and inertia coefficients CD and CM ranging from 1.16–3.03 and 0.25 to 1.25. To derive geometrical models of the mussel dropper lines, 3-D point clouds were prepared by means of 3-D laser scanning to obtain a realistic surface model. Centered on the 3-D point cloud, a suitable descriptor for the mass distribution over the surface was identified and three 3-D printed surrogates of the blue mussel were developed for further testing. These were evaluated regarding their fit to the original 3-D point cloud of the live blue mussels via the chosen surface descriptor.

Description: Studying phytoplankton functional types (PFTs) from space is possible due to recent advances in remote sensing. Though a variety of products are available, the limited number of wavelengths available compared to the number of model parameters needed to be retrieved is still a major problem in using ocean-color data for PFT retrievals. Here, we investigated which band placement could improve retrievals of three particular PFTs (diatoms, coccolithophores and cyanobacteria). In addition to analyzing dominant spectral features in the absorption spectra of the target PFTs, two previously-developed methods using measured spectra were applied to simulated data. Such a synthetic dataset allowed for significantly increasing the number of scenarios and enabled a full control over parameters causing spectral changes. We evaluated the chosen band placement by applying an adapted ocean reflectance inversion, as utilized in the generalized inherent optical properties (GIOP) retrieval. Results show that the optimal band settings depend on the method applied to determine the bands placement, as well as on the internal variability of the dataset investigated. Therefore, continuous hyperspectral instruments would be most beneficial for discriminating multiple PFTs, though a small improvement in spectral sampling and resolution does not significantly modify the results. Bands, which could be added to future instruments (e.g., Ocean and Land Colour Instrument (OLCI) instrument on the upcoming Sentinel-3B,-3C,-3D, etc., and further satellites) in order to enhance PFT retrieval capabilities, were also determined.

Description: We analyzed chlorophyll-a and Colored Dissolved Organic Matter (CDOM) dynamics from field measurements and assessed the potential of multispectral satellite data for retrieving water-quality parameters in three small surface reservoirs in the Brazilian semiarid region. More specifically, this work is comprised of: (i) analysis of Chl-a and trophic dynamics; (ii) characterization of CDOM; (iii) estimation of Chl-a and CDOM from OLI/Landsat-8 and RapidEye imagery. The monitoring lasted 20 months within a multi-year drought, which contributed to water-quality deterioration. Chl-a and trophic state analysis showed a highly eutrophic status for the perennial reservoir during the entire study period, while the non-perennial reservoirs ranged from oligotrophic to eutrophic, with changes associated with the first events of the rainy season. CDOM characterization suggests that the perennial reservoir is mostly influenced by autochthonous sources, while allochthonous sources dominate the non-perennial ones. Spectral-group classification assigned the perennial reservoir as a CDOM-moderate and highly eutrophic reservoir, whereas the non-perennial ones were assigned as CDOM-rich and oligotrophic-dystrophic reservoirs. The remote sensing initiative was partially successful: the Chl-a was best modelled using RapidEye for the perennial one; whereas CDOM performed best with Landsat-8 for non-perennial reservoirs. This investigation showed potential for retrieving water quality parameters in dry areas with small reservoirs

Description: In this study, we analyze interactions in lake and lake catchment systems of a continuous permafrost area. We assessed colored dissolved organic matter (CDOM) absorption at 440 nm (a(440)CDOM) and absorption slope (S300–500) in lakes using field sampling and optical remote sensing data for an area of 350 km2 in Central Yamal, Siberia. Applying a CDOM algorithm (ratio of green and red band reflectance) for two high spatial resolution multispectral GeoEye-1 and Worldview-2 satellite images, we were able to extrapolate the a(λ)CDOM data from 18 lakes sampled in the field to 356 lakes in the study area (model R2 = 0.79). Values of a(440)CDOM in 356 lakes varied from 0.48 to 8.35 m−1 with a median of 1.43 m−1. This a(λ)CDOM dataset was used to relate lake CDOM to 17 lake and lake catchment parameters derived from optical and radar remote sensing data and from digital elevation model analysis in order to establish the parameters controlling CDOM in lakes on the Yamal Peninsula. Regression tree model and boosted regression tree analysis showed that the activity of cryogenic processes (thermocirques) in the lake shores and lake water level were the two most important controls, explaining 48.4% and 28.4% of lake CDOM, respectively (R2 = 0.61). Activation of thermocirques led to a large input of terrestrial organic matter and sediments from catchments and thawed permafrost to lakes (n = 15, mean a(440)CDOM = 5.3 m−1). Large lakes on the floodplain with a connection to Mordy-Yakha River received more CDOM (n = 7, mean a(440)CDOM = 3.8 m−1) compared to lakes located on higher terraces.

Description: We studied two issues to be considered in the calculation of parameters characterizing sea ice deformation: the effect of uncertainties in an automatically retrieved sea ice drift field, and the influence of the type of drift vector grid. Sea ice deformation changes the local ice mass balance and the interaction between atmosphere, ice, and ocean, and constitutes a hazard to marine traffic and operations. Due to numerical effects, the results of deformation retrievals may predict, e.g., openings and closings of the ice cover that do not exist in reality. We focus specifically on fields of ice drift obtained from synthetic aperture radar (SAR) imagery and analyze the Propagated Drift Retrieval Error (PDRE) and the Boundary Definition Error (BDE). From the theory of error propagation, the PDRE for the calculated deformation parameters can be estimated. To quantify the BDE, we devise five different grid types and compare theoretical expectation and numerical results for different deformation parameters assuming three scenarios: pure divergence, pure shear, and a mixture of both. Our findings for both sources of error help to set up optimal deformation retrieval schemes and are also useful for other applications working with vector fields and scalar parameters derived therefrom.

Description: Abstract: The conservation of architectural heritage usually requires a multidisciplinary approach involving a variety of specialist expertise and techniques. Nevertheless, destructive techniques should be avoided, wherever possible, in order to preserve the integrity of the historical buildings, therefore the development of non-destructive and non-contact techniques is extremely important. In this framework, a methodology for combining the terrestrial laser scanning and the infrared thermal images is proposed, in order to obtain a reconnaissance of the conservation state of a historical building. The proposed case study is represented by St. Augustine Monumental Compound, located in the historical centre of the town of Cosenza (Calabria, South Italy). Adopting the proposed methodology, the paper illustrates the main results obtained for the building test overlaying and comparing the collected data with both techniques, in order to outline the capabilities both to detect the anomalies and to improve the knowledge on health state of the masonry building. The 3D model, also, allows to provide a reference model, laying the groundwork for implementation of a monitoring multisensor system based on the use of non-destructive techniques.

Description: The presented work has been carried out in the PON Monitoraggio in Area Sismica di SIstemi MOnumentali (MASSIMO) project framework, managed by the Italian National Institute of Geophysics and Volcanology (INGV) and funded by the Italian Ministry of Education, University and Research

Description: Published

Description: 194-213

Description: 6A. Monitoraggio ambientale, sicurezza e territorio

Description: JCR Journal

Description: open

Description: The three volcanoes that are the object of this paper show different types of activity that are representative of the large variety of volcanism present in the Central Mediterranean area. Etna and Stromboli are sub-aerial volcanoes, with significant part of their structure under the sea, while the Marsili Seamount is submerged, and its activity is still open to debate. The study of these volcanoes can benefit from multi-parametric observations from the seafloor. Each volcano was studied with a different kind of observation system. Stromboli seismic recordings are acquired by means of a single Ocean Bottom Seismometer (OBS). From these data, it was possible to identify two different magma chambers at different depths. At Marsili Seamount, gravimetric and seismic signals are recorded by a battery-powered multi-disciplinary observatory (GEOSTAR). Gravimetric variations and seismic Short Duration Events (SDE) confirm the presence of hydrothermal activity. At the Etna observation site, seismic signals, water pressure, magnetic field and acoustic echo intensity are acquired in real-time thanks to a cabled multi-disciplinary observatory (NEMO-SN1 ). This observatory is one of the operative nodes of the European Multidisciplinary Seafloor and water-column Observatory (EMSO; www.emso-eu.org) research infrastructure. Through a multidisciplinary approach, we speculate about deep Etna sources and follow some significant events, such as volcanic ash diffusion in the seawater.

Description: Published

Description: 298

Description: 3A. Ambiente Marino

Description: JCR Journal

Description: restricted

Description: Automatic detection of icebergs in satellite images is regarded a useful tool to provide information necessary for safety in Arctic shipping or operations over large ocean areas in near-real time. In this work, we investigated the feasibility of automatic iceberg detection in Sentinel-1 Extra Wide Swath (EWS) SAR images which follow the preferred image mode in operational ice charting. As test region, we selected the Barents Sea where the size of many icebergs is on the order of the spatial resolution of the EWS-mode. We tested a new approach for a detection scheme. It is based on a combination of a filter for enhancing the contrast between icebergs and background, subsequent blob detection, and final application of a Constant False Alarm Rate (CFAR) algorithm. The filter relies mainly on the HV-polarized intensity which often reveals a larger difference between icebergs and sea ice or open water. The blob detector identifies locations of potential icebergs and thus shortens computation time. The final detection is performed on the identified blobs using the CFAR algorithm. About 2000 icebergs captured in fast ice were visually identified in Sentinel-2 Multi Spectral Imager (MSI) data and exploited for an assessment of the detection scheme performance using confusion matrices. For our performance tests, we used four Sentinel-1 EWS images. For judging the effect of spatial resolution, we carried out an additional test with one Sentinel-1 Interferometric Wide Swath (IWS) mode image. Our results show that only 8–22 percent of the icebergs could be detected in the EWS images, and over 90 percent of all detections were false alarms. In IWS mode, the number of correctly identified icebergs increased to 38 percent. However, we obtained a larger number of false alarms in the IWS image than in the corresponding EWS image. We identified two problems for iceberg detection: 1) with the given frequency–polarization combination, not all icebergs are strong scatterers at HV-polarization, and (2) icebergs and deformation structures present on fast ice can often not be distinguished since both may reveal equally strong responses at HV-polarization.

Description: Thermokarst lakes in the Arctic and Subarctic release carbon from thawing permafrost in the form of methane and carbon dioxide with important implications for regional and global carbon cycles. Lake ice impedes the release of gas during the winter. For instance, bubbles released from lake sediments become trapped in downward growing lake ice, resulting in vertically-oriented bubble columns in the ice that are visible on the lake surface. We here describe a classification technique using an object-based image analysis (OBIA) framework to successfully map ebullition bubbles in airborne imagery of early winter ice on an interior Alaska thermokarst lake. Ebullition bubbles appear as white patches in high-resolution optical remote sensing images of snow-free lake ice acquired in early winter and, thus, can be mapped across whole lake areas. We used high-resolution (9–11 cm) aerial images acquired two and four days following freeze-up in the years 2011 and 2012, respectively. The design of multiresolution segmentation and region-specific classification rulesets allowed the identification of bubble features and separation from other confounding factors such as snow, submerged and floating vegetation, shadows, and open water. The OBIA technique had an accuracy of 〉95% for mapping ebullition bubble patches in early winter lake ice. Overall, we mapped 1195 and 1860 ebullition bubble patches in the 2011 and 2012 images, respectively. The percent surface area of lake ice covered with ebullition bubble patches for 2011 was 2.14% and for 2012 was 2.67%, representing a conservative whole lake estimate of bubble patches compared to ground surveys usually conducted on thicker ice 10 or more days after freeze-up. Our findings suggest that the information derived from high-resolution optical images of lake ice can supplement spatially limited field sampling methods to better estimate methane flux from individual lakes. The method can also be used to improve estimates of methane ebullition from numerous lakes within larger regions.

Description: Light microscopy analysis of diatom frustules is widely used in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. Although there is a need for automation in these applications, various developments in image processing and analysis methodology supporting these tasks have not become widespread in diatom-based analyses. We have addressed this issue by combining our automated diatom image analysis software SHERPA with a commercial slide-scanning microscope. The resulting workflow enables mass-analyses of a broad range of morphometric features from individual frustules mounted on permanent slides. Extensive automation and internal quality control of the results helps to minimize user intervention, but care was taken to allow the user to stay in control of the most critical steps (exact segmentation of valve outlines and selection of objects of interest) using interactive functions for reviewing and revising results. In this contribution, we describe our workflow and give an overview of factors critical for success, ranging from preparation and mounting through slide scanning and autofocus finding to final morphometric data extraction. To demonstrate the usability of our methods we finally provide an example application by analysing Fragilariopsis kerguelensis valves originating from a sediment core, which substantially extends the size range reported in the literature.

Description: We present an annotated list of new finds of red algae from Hainan Island, Southern China, including those found in 1990 and 1992 during the German-Chinese expeditions to Hainan Island and in 2008–2016 by Titlyanova, Titlyanov, and Li. Between 1990 and 1992, a total of 64 taxa of red algae were newly recorded for Hainan Island. Of these 15 species were new records for China. During the period 2008–2016, a further 54 taxa were newly recorded for Hainan Island, of which 20 were new records for China. The full list of new taxa includes taxonomic forms, dates, and locales, together with known biogeographical distributions. During both periods, the apparent enrichment of red algal marine flora has occurred in a similar way—mainly at the expense of epiphytes with filamentous, thin-filamentous, and finely branched forms. We believe that the changes in the flora of Hainan Island have been influenced by both anthropogenic and natural factors including in particular exploitation of herbivores, nutrient pollution, and coral bleaching.

Description: Alexandrium ostenfeldii is a toxic dinoflagellate that has recently bloomed in Ouwerkerkse Kreek, The Netherlands, and which is able to cause a serious threat to shellfish consumers and aquacultures. We used a large set of 68 strains to the aim of fully characterizing the toxin profiles of the Dutch A. ostenfeldii in consideration of recent reports of novel toxins. Alexandrium ostenfeldii is known as a causative species of paralytic shellfish poisoning, and consistently in the Dutch population we determined the presence of several paralytic shellfish toxins (PST) including saxitoxin (STX), GTX2/3 (gonyautoxins), B1 and C1/C2. We also examined the production of spiroimine toxins by the Dutch A. ostenfeldii strains. An extensive liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed a high intraspecific variability of spirolides (SPX) and gymnodimines (GYM). Spirolides included 13-desMethyl-spirolide C generally as the major compound and several other mostly unknown SPX-like compounds that were detected and characterized. Besides spirolides, the presence of gymnodimine A and 12-Methyl-gymnodimine A was confirmed, together with two new gymnodimines. One of these was tentatively identified as an analogue of gymnodimine D and was the most abundant gymnodimine (calculated cell quota up to 274 pg cell−1, expressed as GYM A equivalents). Our multi-clonal approach adds new analogues to the increasing number of compounds in these toxin classes and revealed a high strain variability in cell quota and in toxin profile of toxic compounds within a single population.

Description: Lakes are a ubiquitous landscape feature in northern permafrost regions. They have a strong impact on carbon, energy and water fluxes and can be quite responsive to climate change. The monitoring of lake change in northern high latitudes, at a sufficiently accurate spatial and temporal resolution, is crucial for understanding the underlying processes driving lake change. To date, lake change studies in permafrost regions were based on a variety of different sources, image acquisition periods and single snapshots, and localized analysis, which hinders the comparison of different regions. Here, we present a methodology based on machine-learning based classification of robust trends of multi-spectral indices of Landsat data (TM, ETM+, OLI) and object-based lake detection, to analyze and compare the individual, local and regional lake dynamics of four different study sites (Alaska North Slope, Western Alaska, Central Yakutia, Kolyma Lowland) in the northern permafrost zone from 1999 to 2014. Regional patterns of lake area change on the Alaska North Slope (−0.69%), Western Alaska (−2.82%), and Kolyma Lowland (−0.51%) largely include increases due to thermokarst lake expansion, but more dominant lake area losses due to catastrophic lake drainage events. In contrast, Central Yakutia showed a remarkable increase in lake area of 48.48%, likely resulting from warmer and wetter climate conditions over the latter half of the study period. Within all study regions, variability in lake dynamics was associated with differences in permafrost characteristics, landscape position (i.e., upland vs. lowland), and surface geology. With the global availability of Landsat data and a consistent methodology for processing the input data derived from robust trends of multi-spectral indices, we demonstrate a transferability, scalability and consistency of lake change analysis within the northern permafrost region.

Description: In permafrost areas, seasonal freeze-thaw cycles result in upward and downward movements of the ground. For some permafrost areas, long-term downward movements were reported during the last decade. We measured seasonal and multi-year ground movements in a yedoma region of the Lena River Delta, Siberia, in 2013–2017, using reference rods installed deep in the permafrost. The seasonal subsidence was 1.7 +- 1.5 cm in the cold summer of 2013 and 4.8 +- 2 cm in the warm summer of 2014. Furthermore, we measured a pronounced multi-year net subsidence of 9.3 +- 5.7 cm from spring 2013 to the end of summer 2017. Importantly, we observed a high spatial variability of subsidence of up to 6 cm across a sub-meter horizontal scale. In summer 2013, we accompanied our field measurements with Differential Synthetic Aperture Radar Interferometry (DInSAR) on repeat-pass TerraSAR-X (TSX) data from the summer of 2013 to detect summer thaw subsidence over the same study area. Interferometry was strongly affected by a fast phase coherence loss, atmospheric artifacts, and possibly the choice of reference point. A cumulative ground movement map, built from a continuous interferogram stack, did not reveal a subsidence on the upland but showed a distinct subsidence of up to 2 cm in most of the thermokarst basins. There, the spatial pattern of DInSAR-measured subsidence corresponded well with relative surface wetness identified with the near infra-red band of a high-resolution optical image. Our study suggests that (i) although X-band SAR has serious limitations for ground movement monitoring in permafrost landscapes, it can provide valuable information for specific environments like thermokarst basins, and (ii) due to the high sub-pixel spatial variability of ground movements, a validation scheme needs to be developed and implemented for future DInSAR studies in permafrost environments.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 90, doi:10.3389/fmars.2018.00090.

Description: Sea turtles inhabiting coastal environments routinely encounter anthropogenic hazards, including fisheries, vessel traffic, pollution, dredging, and drilling. To support mitigation of potential threats, it is important to understand fine-scale sea turtle behaviors in a variety of habitats. Recent advancements in autonomous underwater vehicles (AUVs) now make it possible to directly observe and study the subsurface behaviors and habitats of marine megafauna, including sea turtles. Here, we describe a “smart” AUV capability developed to study free-swimming marine animals, and demonstrate the utility of this technology in a pilot study investigating the behaviors and habitat of leatherback turtles (Dermochelys coriacea). We used a Remote Environmental Monitoring UnitS (REMUS-100) AUV, designated “TurtleCam,” that was modified to locate, follow and film tagged turtles for up to 8 h while simultaneously collecting environmental data. The TurtleCam system consists of a 100-m depth rated vehicle outfitted with a circular Ultra-Short BaseLine receiver array for omni-directional tracking of a tagged animal via a custom transponder tag that we attached to the turtle with two suction cups. The AUV collects video with six high-definition cameras (five mounted in the vehicle nose and one mounted aft) and we added a camera to the animal-borne transponder tag to record behavior from the turtle's perspective. Since behavior is likely a response to habitat factors, we collected concurrent in situ oceanographic data (bathymetry, temperature, salinity, chlorophyll-a, turbidity, currents) along the turtle's track. We tested the TurtleCam system during 2016 and 2017 in a densely populated coastal region off Cape Cod, Massachusetts, USA, where foraging leatherbacks overlap with fixed fishing gear and concentrated commercial and recreational vessel traffic. Here we present example data from one leatherback turtle to demonstrate the utility of TurtleCam. The concurrent video, localization, depth and environmental data allowed us to characterize leatherback diving behavior, foraging ecology, and habitat use, and to assess how turtle behavior mediates risk to impacts from anthropogenic activities. Our study demonstrates that an AUV can successfully track and image leatherback turtles feeding in a coastal environment, resulting in novel observations of three-dimensional subsurface behaviors and habitat use, with implications for sea turtle management and conservation.

Description: This research was funded by National Oceanic and Atmospheric Administration Grant #NA16NMF4720074 to the Massachusetts Division of Marine Fisheries under the Species Recovery Grants to States program. Additional funding was provided by Jean Tempel, Hydroid Inc., and over 100 Project WHOI donors.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 241, doi:10.3389/fmars.2018.00241.

Description: Cryptophyte algae are globally distributed photosynthetic flagellates found in freshwater, estuarine, and neritic ecosystems. While cryptophytes can be highly abundant and are consumed by a wide variety of protistan predators, few studies have sought to quantify in situ grazing rates on their populations. Here we show that autumnal grazing rates on in situ communities of cryptophyte algae in Chesapeake Bay are high throughout the system, while growth rates, particularly in the lower bay, were low. Analysis of the genetic diversity of cryptophyte populations within dilution experiments suggests that microzooplankton may be selectively grazing the fastest-growing members of the population, which were generally Teleaulax spp. We also demonstrate that potential grazing rates of ciliates and dinoflagellates on fluorescently labeled (FL) Rhodomonas salina, Storeatula major, and Teleaulax amphioxeia can be high (up to 149 prey predator−1 d−1), and that a Gyrodinium sp. and Mesodinium rubrum could be selective grazers. Potential grazing was highest for heterotrophic dinoflagellates, but due to its abundance, M. rubrum also had a high overall impact. This study reveals that cryptophyte algae in Chesapeake Bay can experience extremely high grazing pressure from phagotrophic protists, and that this grazing likely shapes their community diversity.

Description: The authors thank the National Science Foundation (OCE 1031718 and 1436169) for providing support for this research.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 647, doi:10.3389/fmicb.2014.00647.

Description: The Southern Ocean is currently subject to intense investigations, mainly related to its importance for global biogeochemical cycles and its alarming rate of warming in response to climate change. Microbes play an essential role in the functioning of this ecosystem and are the main drivers of the biogeochemical cycling of elements. Yet, the diversity and abundance of microorganisms in this system remain poorly studied, in particular with regards to changes along environmental gradients. Here, we used amplicon sequencing of 16S rRNA gene tags using primers covering both Bacteria and Archaea to assess the composition and diversity of the microbial communities from four sampling depths (surface, the maximum and minimum of the oxygen concentration, and near the seafloor) at 10 oceanographic stations located in Bransfield Strait [northwest of the Antarctic Peninsula (AP)] and near the sea ice edge (north of the AP). Samples collected near the seafloor and at the oxygen minimum exhibited a higher diversity than those from the surface and oxygen maximum for both bacterial and archaeal communities. The main taxonomic groups identified below 100 m were Thaumarchaeota, Euryarchaeota and Proteobacteria (Gamma-, Delta-, Beta-, and Alphaproteobacteria), whereas in the mixed layer above 100 m Bacteroidetes and Proteobacteria (mainly Alpha- and Gammaproteobacteria) were found to be dominant. A combination of environmental factors seems to influence the microbial community composition. Our results help to understand how the dynamic seascape of the Southern Ocean shapes the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes.

Description: This work was supported by the Brazilian National Counsel of Technological and Scientific Development (Polar Canion CNPq 556848/2009-8, ProOasis CNPq 565040/2010-3, Interbiota CNPq 407889/2013-2 and INCT-MAR-COI). Alex Enrich-Prast received a CNPq Productivity fellowship. Camila N. Signori was supported by a WHOI Mary Sears Visitor Award (for the microbial community analyses) and by the Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES) for the “Doctorate Sandwich” scholarship (n. 18835/12-0).

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 882, doi:10.3389/fmicb.2017.00882.

Description: Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and 〉2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.

Description: This research is funded by the Gordon and Betty Moore Foundation (GBMF 2293 and 2928), the U.S. National Science Foundation (OCE-0934095, OCE-0424602, DEB-1256724), and the São Paulo Research Foundation (FAPESP 12/51187-0).

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 1496, doi:10.3389/fmicb.2017.01496.

Description: Synechococcus are ubiquitous and cosmopolitan cyanobacteria that play important roles in global productivity and biogeochemical cycles. This study investigated the fine scale microdiversity, seasonal patterns, and spatial distributions of Synechococcus in estuarine waters of Little Sippewissett salt marsh (LSM) on Cape Cod, MA. The proportion of Synechococcus reads was higher in the summer than winter, and higher in coastal waters than within the estuary. Variations in the V4–V6 region of the bacterial 16S rRNA gene revealed 12 unique Synechococcus oligotypes. Two distinct communities emerged in early and late summer, each comprising a different set of statistically co-occurring Synechococcus oligotypes from different clades. The early summer community included clades I and IV, which correlated with lower temperature and higher dissolved oxygen levels. The late summer community included clades CB5, I, IV, and VI, which correlated with higher temperatures and higher salinity levels. Four rare oligotypes occurred in the late summer community, and their relative abundances more strongly correlated with high salinity than did other co-occurring oligotypes. The analysis revealed that multiple, closely related oligotypes comprised certain abundant clades (e.g., clade 1 in the early summer and clade CB5 in the late summer), but the correlations between these oligotypes varied from pair to pair, suggesting they had slightly different niches despite being closely related at the clade level. Lack of tidal water exchange between sampling stations gave rise to a unique oligotype not abundant at other locations in the estuary, suggesting physical isolation plays a role in generating additional microdiversity within the community. Together, these results contribute to our understanding of the environmental and ecological factors that influence patterns of Synechococcus microbial community composition over space and time in salt marsh estuarine waters.

Description: This work was supported through a subcontract from the Woods Hole Center for Oceans and Human Health, from the National Institutes of Health and the National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724), a National Research Council Research Associateship Award and L'Oreal USA Fellowship (JH), an Alfred P. Sloan Research Fellowship in Ocean Sciences and the Clare Boothe Luce Program (KM), NASA Astrobiology Institute Cooperative Agreement NNA04CC04A (MS), the Alfred P. Sloan Foundation's ICoMM field project, and the W. M. Keck Foundation.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 337, doi:10.3389/fmars.2017.00337.

Description: The fishery for American lobster is currently the highest-valued commercial fishery in the United States, worth over US$620 million in dockside value in 2015. During a marine heat wave in 2012, the fishery was disrupted by the early warming of spring ocean temperatures and subsequent influx of lobster landings. This situation resulted in a price collapse, as the supply chain was not prepared for the early and abundant landings of lobsters. Motivated by this series of events, we have developed a forecast of when the Maine (USA) lobster fishery will shift into its high volume summer landings period. The forecast uses a regression approach to relate spring ocean temperatures derived from four NERACOOS buoys along the coast of Maine to the start day of the high landings period of the fishery. Tested against conditions in past years, the forecast is able to predict the start day to within 1 week of the actual start, and the forecast can be issued 3–4 months prior to the onset of the high-landings period, providing valuable lead-time for the fishery and its associated supply chain to prepare for the upcoming season. Forecast results are conveyed in a probabilistic manner and are updated weekly over a 6-week forecasting period so that users can assess the certainty and consistency of the forecast and factor the uncertainty into their use of the information in a given year. By focusing on the timing of events, this type of seasonal forecast provides climate-relevant information to users at time scales that are meaningful for operational decisions. As climate change alters seasonal phenology and reduces the reliability of past experience as a guide for future expectations, this type of forecast can enable fishing industry participants to better adjust to and prepare for operating in the context of climate change.

Description: This forecast was initiated with support from NSF Coastal SEES (OCE 1325484) and was developed with funds from NASA EPSCoR through Maine Space Grant Consortium (EP-15-03).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 168, doi:10.3389/fmars.2018.00168.

Description: North Atlantic right whales (Eubalaena glacialis) are highly endangered and frequently exposed to a myriad of human activities and stressors in their industrialized habitat. Entanglements in fixed fishing gear represent a particularly pervasive and often drawn-out source of anthropogenic morbidity and mortality to the species. To better understand both the physiological response to entanglement, and to determine fundamental parameters such as acquisition, duration, and severity of entanglement, we measured a suite of biogeochemical markers in the baleen of an adult female that died from a well-documented chronic entanglement in 2005 (whale Eg2301). Steroid hormones (cortisol, corticosterone, estradiol, and progesterone), thyroid hormones (triiodothyronine (T3) and thyroxine (T4)), and stable isotopes (δ13C and δ15N) were all measured in a longitudinally sampled baleen plate. This yielded an 8-year profile of foraging and migration behavior, stress response, and reproduction. Stable isotopes cycled in annual patterns that reflect the animal's north-south migration behavior and seasonally abundant zooplankton diet. A progesterone peak, lasting approximately 23 months, was associated with the single known calving event (in 2002) for this female. Estradiol, cortisol, corticosterone, T3, and T4 were also elevated, although variably so, during the progesterone peak. This whale was initially sighted with a fishing gear entanglement in September 2004, but the hormone panel suggests that the animal first interacted with the gear as early as June 2004. Elevated δ15N, T3, and T4 indicate that Eg2301 potentially experienced increased energy expenditure, significant lipid catabolism, and thermal stress approximately 3 months before the initial sighting with fishing gear. All hormones in the panel (except cortisol) were elevated above baseline by September 2004. This novel study illustrates the value of using baleen to reconstruct recent temporal profiles and as a comparative matrix in which key physiological indicators of individual whales can be used to understand the impacts of anthropogenic activity on threatened whale populations.

Description: The Woods Hole Oceanographic Institution's Ocean Life Institute and Marine Mammal Center funded this study and NL was supported by a Postdoctoral Fellowship from Baylor University.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 772, doi:10.3389/fmicb.2018.00772.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 25, doi:10.3389/fmars.2018.00025.

Description: Basking shark (Cetorhinus maximus) populations are considered “vulnerable” globally and “endangered” in the northeast Atlantic by the International Union for the Conservation of Nature (IUCN). Much of our knowledge of this species comes from surface observations in coastal waters, yet recent evidence suggests the majority of their lives may be spent in the deep ocean. Depth preferences of basking sharks have significantly limited movement studies that used pop-up satellite archival transmitting (PSAT) tags as conventional light-based geolocation is impossible for tagged animals that spend significant time below the photic zone. We tagged 57 basking sharks with PSAT tags in the NW Atlantic from 2004 to 2011. Many individuals spent several months at meso- and bathy-pelagic depths where accurate light-level geolocation was impossible during fall, winter and spring. We applied a newly-developed geolocation approach for the PSAT data by comparing three-dimensional depth-temperature profile data recorded by the tags to modeled in situ oceanographic data from the high-resolution HYbrid Coordinate Ocean Model (HYCOM). Observation-based likelihoods were leveraged within a state-space hidden Markov model (HMM). The combined tracks revealed that basking sharks moved from waters around Cape Cod, MA to as far as the SE coast of Brazil (20°S), a total distance of over 17,000 km. Moreover, 59% of tagged individuals with sufficient deployment durations (〉250 days) demonstrated seasonal fidelity to Cape Cod and the Gulf of Maine, with one individual returning to within 60 km of its tagging location 1 year later. Tagged sharks spent most of their time at epipelagic depths during summer months around Cape Cod and in the Gulf of Maine. During winter months, sharks spent extended periods at depths of at least 600 m while moving south to the Sargasso Sea, the Caribbean Sea, or the western tropical Atlantic. Our work demonstrates the utility of applying advances in oceanographic modeling to understanding habitat use of highly migratory, often meso- and bathy-pelagic, ocean megafauna. The large-scale movement patterns of tagged sharks highlight the need for international cooperation when designing and implementing conservation strategies to ensure that the species recovers from the historical effects of over-fishing throughout the North Atlantic Ocean.

Description: We gratefully acknowledge funding from the US National Science Foundation (OCE 0825148), the National Aeronautics and Space Administration (NNS06AA96G), the Massachusetts Environmental Trust, and the Federal Aid in Sport Fish Restoration Program. CB was funded by the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology, the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution, and the NASA Earth and Space Science Fellowship. Funding for the development of HYCOM has been provided by the National Ocean Partnership Program and the Office of Naval Research.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 840, doi:10.3389/fmicb.2018.00840.

Description: Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.

Description: We wish to acknowledge the support of the Sloan Foundation and the Deep Carbon Observatory and the Department of Energy, Office of Fossil Energy (Colwell).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Earth Science 6 (2018): 147, doi:10.3389/feart.2018.00147.

Description: Silicic effusive eruptions in deep submarine environments have not yet been directly observed and very few modern submarine silicic lavas and domes have been described. The eruption of Havre caldera volcano in the Kermadec arc in 2012 provided an outstanding database for research on deep submarine silicic effusive eruptions because it produced 15 rhyolite (70–72 wt.% SiO2) lavas and domes with a total volume of ∼0.21 km3 from 14 separate seafloor vents. Moreover, in 2015, the seafloor products were observed, mapped and sampled in exceptional detail (1-m resolution) using AUV Sentry and ROV Jason2 deployed from R/V Roger Revelle. Vent positions are strongly aligned, defining NW-SE and E-W trends along the southwestern and southern Havre caldera margin, respectively. The alignment of the vents suggests magma ascent along dykes which probably occupy faults related to the caldera margin. Four vents part way up the steeply sloping southwestern caldera wall at 1,200–1,300 m below sea level (bsl) and one on the caldera rim (1,060 m bsl) produced elongate lavas. On the steep caldera wall, the lavas consist of narrow tongues that have triangular cross-section shapes. Two of the narrow-tongue segments are connected to wide lobes on the flat caldera floor at ∼1,500 m bsl. The lavas are characterized by arcuate surface ridges oriented perpendicular to the propagation direction. Eight domes were erupted onto relatively flat sea floor from vents at ∼1,000 m bsl along the southern and southwestern caldera rim. They are characterized by steep margins and gently convex-up upper surfaces. With one exception, the domes have narrow spines and deep clefts above the inferred vent positions. One dome has a relatively smooth upper surface. The lavas and domes all consist of combinations of coherent rhyolite and monomictic rhyolite breccia. Despite eruption from deep-water vents (most 〉900 m bsl), the Havre 2012 rhyolite lavas and domes are very similar to subaerial rhyolite lavas and domes in terms of dimensions, volumes, aspect ratio, textures and morphology. They show that lava morphology was strongly controlled by the pre-existing seafloor topography: domes and wide lobes formed where the rhyolite was emplaced onto flat sea floor, whereas narrow tongues formed where the rhyolite was emplaced on the steep slopes of the caldera wall.

Description: This research was funded by an Australian Research Council Postdoctoral fellowship to RJC (DP110102196 and DE150101190), and National Science Foundation grants OCE1357443 and OCE1357216. FI was supported by a Tasmanian Government Postgraduate Award.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 10 (2019): 115, doi:10.3389/fmicb.2019.00115.

Description: This Research Topic was supported by the National Key Research and Development Program of China grant 2016YFA0601303, China Ocean Mineral Resources R&D Association grant DY135-E2-1-04, China SOA grant GASI-03-01-02-05, NSFC grants 41676122, 91328209, and 91428308, and CNOOC grant CNOOC-KJ125FZDXM00TJ001-2014.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wurch, L. L., Alexander, H., Frischkorn, K. R., Haley, S. T., Gobler, C. J., & Dyhrman, S. T. Transcriptional shifts highlight the role of nutrients in harmful brown tide dynamics. Frontiers in Microbiology, 10, (2019):136, doi:10.3389/fmicb.2019.00136.

Description: Harmful algal blooms (HABs) threaten ecosystems and human health worldwide. Controlling nitrogen inputs to coastal waters is a common HAB management strategy, as nutrient concentrations often suggest coastal blooms are nitrogen-limited. However, defining best nutrient management practices is a long-standing challenge: in part, because of difficulties in directly tracking the nutritional physiology of harmful species in mixed communities. Using metatranscriptome sequencing and incubation experiments, we addressed this challenge by assaying the in situ physiological ecology of the ecosystem destructive alga, Aureococcus anophagefferens. Here we show that gene markers of phosphorus deficiency were expressed in situ, and modulated by the enrichment of phosphorus, which was consistent with the observed growth rate responses. These data demonstrate the importance of phosphorus in controlling brown-tide dynamics, suggesting that phosphorus, in addition to nitrogen, should be evaluated in the management and mitigation of these blooms. Given that nutrient concentrations alone were suggestive of a nitrogen-limited ecosystem, this study underscores the value of directly assaying harmful algae in situ for the development of management strategies.

Description: This research was funded by NOAA Grant NA15NOS4780199 (SD), NA09NOA4780206 (SD and CG), and NA15NOS4780183 (CG) through the ECOHAB Program, publication number ECO929. Partial support was also provided by the World Surf League through the Columbia Center for Climate and Life, the Woods Hole Oceanographic Institution Coastal Ocean Institute, and the Link Foundation. Kyle Frischkorn was funded under a National Science Foundation Graduate Research Fellowship.

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 104, doi:10.3389/fmicb.2015.00104.

Description: Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.

Description: This work was supported by funding from the University of Massachusetts Amherst to DeAngelis and the National Science Foundation Long-term Ecological Research (LTER) Program.

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 90, doi:10.3389/fmicb.2015.00090.

Description: Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture.

Description: SAW, MA, CN, and CAP were supported by NSF PIRE grant OISE-0968211. GeoChip analysis was supported by the Office of the Vice President for Research at the University of Oklahoma and NSF MacroSystems Biology program EF-1065844 to JZ.

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Cellular Neuroscience 8 (2015): 455, doi:10.3389/fncel.2014.00455.

Description: Here we summarize the evidence from two “giant” presynaptic terminals—the squid giant synapse and the mammalian calyx of Held—supporting the involvement of nanodomain calcium signals in triggering of neurotransmitter release. At the squid synapse, there are three main lines of experimental evidence for nanodomain signaling. First, changing the size of the unitary calcium channel current by altering external calcium concentration causes a non-linear change in transmitter release, while changing the number of open channels by broadening the presynaptic action potential causes a linear change in release. Second, low-affinity calcium indicators, calcium chelators, and uncaging of calcium all suggest that presynaptic calcium concentrations are as high as hundreds of micromolar, which is more compatible with a nanodomain type of calcium signal. Finally, neurotransmitter release is much less affected by the slow calcium chelator, ethylene glycol tetraacetic acid (EGTA), in comparison to the rapid chelator 1,2-bis(o-aminophenoxy)ethane-N,N,N’,N’-tetraacetic acid (BAPTA). Similarly, as the calyx of Held synapse matures, EGTA becomes less effective in attenuating transmitter release while the number of calcium channels required to trigger a single fusion event declines. This suggests a developmental transformation of microdomain to nanodomain coupling between calcium channels and transmitter release. Calcium imaging and uncaging experiments, in combination with simulations of calcium diffusion, indicate the peak calcium concentration seen by presynaptic calcium sensors reaches at least tens of micromolar at the calyx of Held. Taken together, data from these provide a compelling argument that nanodomain calcium signaling gates very rapid transmitter release.

Description: This work was supported by a CRP grant from the National Research Foundation of Singapore and by the World Class Institute (WCI) Program of the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology of Korea (MEST) (NRF Grant Number: WCI 2009-003) (to George J. Augustine), and by Operating Grants from the Canadian Institutes of Health Research (MOP-77610, MOP-81159, MOP-14692, VIH-105441) and Canada Research Chair (to Lu-Yang Wang).

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 1288, doi:10.3389/fmicb.2015.01288.

Description: We used culture-based and culture-independent approaches to discover diversity and ecology of anaerobic jakobids (Excavata: Jakobida), an overlooked, deep-branching lineage of free-living nanoflagellates related to Euglenozoa. Jakobids are among a few lineages of nanoflagellates frequently detected in anoxic habitats by PCR-based studies, however only two strains of a single jakobid species have been isolated from those habitats. We recovered 712 environmental sequences and cultured 21 new isolates of anaerobic jakobids that collectively represent at least ten different species in total, from which four are uncultured. Two cultured species have never been detected by environmental, PCR-based methods. Surprisingly, culture-based and culture-independent approaches were able to reveal a relatively high proportion of overall species diversity of anaerobic jakobids—60 or 80%, respectively. Our phylogenetic analyses based on SSU rDNA and six protein-coding genes showed that anaerobic jakobids constitute a clade of morphologically similar, but genetically and ecologically diverse protists—Stygiellidae fam. nov. Our investigation combines culture-based and environmental molecular-based approaches to capture a wider extent of species diversity and shows Stygiellidae as a group that ordinarily inhabits anoxic, sulfide- and ammonium-rich marine habitats worldwide.

Description: This work was supported by grants from the Czech Science Foundation (project GA14-14105S), the Grant Agency of Charles University (project 301711), Charles University Specific Research SVV 260208/2015. VE and MP acknowledge support from NSF OCE-0849578 and OCE-0326175 for DHAB and Cariaco data. Unpublished data from Saanich Inlet were generously provided by Steven Hallam whose long-term research at this site is made possible through funding from the Tula Foundation-funded Centre for Microbial Diversity and Evolution, the Natural Sciences and Engineering Research Council of Canada, the Canada Foundation for Innovation, and the Canadian Institute for Advanced Research for Saanich Inlet data.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1731, doi: 10.3389/fmicb.2016.01731.

Description: The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.

Description: CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 264, doi:10.3389/fmicb.2017.00264.

Description: The occurrence of bacteria in the food processing environments plays a key role in food contamination and development of spoilage. Species of the genus Pseudomonas are recognized as major food spoilers and the capability to actually determine spoilage can be species- as well as strain-dependent. In order to improve the taxonomic resolution of 16S rRNA gene amplicons, in this study we used oligotyping to investigate the diversity of Pseudomonas populations in meat and dairy processing environments. Sequences of the V1–V3 regions from previous studies were used, including environmental swabs and food samples from both meat and dairy processing plants. We showed that the most frequently found oligotypes belonged to Pseudomonas fragi and P. fluorescens, that the most abundant oligotypes co-occurred, and were shared between the meat and dairy datasets. All the oligotypes occurring in foods were also identified in the environmental samples of the corresponding plants, highlighting the important role of the environment as a source of strains for food contamination. Oligotypes of the same species showed different levels depending on food processing and type of sample, suggesting that different strains of the same species can have different adaptation efficiency, leading to resilient bacterial associations.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 109, doi:10.3389/fmars.2017.00109.

Description: Assessment of underwater noise is of particular interest given the increase in noise-generating human activities and the potential negative effects on marine mammals which depend on sound for many vital processes. The Azores archipelago is an important migratory and feeding habitat for blue (Balaenoptera musculus), fin (Balaenoptera physalus) and sei whales (Balaenoptera borealis) en route to summering grounds in northern Atlantic waters. High levels of low frequency noise in this area could displace whales or interfere with foraging behavior, impacting energy intake during a critical stage of their annual cycle. In this study, bottom-mounted Ecological Acoustic Recorders were deployed at three Azorean seamounts (Condor, Açores, and Gigante) to measure temporal variations in background noise levels and ship noise in the 18–1,000 Hz frequency band, used by baleen whales to emit and receive sounds. Monthly average noise levels ranged from 90.3 dB re 1 μPa (Açores seamount) to 103.1 dB re 1 μPa (Condor seamount) and local ship noise was present up to 13% of the recording time in Condor. At this location, average contribution of local boat noise to background noise levels is almost 10 dB higher than wind contribution, which might temporally affect detection ranges for baleen whale calls and difficult communication at long ranges. Given the low time percentatge with noise levels above 120 dB re 1 μPa found here (3.3% at Condor), we woud expect limited behavioral responses to ships from baleen whales. Sound pressure levels measured in the Azores are lower than those reported for the Mediterranean basin and the Strait of Gibraltar. However, the currently unknown effects of baleen whale vocalization masking and the increasing presence of boats at the monitored sites underline the need for continuous monitoring to understand any long-term impacts on whales.

Description: Fundação para a Ciência e a Tecnologia (FCT) and Fundo Regional da Ciência e Tecnologia (FRCT), through research projects TRACE (PTDC/MAR/74071/2006), MAPCET (M2.1.2/F/012/2011), and FCT Exploratory project (IF/00943/2013/CP1199/CT0001), supported by funds from FEDER, the Competitiveness Factors Operational (COMPETE), QREN, POPH, European Social Fund, Portuguese Ministry for Science and Education, and Proconvergencia Açores/EU Program. We also acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013, that also supported fees for this open access publication. MR is supported by a DRCT doctoral grant (M3.1.a/F/028/2015), IC was supported by a FCT doctoral grant (SFRH/BD/41192/2007) and MAS is supported by an FCT-Investigator contract (IF/00943/2013).

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 682, doi:10.3389/fmicb.2017.00682.

Description: The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.

Description: The study was supported by a Discovery Outstanding Researcher Award (DP120103498) and an Australian Laureate Fellowship (FL150100038) from the Australian Research Council.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 334, doi:10.3389/fmars.2017.00334.

Description: Scattering structures, including deep (〉200 m) scattering layers are common in most oceans, but have not previously been properly documented in the Arctic Ocean. In this work, we combine acoustic data for distribution and abundance estimation of zooplankton and fish with biological sampling from the region west and north of Svalbard, to examine high latitude meso- and epipelagic scattering layers and their biological constituents. Our results show that typically, there was strong patchy scattering in the upper part of the epipelagic zone (〈50 m) throughout the area. It was mainly dominated by copepods, krill, and amphipods in addition to 0-group fish that were particularly abundant west of the Spitsbergen Archipelago. Off-shelf there was a distinct deep scattering layer (DSL) between 250 and 600 m containing a range of larger longer lived organisms (mesopelagic fish and macrozooplankton). In eastern Fram Strait, the DSL also included and was in fact dominated by larger fish close to the shelf/slope break that were associated with Warm Atlantic Water moving north toward the Arctic Ocean, but switched to dominance by species having weaker scattering signatures further offshore. The Weighted Mean Depths of the DSL were deeper (WMD 〉 440 m) in the Arctic habitat north of Svalbard compared to those south in the Fram Strait west of Svalbard (WMD ~400 m). The surface integrated backscatter [Nautical Area-Scattering Coefficient, NASC, sA (m2 nmi−2)] was considerably lower in the waters around Svalbard compared to the more southern regions (62–69°N). Also, the integrated DSL nautical area scattering coefficient was a factor of ~6–10 lower around Svalbard compared to the areas in the south-eastern part of the Norwegian Sea ~62°30′N. The documented patterns and structures, particularly the DSL and its constituents, will be key reference points for understanding and quantifying future changes in the pelagic ecosystem at the entrance to the Arctic Ocean.

Description: The Research Council of Norway is thanked for the financial support through the projects “The Arctic Ocean Ecosystem”—(SI_ARCTIC, RCN 228896), the “Effects of climate change on the Calanus complex”—(ECCO, RCN 200508), “Harvesting marine cold water plankton species—abundance estimation and stock assessment”—(Harvest II, RCN 203871) as well as the Institute of Marine Research, Bergen.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 49, doi:10.3389/fmars.2018.00049.

Description: Species inhabiting deep-sea hydrothermal vents are strongly influenced by the geological setting, as it provides the chemical-rich fluids supporting the food web, creates the patchwork of seafloor habitat, and generates catastrophic disturbances that can eradicate entire communities. The patches of vent habitat host a network of communities (a metacommunity) connected by dispersal of planktonic larvae. The dynamics of the metacommunity are influenced not only by birth rates, death rates and interactions of populations at the local site, but also by regional influences on dispersal from different sites. The connections to other communities provide a mechanism for dynamics at a local site to affect features of the regional biota. In this paper, we explore the challenges and potential benefits of applying metacommunity theory to vent communities, with a particular focus on effects of disturbance. We synthesize field observations to inform models and identify data gaps that need to be addressed to answer key questions including: (1) what is the influence of the magnitude and rate of disturbance on ecological attributes, such as time to extinction or resilience in a metacommunity; (2) what interactions between local and regional processes control species diversity, and (3) which communities are “hot spots” of key ecological significance. We conclude by assessing our ability to evaluate resilience of vent metacommunities to human disturbance (e.g., deep-sea mining). Although the resilience of a few highly disturbed vent systems in the eastern Pacific has been quantified, these values cannot be generalized to remote locales in the western Pacific or mid Atlantic where disturbance rates are different and information on local controls is missing.

Description: LM was supported by NSF OCE 1356738 and DEB 1558904. SB was supported by the NSF DEB 1558904 and the Investment in Science Fund at Woods Hole Oceanographic Institution. MB was supported by the Austrian Science Fund grants P20190-B17 and P16774-B03. LL was supported by NSF OCE 1634172 and the JM Kaplan Fund. MN was supported by NSF DEB 1558904. Y-JW was supported by a Korean Institute of Ocean Science and Technology (KIOST) grant PM60210.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 158, doi:10.3389/fmars.2018.00158.

Description: In autumn 2015, several sources reported observations of large amounts of gelatinous material in a large north Norwegian fjord system, either caught when trawling for other organisms or fouling fishing gear. The responsible organism was identified as a physonect siphonophore, Nanomia cara, while a ctenophore, Beroe cucumis, and a hydromedusa, Modeeria rotunda, were also registered in high abundances on a couple of occasions. To document the phenomena, we have compiled a variety of data from concurrent fisheries surveys and local fishermen, including physical samples, trawl catch, and acoustic data, photo and video evidence, and environmental data. Because of the gas-filled pneumatophore, characteristic for these types of siphonophores, acoustics provided detailed and unique insight to the horizontal and vertical distribution and potential abundances (~0.2–20 colonies·m−3) of N. cara with the highest concentrations observed in the near bottom region at ~320 m depth in the study area. This suggests that these animals were retained and accumulated in the deep basins of the fjord system possibly blooming here because of favorable environmental conditions and potentially higher prey availability compared to the shallower shelf areas to the north. Few cues as to the origin and onset of the bloom were found, but it may have originated from locally resident siphonophores. The characteristics of the deep-water masses in the fjord basins were different compared to the deep water outside the fjord system, suggesting no recent deep-water import to the fjords. However, water-masses containing siphonophores (not necessarily very abundant), may have been additionally introduced to the fjords at intermediate depths, with the animals subsequently trapped in the deeper fjord basins. The simultaneous observations of abundant siphonophores, hydromedusae, and ctenophores in the Lyngen-Kvænangen fjord system are intriguing, but difficult to provide a unified explanation for, as the organisms differ in their biology and ecology. Nanomia and Beroe spp. are holopelagic, while M. rotunda has a benthic hydroid stage. The species also have different trophic ecologies and dietary preferences. Only by combining information from acoustics, trawling, genetics, and local fishermen, were the identity, abundance, and the vertical and horizontal distribution of the physonect siphonophore, N. cara, established.

Description: The work was funded by the Ministry of Fisheries and Coastal Affairs through the Institute of Marine Research (IMR), while the Research Council of Norway (RCN) is thanked for the financial support through the project The Arctic Ocean Ecosystem—(SI_ARCTIC, RCN 228896). AH was supported by the Norwegian Taxonony Initiative (NTI 70184233) and ForBio Research School funding (RCN 248799 and NTI 70184215).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 1201, doi:10.3389/fmicb.2018.01201.

Description: Interactions between microorganisms and algae during bloom events significantly impacts their physiology, alters ambient chemistry, and shapes ecosystem diversity. The potential role these interactions have in bloom development and decline are also of particular interest given the ecosystem impacts of algal blooms. We hypothesized that microbial community structure and succession is linked to specific bloom stages, and reflects complex interactions among taxa comprising the phycosphere environment. This investigation used pyrosequencing and correlation approaches to assess patterns and associations among bacteria, archaea, and microeukaryotes during a spring bloom of the dinoflagellate Alexandrium catenella. Within the bacterial community, Gammaproteobacteria and Bacteroidetes were predominant during the initial bloom stage, while Alphaproteobacteria, Cyanobacteria, and Actinobacteria were the most abundant taxa present during bloom onset and termination. In the archaea biosphere, methanogenic members were present during the early bloom period while the majority of species identified in the late bloom stage were ammonia-oxidizing archaea and Halobacteriales. Dinoflagellates were the major eukaryotic group present during most stages of the bloom, whereas a mixed assemblage comprising diatoms, green-algae, rotifera, and other microzooplankton were present during bloom termination. Temperature and salinity were key environmental factors associated with changes in bacterial and archaeal community structure, respectively, whereas inorganic nitrogen and inorganic phosphate were associated with eukaryotic variation. The relative contribution of environmental parameters measured during the bloom to variability among samples was 35.3%. Interaction analysis showed that Maxillopoda, Spirotrichea, Dinoflagellata, and Halobacteria were keystone taxa within the positive-correlation network, while Halobacteria, Dictyochophyceae, Mamiellophyceae, and Gammaproteobacteria were the main contributors to the negative-correlation network. The positive and negative relationships were the primary drivers of mutualist and competitive interactions that impacted algal bloom fate, respectively. Functional predictions showed that blooms enhance microbial carbohydrate and energy metabolism, and alter the sulfur cycle. Our results suggest that microbial community structure is strongly linked to bloom progression, although specific drivers of community interactions and responses are not well understood. The importance of considering biotic interactions (e.g., competition, symbiosis, and predation) when investigating the link between microbial ecological behavior and an algal bloom’s trajectory is also highlighted.

Description: This work was supported by NSFC (41476092, 41741015), S&T Projects of Shenzhen Science and Technology Innovation Committee (JCYJ20150831192329178, JCYJ20170817160708491, and JCYJ20170412171959157), Key Research and Development Plan of Ministry of Science and Technology of China (2017YFC1403600), as well as by the Woods Hole Center for Oceans and Human Health through the National Science Foundation (Grant OCE-1314642), and National Institute of Environmental Health Sciences (Grant 1-P01-ES021923-01).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 9 (2018): 838, doi: 10.3389/fphys.2018.00838.

Description: Bottlenose dolphins (Tursiops truncatus) are highly versatile breath-holding predators that have adapted to a wide range of foraging niches from rivers and coastal ecosystems to deep-water oceanic habitats. Considerable research has been done to understand how bottlenose dolphins manage O2 during diving, but little information exists on other gases or how pressure affects gas exchange. Here we used a dynamic multi-compartment gas exchange model to estimate blood and tissue O2, CO2, and N2 from high-resolution dive records of two different common bottlenose dolphin ecotypes inhabiting shallow (Sarasota Bay) and deep (Bermuda) habitats. The objective was to compare potential physiological strategies used by the two populations to manage shallow and deep diving life styles. We informed the model using species-specific parameters for blood hematocrit, resting metabolic rate, and lung compliance. The model suggested that the known O2 stores were sufficient for Sarasota Bay dolphins to remain within the calculated aerobic dive limit (cADL), but insufficient for Bermuda dolphins that regularly exceeded their cADL. By adjusting the model to reflect the body composition of deep diving Bermuda dolphins, with elevated muscle mass, muscle myoglobin concentration and blood volume, the cADL increased beyond the longest dive duration, thus reflecting the necessary physiological and morphological changes to maintain their deep-diving life-style. The results indicate that cardiac output had to remain elevated during surface intervals for both ecotypes, and suggests that cardiac output has to remain elevated during shallow dives in-between deep dives to allow sufficient restoration of O2 stores for Bermuda dolphins. Our integrated modeling approach contradicts predictions from simple models, emphasizing the complex nature of physiological interactions between circulation, lung compression, and gas exchange.

Description: AF (N00014-17-1-2756), PT (N000141512553) and FHJ (N00014-14-1-0410) were supported by the Office of Naval Research, and FHJ by an AIASCOFUND fellowship from Aarhus Institute of Advanced Studies, Aarhus University, under EU's FP7 program (Agreement No. 609033). PT received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) and their support is gratefully acknowledged.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sathyendranath, S., Brewin, R. J. W., Brockmann, C., Brotas, V., Calton, B., Chuprin, A., Cipollini, P., Couto, A. B., Dingle, J., Doerffer, R., Donlon, C., Dowell, M., Farman, A., Grant, M., Groom, S., Horseman, A., Jackson, T., Krasemann, H., Lavender, S., Martinez-Vicente, V., Mazeran, C., Melin, F., Moore, T. S., Muller, D., Regner, P., Roy, S., Steele, C. J., Steinmetz, F., Swinton, J., Taberner, M., Thompson, A., Valente, A., Zuhlke, M., Brando, V. E., Feng, H., Feldman, G., Franz, B. A., Frouin, R., Gould, R. W., Hooker, S. B., Kahru, M., Kratzer, S., Mitchell, B. G., Muller-Karger, F. E., Sosik, H. M., Voss, K. J., Werdell, J., & Platt, T. An ocean-colour time series for use in climate studies: The experience of the ocean-colour climate change initiative (OC-CCI). Sensors, 19(19), (2019): 4285, doi: 10.3390/s19194285.

Description: Ocean colour is recognised as an Essential Climate Variable (ECV) by the Global Climate Observing System (GCOS); and spectrally-resolved water-leaving radiances (or remote-sensing reflectances) in the visible domain, and chlorophyll-a concentration are identified as required ECV products. Time series of the products at the global scale and at high spatial resolution, derived from ocean-colour data, are key to studying the dynamics of phytoplankton at seasonal and inter-annual scales; their role in marine biogeochemistry; the global carbon cycle; the modulation of how phytoplankton distribute solar-induced heat in the upper layers of the ocean; and the response of the marine ecosystem to climate variability and change. However, generating a long time series of these products from ocean-colour data is not a trivial task: algorithms that are best suited for climate studies have to be selected from a number that are available for atmospheric correction of the satellite signal and for retrieval of chlorophyll-a concentration; since satellites have a finite life span, data from multiple sensors have to be merged to create a single time series, and any uncorrected inter-sensor biases could introduce artefacts in the series, e.g., different sensors monitor radiances at different wavebands such that producing a consistent time series of reflectances is not straightforward. Another requirement is that the products have to be validated against in situ observations. Furthermore, the uncertainties in the products have to be quantified, ideally on a pixel-by-pixel basis, to facilitate applications and interpretations that are consistent with the quality of the data. This paper outlines an approach that was adopted for generating an ocean-colour time series for climate studies, using data from the MERIS (MEdium spectral Resolution Imaging Spectrometer) sensor of the European Space Agency; the SeaWiFS (Sea-viewing Wide-Field-of-view Sensor) and MODIS-Aqua (Moderate-resolution Imaging Spectroradiometer-Aqua) sensors from the National Aeronautics and Space Administration (USA); and VIIRS (Visible and Infrared Imaging Radiometer Suite) from the National Oceanic and Atmospheric Administration (USA). The time series now covers the period from late 1997 to end of 2018. To ensure that the products meet, as well as possible, the requirements of the user community, marine-ecosystem modellers, and remote-sensing scientists were consulted at the outset on their immediate and longer-term requirements as well as on their expectations of ocean-colour data for use in climate research. Taking the user requirements into account, a series of objective criteria were established, against which available algorithms for processing ocean-colour data were evaluated and ranked. The algorithms that performed best with respect to the climate user requirements were selected to process data from the satellite sensors. Remote-sensing reflectance data from MODIS-Aqua, MERIS, and VIIRS were band-shifted to match the wavebands of SeaWiFS. Overlapping data were used to correct for mean biases between sensors at every pixel. The remote-sensing reflectance data derived from the sensors were merged, and the selected in-water algorithm was applied to the merged data to generate maps of chlorophyll concentration, inherent optical properties at SeaWiFS wavelengths, and the diffuse attenuation coefficient at 490 nm. The merged products were validated against in situ observations. The uncertainties established on the basis of comparisons with in situ data were combined with an optical classification of the remote-sensing reflectance data using a fuzzy-logic approach, and were used to generate uncertainties (root mean square difference and bias) for each product at each pixel.

Description: This work was funded by the Ocean Colour Climate Change initiative of the European Space Agency (Grant Number 4000101437/10/I-LG). We acknowledge additional funding support by NERC through the National Centre for Earth Observation (Grant Number PR140015). Additional funding from a Simons Foundation Grant (549947, SS) is also gratefully acknowledged. V.B. also acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Programme grant agreement N_ 810139: Project Portugal Twinning for Innovation and Excellence in Marine Science and Earth Observation – PORTWIMS.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published invan der Hoop, J. M., Fahlman, A., Shorter, K. A., Gabaldon, J., Rocho-Levine, J., Petrov, V., & Moore, M. J. Swimming energy economy in bottlenose dolphins under variable drag loading. Frontiers in Marine Science, 5, (2018):465, doi:10.3389/fmars.2018.00465.

Description: Instrumenting animals with tags contributes additional resistive forces (weight, buoyancy, lift, and drag) that may result in increased energetic costs; however, additional metabolic expense can be moderated by adjusting behavior to maintain power output. We sought to increase hydrodynamic drag for near-surface swimming bottlenose dolphins, to investigate the metabolic effect of instrumentation. In this experiment, we investigate whether (1) metabolic rate increases systematically with hydrodynamic drag loading from tags of different sizes or (2) whether tagged individuals modulate speed, swimming distance, and/or fluking motions under increased drag loading. We detected no significant difference in oxygen consumption rates when four male dolphins performed a repeated swimming task, but measured swimming speeds that were 34% (〉1 m s-1) slower in the highest drag condition. To further investigate this observed response, we incrementally decreased and then increased drag in six loading conditions. When drag was reduced, dolphins increased swimming speed (+1.4 m s-1; +45%) and fluking frequency (+0.28 Hz; +16%). As drag was increased, swimming speed (-0.96 m s-1; -23%) and fluking frequency (-14 Hz; 7%) decreased again. Results from computational fluid dynamics simulations indicate that the experimentally observed changes in swimming speed would have maintained the level of external drag forces experienced by the animals. Together, these results indicate that dolphins may adjust swimming speed to modulate the drag force opposing their motion during swimming, adapting their behavior to maintain a level of energy economy during locomotion.

Description: Funding for this project was provided by the National Oceanographic Partnership Program (National Science Foundation via the Office of Naval Research N00014-11-1-0113 to MM) and the Office of Naval Research (ONR YIP Award N000141410563 to AF). Dolphin Quest provided in-kind support of animals, crew, and access to resources. JvdH was supported by a Postgraduate Scholarship from the Natural Sciences and Engineering Research Council of Canada.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Battefeld, A., Popovic, M. A., van der Werf, D., & Kole, M. H. P. (2019). A versatile and open-source rapid LED switching system for one-photon imaging and photo-activation. Frontiers in Cellular Neuroscience, 12, (2019): 530. doi:10.3389/fncel.2018.00530.

Description: Combining fluorescence and transmitted light sources for microscopy is an invaluable method in cellular neuroscience to probe the molecular and cellular mechanisms of cells. This approach enables the targeted recording from fluorescent reporter protein expressing neurons or glial cells in brain slices and fluorescence-assisted electrophysiological recordings from subcellular structures. However, the existing tools to mix multiple light sources in one-photon microscopy are limited. Here, we present the development of several microcontroller devices that provide temporal and intensity control of light emitting diodes (LEDs) for computer controlled microscopy illumination. We interfaced one microcontroller with μManager for rapid and dynamic overlay of transmitted and fluorescent images. Moreover, on the basis of this illumination system we implemented an electronic circuit to combine two pulsed LED light sources for fast (up to 1 kHz) ratiometric calcium (Ca2+) imaging. This microcontroller enabled the calibration of intracellular Ca2+ concentration and furthermore the combination of Ca2+ imaging with optogenetic activation. The devices are based on affordable components and open-source hardware and software. Integration into existing bright-field microscope systems will take ∼1 day. The microcontroller based LED imaging substantially advances conventional illumination methods by limiting light exposure and adding versatility and speed.

Description: This work was supported by grants to MK: European Research Council (FP7/2007-2013)/ERC grant agreement P261114, National Multiple Sclerosis Society grant (RG 4924A1/1) and a NWO-Vici grant 865.17.003. AB received a Grass Fellowship from the Grass Foundation.

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 596, doi:10.3389/fmicb.2015.00596.

Description: Mercury (Hg) is a toxic heavy metal that poses significant environmental and human health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. Here, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanisms at play. We show that the abundant and widespread sulfur-oxidizing bacteria of the genus Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus thioparus cultures led to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of thiosulfate, which served a dual role by enhancing HgS dissolution through Hg complexation and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. They also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment.

Description: This work was supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-0644491 awarded to AV.

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 901, doi:10.3389/fmicb.2015.00901.

Description: Many deep-sea hydrothermal vent systems are regularly impacted by volcanic eruptions, leaving fresh basalt where abundant animal and microbial communities once thrived. After an eruption, microbial biofilms are often the first visible evidence of biotic re-colonization. The present study is the first to investigate microbial colonization of newly exposed basalt surfaces in the context of vent fluid chemistry over an extended period of time (4–293 days) by deploying basalt blocks within an established diffuse-flow vent at the 9°50′ N vent field on the East Pacific Rise. Additionally, samples obtained after a recent eruption at the same vent field allowed for comparison between experimental results and those from natural microbial re-colonization. Over 9 months, the community changed from being composed almost exclusively of Epsilonproteobacteria to a more diverse assemblage, corresponding with a potential expansion of metabolic capabilities. The process of biofilm formation appears to generate similar surface-associated communities within and across sites by selecting for a subset of fluid-associated microbes, via species sorting. Furthermore, the high incidence of shared operational taxonomic units over time and across different vent sites suggests that the microbial communities colonizing new surfaces at diffuse-flow vent sites might follow a predictable successional pattern.

Description: This work was partly supported by grants from the US National Science Foundation to SS (OCE-0452333, 1136727), to TS (OCE-0117117, 0525907, 0961186, 1043064, 0327261, 1131620), to WS and KD (1434798), as well as a grant by the WHOI Deep Ocean Exploration Institute to SB, TS, and SS.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Chemistry 4 (2016): 5, doi:10.3389/fchem.2016.00005.

Description: Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H2O2) and superoxide (O−2) likely have significant effects on the cycling of trace metals and carbon in marine systems. In this study, extracellular production rates of H2O2 and O−2 were determined for five species of marine diatoms in the presence and absence of light. Production of both ROS was measured in parallel by suspending cells on filters and measuring the ROS downstream using chemiluminescence probes. In addition, the ability of these organisms to break down O−2 and H2O2 was examined by measuring recovery of O−2 and H2O2 added to the influent medium. O−2 production rates ranged from undetectable to 7.3 × 10−16 mol cell−1 h−1, while H2O2 production rates ranged from undetectable to 3.4 × 10−16 mol cell−1 h−1. Results suggest that extracellular ROS production occurs through a variety of pathways even amongst organisms of the same genus. Thalassiosira spp. produced more O−2 in light than dark, even when the organisms were killed, indicating that O−2 is produced via a passive photochemical process on the cell surface. The ratio of H2O2 to O−2 production rates was consistent with production of H2O2 solely through dismutation of O−2 for T. oceanica, while T. pseudonana made much more H2O2 than O−2. T. weissflogii only produced H2O2 when stressed or killed. P. tricornutum cells did not make cell-associated ROS, but did secrete H2O2-producing substances into the growth medium. In all organisms, recovery rates for killed cultures (94–100% H2O2; 10–80% O−2) were consistently higher than those for live cultures (65–95% H2O2; 10–50% O−2). While recovery rates for killed cultures in H2O2 indicate that nearly all H2O2 was degraded by active cell processes, O−2 decay appeared to occur via a combination of active and passive processes. Overall, this study shows that the rates and pathways for ROS production and decay vary greatly among diatom species, even between those that are closely related, and as a function of light conditions.

Description: This research was supported by NSF grant OCE-1131734/1246174 to BV and CH.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1318, doi:10.3389/fmicb.2016.01318.

Description: Characterizing the community structure of naturally occurring microbes through marker gene amplicons has gained widespread acceptance for profiling microbial populations. The 16S ribosomal RNA (rRNA) gene provides a suitable target for most studies since (1) it meets the criteria for robust markers of evolution, e.g., both conserved and rapidly evolving regions that do not undergo horizontal gene transfer, (2) microbial ecologists have identified widely adopted primers and protocols for generating amplicons for sequencing, (3) analyses of both cultivars and environmental DNA have generated well-curated databases for taxonomic profiling, and (4) bioinformaticians and computational biologists have published comprehensive software tools for interpreting the data and generating publication-ready figures. Since the initial descriptions of high-throughput sequencing of 16S rRNA gene amplicons to survey microbial diversity, we have witnessed an explosion of association-based inferences of interactions between microbes and their environment.

Description: AME was supported by the University of Chicago and the Marine Biological Laboratory collaboration award.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 1786, doi:10.3389/fmicb.2017.01786.

Description: Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.

Description: Financial support for this work was provided by the National Science Foundation Center for Microbial Oceanography: Research and Education (award #EF0424599 to DK and ED), the National Science Foundation HOT program (OCE-1260164 to M. J. Church and DK), the Gordon and Betty Moore Foundation (grants #492.01 and #3777 to ED, #3298 to DR, and #3794 to DK), and the Simons Foundation (award ID 329108 to DK, DR, and ED). Additional support was provided by the Agouron Institute through a fellowship to OS.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 13, doi:10.3389/fmars.2018.00013.

Description: Identifying putative mixotrophic protist species in the environment is important for understanding their behavior, with the recovery of these species in culture essential for determining the triggers of feeding, grazing rates, and overall impact on bacterial standing stocks. In this project, mixotroph abundances determined using tracer ingestion in water and sea ice samples collected in the Ross Sea, Antarctica during the summer of 2011 were compared with data from the spring (Ross Sea) and fall (Arctic) to examine the impacts of bacterivory/mixotrophy. Mixotrophic nanoplankton (MNAN) were usually less abundant than heterotrophs, but consumed more of the bacterial standing stock per day due to relatively higher ingestion rates (1–7 bacteria mixotroph−1 h−1 vs. 0.1–4 bacteria heterotroph−1 h−1). Yet, even with these high rates observed in the Antarctic summer, mixotrophs appeared to have a smaller contribution to bacterivory than in the Antarctic spring. Additionally, putative mixotroph taxa were identified through incubation experiments accomplished with bromodeoxyuridine-labeled bacteria as food, immunoprecipitation (IP) of labeled DNA, and amplification and high throughput sequencing of the eukaryotic ribosomal V9 region. Putative mixotroph OTUs were identified in the IP samples by taxonomic similarity to known phototroph taxa. OTUs that had increased abundance in IP samples compared to the non-IP samples from both surface and chlorophyll maximum (CM) depths were considered to represent active mixotrophy and include ones taxonomically similar to Dictyocha, Gymnodinium, Pentapharsodinium, and Symbiodinium. These OTUs represent target taxa for isolation and laboratory experiments on triggers for mixotrophy, to be combined with qPCR to estimate their abundance, seasonal distribution and potential impact.

Description: This work was supported by National Science Foundation Grants OPP-0838955 (RG) and OPP-0838847 (RS).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 61, doi:10.3389/fmars.2018.00061.

Description: The distribution of dissolved iron (Fe), total organic Fe-binding ligands, and siderophores were measured between the surface and 400 m at Station ALOHA, a long term ecological study site in the North Pacific Subtropical Gyre. Dissolved Fe concentrations were low throughout the water column and strong organic Fe-binding ligands exceeded dissolved Fe at all depths; varying from 0.9 nmol L−1 in the surface to 1.6 nmol L−1 below 150 m. Although Fe does not appear to limit microbial production, we nevertheless found siderophores at nearly all depths, indicating some populations of microbes were responding to Fe stress. Ferrioxamine siderophores were most abundant in the upper water column, with concentrations between 0.1 and 2 pmol L−1, while a suite of amphibactins were found below 200 m with concentrations between 0.8 and 11 pmol L−1. The distinct vertical distribution of ferrioxamines and amphibactins may indicate disparate strategies for acquiring Fe from dust in the upper water column and recycled organic matter in the lower water column. Amphibactins were found to have conditional stability constants (log KcondFeL1,Fe′) ranging from 12.0 to 12.5, while ferrioxamines had much stronger conditional stability constants ranging from 14.0 to 14.4, within the range of observed L1 ligands by voltammetry. We used our data to calculate equilibrium Fe speciation at Station ALOHA to compare the relative concentration of inorganic and siderophore complexed Fe. The results indicate that the concentration of Fe bound to siderophores was up to two orders of magnitude higher than inorganic Fe, suggesting that even if less bioavailable, siderophores were nevertheless a viable pathway for Fe acquisition by microbes at our study site. Finally, we observed rapid production of ferrioxamine E by particle-associated bacteria during incubation of freshly collected sinking organic matter. Fe-limitation may therefore be a factor in regulating carbon metabolism and nutrient regeneration in the mesopelagic.

Description: This work was funded by the Woods Hole Oceanographic Postdoctoral Fellowship for RaB, the Simons Foundation (Award 329108), and the National Science Foundation (OCE-1356747).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 170, doi:10.3389/fmars.2018.00170.

Description: Understanding the mechanisms of coral calcification is critical for accurately projecting coral reef futures under ocean acidification and warming. Recent suggestions that calcification is primarily controlled by organic molecules and the biological activity of the coral polyp imply that ocean acidification may not affect skeletal accretion. The basis for these suggestions relies heavily on correlating the presence of organic matter with the orientation and disorder of aragonite crystals in the skeleton, carrying the assumption that organic matter observed in the skeleton was produced by the polyp to control calcification. Here we use Raman spectroscopy to test whether there are differences in organic matter content between coral skeleton and abiogenic aragonites precipitated from seawater, both before and after thermal annealing (heating). We measured the background fluxorescence and intensity of C-H bonding signals in the Raman spectra, which are commonly attributed to coral polyp-derived skeletal organic matrix (SOM) and have been used to map its distribution. Surprisingly, we found no differences in either fluorescence or C-H bonding between abiogenic aragonite and coral skeleton. Annealing reduced the molecular disorder in coral skeleton, potentially due to removal of organic matter, but the same effect was also observed in the abiogenic aragonites. The presence of organic molecules in the abiogenic aragonites is further supported by measurements of N content and δ15N. Together, our data suggest that some of what has been interpreted in previous studies as polyp-derived SOM may actually be seawater-sourced organic matter or some other signal not unique to biogenic aragonite. Finally, we create a high-resolution Raman map of a Pocillopora skeleton to demonstrate how patterns of fluorescence and elevated calcifying fluid aragonite saturation state (ΩAr) along centers of calcification are consistent with both biological and physico-chemical controls. Our aim is to advance discussion on biological mediation of calcification and the implications for coral resilience in a high-CO2 world.

Description: This study was supported by an ARC Laureate Fellowship (FL120100049) awarded to Professor Malcolm McCulloch and the ARC Centre of Excellence for Coral Reef Studies (CE140100020).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Cellular Neuroscience 12 (2018): 156, doi:10.3389/fncel.2018.00156.

Description: Electrical synapses are ubiquitous in interneuron networks. They form intercellular pathways, allowing electrical currents to leak between coupled interneurons. I explored the impact of electrical coupling on the integration of excitatory signals and on the coincidence detection abilities of electrically-coupled cerebellar basket cells (BCs). In order to do so, I quantified the influence of electrical coupling on the rate, the probability and the latency at which BCs generate action potentials when stimulated. The long-lasting simultaneous suprathreshold depolarization of a coupled cell evoked an increase in firing rate and a shortening of action potential latency in a reference basket cell, compared to its depolarization alone. Likewise, the action potential probability of coupled cells was strongly increased when they were simultaneously stimulated with trains of short-duration near-threshold current pulses (mimicking the activation of presynaptic granule cells) at 10 Hz, and to a lesser extent at 50 Hz, an effect that was absent in non-coupled cells. Moreover, action potential probability was increased and action potential latency was shortened in response to synaptic stimulations in mice lacking the protein that forms gap junctions between BCs, connexin36, relative to wild-type (WT) controls. These results suggest that electrical synapses between BCs decrease the probability and increase the latency of stimulus-triggered action potentials, both effects being reverted upon simultaneous excitation of coupled cells. Interestingly, varying the delay at which coupled cells are stimulated revealed that the probability and the speed of action potential generation are facilitated maximally when a basket cell is stimulated shortly after a coupled cell. These findings suggest that electrically-coupled interneurons behave as coincidence and sequence detectors that dynamically regulate the latency and the strength of inhibition onto postsynaptic targets depending on the degree of input synchrony in the coupled interneuron network.

Description: This work was supported by the laboratory of Brain Physiology at Paris Descartes University (UMR8118), the Centre National de la Recherche Scientifique, the Agence Nationale de la Recherche Grant INterneuron NETwork (INNET), the Laboratory of Cellular and Systemic Neurophysiology, Institute for Physiology I at the University of Freiburg, and the Grass foundation.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 362, doi:10.3389/fmars.2018.00362.

Description: Major changes to Arctic marine ecosystems have resulted in longer growing seasons with increased phytoplankton production over larger areas. In the Chukchi Sea, the high productivity fuels intense benthic denitrification creating a nitrogen (N) deficit that is transported through the Arctic to the Atlantic Ocean, where it likely fuels N fixation. Given the rapid pace of environmental change and the potentially globally significant N deficit, we conducted experiments aimed at understanding phytoplankton and microbial N utilization in the Chukchi Sea. Ship-board experiments tested the effect of nitrate (NO3-) additions on both phytoplankton and heterotrophic prokaryote abundance, community composition, photophysiology, carbon fixation and NO3- uptake rates. Results support the critical role of NO3- in limiting summer phytoplankton communities to small cells with low production rates. NO3- additions increased particulate concentrations, abundance of large diatoms, and rates of carbon fixation and NO3- uptake by cells 〉1 μm. Increases in the quantum yield and electron turnover rate of photosystem II in +NO3- treatments suggested that phytoplankton in the ambient dissolved N environment were N starved and unable to build new, or repair damaged, reaction centers. While some increases in heterotrophic prokaryote abundance and production were noted with NO3- amendments, phytoplankton competition or grazers likely dampened these responses. Trends toward a warmer more stratified Chukchi Sea will likely enhance summer oligotrophic conditions and further N starve Chukchi Sea phytoplankton communities.

Description: Fieldwork and analysis for the ICESCAPE program was supported by Ocean Biology and Biogeochemistry Program of the National Aeronautic and Space Administration under Grant No. NNX10AF42G to KA.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Torres-Beltran, M., Mueller, A., Scofield, M., Pachiadaki, M. G., Taylor, C., Tyshchenko, K., Michiels, C., Lam, P., Ulloa, O., Jurgens, K., Hyun, J., Edgcomb, V. P., Crowe, S. A., & Hallam, S. J. Sampling and processing methods impact microbial community structure and potential activity in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Frontiers in Marine Science, 6,(2019):132, doi:10.3389/fmars.2019.00132.

Description: The Scientific Committee on Oceanographic Research (SCOR) Working Group 144 Microbial Community Responses to Ocean Deoxygenation workshop held in Vancouver, B.C on July 2014 had the primary objective of initiating a process to standardize operating procedures for compatible process rate and multi-omic (DNA, RNA, protein, and metabolite) data collection in marine oxygen minimum zones and other oxygen depleted waters. Workshop attendees participated in practical sampling and experimental activities in Saanich Inlet, British Columbia, a seasonally anoxic fjord. Experiments were designed to compare and cross-calibrate in situ versus bottle sampling methods to determine effects on microbial community structure and potential activity when using different filter combinations, filtration methods, and sample volumes. Resulting biomass was preserved for small subunit ribosomal RNA (SSU or 16S rRNA) and SSU rRNA gene (rDNA) amplicon sequencing followed by downstream statistical and visual analyses. Results from these analyses showed that significant community shifts occurred between in situ versus on ship processed samples. For example, Bacteroidetes, Alphaproteobacteria, and Opisthokonta associated with on-ship filtration onto 0.4 μm filters increased fivefold compared to on-ship in-line 0.22 μm filters or 0.4 μm filters processed and preserved in situ. In contrast, Planctomycetes associated with 0.4 μm in situ filters increased fivefold compared to on-ship filtration onto 0.4 μm filters and on-ship in-line 0.22 μm filters. In addition, candidate divisions and Chloroflexi were primarily recovered when filtered onto 0.4 μm filters in situ. Results based on rRNA:rDNA ratios for microbial indicator groups revealed previously unrecognized roles of candidate divisions, Desulfarculales, and Desulfuromandales in sulfur cycling, carbon fixation and fermentation within anoxic basin waters. Taken together, filter size and in situ versus on-ship filtration had the largest impact on recovery of microbial groups with the potential to influence downstream metabolic reconstruction and process rate measurements. These observations highlight the need for establishing standardized and reproducible techniques that facilitate cross-scale comparisons and more accurately assess in situ activities of microbial communities.

Description: This work was performed under the auspices of the Scientific Committee on Oceanographic Research (SCOR), the United States Department of Energy (DOE) Joint Genome Institute, an Office of Science User Facility, supported by the Office of Science of the United States Department of Energy under Contract DE-AC02- 05CH11231, the G. Unger Vetlesen and Ambrose Monell Foundations, the Tula Foundation-funded Centre for Microbial Diversity and Evolution, the Natural Sciences and Engineering Research Council of Canada, Genome British Columbia, the Canada Foundation for Innovation, and the Canadian Institute for Advanced Research through grants awarded to SH. McLane Research Laboratories and Connie Lovejoy contributed access to instrumentation for field work. Ship time support was provided by NSERC between 2007 and 2014 through grants awarded to SC, SH and Philippe Tortell MT-B was funded by Consejo Nacional de Ciencia y Tecnología (CONACyT) and the Tula Foundation.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 605, doi:10.3389/fmicb.2014.00605.

Description: Some of the most extreme marine habitats known are the Mediterranean deep hypersaline anoxic basins (DHABs; water depth ∼3500 m). Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB water-column haloclines and brines, the existence and activity of benthic DHAB protists have rarely been explored. Here, we report findings regarding protists and fungi recovered from sediments of three DHAB (Discovery, Urania, L’ Atalante) haloclines, and compare these to communities from sediments underlying normoxic waters of typical Mediterranean salinity. Halocline sediments, where the redoxcline impinges the seafloor, were studied from all three DHABs. Microscopic cell counts suggested that halocline sediments supported denser protist populations than those in adjacent control sediments. Pyrosequencing analysis based on ribosomal RNA detected eukaryotic ribotypes in the halocline sediments from each of the three DHABs, most of which were fungi. Sequences affiliated with Ustilaginomycotina Basidiomycota were the most abundant eukaryotic signatures detected. Benthic communities in these DHABs appeared to differ, as expected, due to differing brine chemistries. Microscopy indicated that only a low proportion of protists appeared to bear associated putative symbionts. In a considerable number of cases, when prokaryotes were associated with a protist, DAPI staining did not reveal presence of any nuclei, suggesting that at least some protists were carcasses inhabited by prokaryotic scavengers.

Description: K. Kormas was partially supported by the University of Thessaly through a sabbatical in 2013. Supported by NSF grants OCE-0849578 to Virginia P. Edgcomb and Joan M. Bernhard and OCE-1061391 to Joan M. Bernhard and Virginia P. Edgcomb.

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2015): 794, doi:10.3389/fmicb.2014.00794.

Description: Atmospheric deposition is a major source of trace metals in marine surface waters and supplies vital micronutrients to phytoplankton, yet measured aerosol trace metal solubility values are operationally defined, and there are relatively few multi-element studies on aerosol-metal solubility in seawater. Here we measure the solubility of aluminum (Al), cadmium (Cd), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) from natural aerosol samples in seawater over a 7 days period to (1) evaluate the role of extraction time in trace metal dissolution behavior and (2) explore how the individual dissolution patterns could influence biota. Dissolution behavior occurs over a continuum ranging from rapid dissolution, in which the majority of soluble metal dissolved immediately upon seawater exposure (Cd and Co in our samples), to gradual dissolution, where metals dissolved slowly over time (Zn, Mn, Cu, and Al in our samples). Additionally, dissolution affected by interactions with particles was observed in which a decline in soluble metal concentration over time occurred (Fe and Pb in our samples). Natural variability in aerosol chemistry between samples can cause metals to display different dissolution kinetics in different samples, and this was particularly evident for Ni, for which samples showed a broad range of dissolution rates. The elemental molar ratio of metals in the bulk aerosols was 23,189Fe: 22,651Al: 445Mn: 348Zn: 71Cu: 48Ni: 23Pb: 9Co: 1Cd, whereas the seawater soluble molar ratio after 7 days of leaching was 11Fe: 620Al: 205Mn: 240Zn: 20Cu: 14Ni: 9Pb: 2Co: 1Cd. The different kinetics and ratios of aerosol metal dissolution have implications for phytoplankton nutrition, and highlight the need for unified extraction protocols that simulate aerosol metal dissolution in the surface ocean.

Description: This work was supported by NSF-OCE grant 0850467 to Adina Paytan, NSF-OCE grant 1233261 to Mak A. Saito, and NATO Science for Peace Grant to Adina Paytan and Anton F. Post (SfP 982161). Katherine R. M. Mackey was supported by a National Science Foundation Postdoctoral Research Fellowship in Biology (Grant No. NSF 1103575) and Chia-Te Chien by an international graduate student fellowship from the ministry of education, Taiwan.

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 197, doi:10.3389/fmicb.2015.00197.

Description: Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw.

Description: This work was fostered by grants from WHOI's Arctic Research Initiative to MJLC and AS, as well as a Center for Dark Energy Biosphere Investigations (CDEBI) grant OCE-0939564 to WDO.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 59, doi:10.3389/fmicb.2016.00059.

Description: Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. However, deciphering the chemical drivers of these interspecies interactions remains challenging. Here, we report the isolation of 2-heptyl-4-quinolone (HHQ), released by Pseudoalteromonas piscicida, a marine gamma-proteobacteria previously reported to induce phytoplankton mortality through a hitherto unknown algicidal mechanism. HHQ functions as both an antibiotic and a bacterial signaling molecule in cell–cell communication in clinical infection models. Co-culture of the bloom-forming coccolithophore, Emiliania huxleyi with both live P. piscicida and cell-free filtrates caused a significant decrease in algal growth. Investigations of the P. piscicida exometabolome revealed HHQ, at nanomolar concentrations, induced mortality in three strains of E. huxleyi. Mortality of E. huxleyi in response to HHQ occurred slowly, implying static growth rather than a singular loss event (e.g., rapid cell lysis). In contrast, the marine chlorophyte, Dunaliella tertiolecta and diatom, Phaeodactylum tricornutum were unaffected by HHQ exposures. These results suggest that HHQ mediates the type of inter-domain interactions that cause shifts in phytoplankton population dynamics. These chemically mediated interactions, and other like it, ultimately influence large-scale oceanographic processes.

Description: This research was support through funding from the Gordon and Betty Moore Foundation through Grant GBMF3301 to MJ and TM; NIH grant from the National Institute of Allergy and Infectious Disease (NIAID – 1R21Al119311-01) to TM and KW; the National Science Foundation (OCE – 1313747) and US National Institute of Environmental Health Science (P01-ES021921) through the Oceans and Human Health Program to BM. Additional financial support was provided to TM from the Flatley Discovery Lab.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 702, doi:10.3389/fmicb.2017.00702.

Description: The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe2+. Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13C-incorporation in the dark allowed the classification of aiC15:0, C15:0, and iC16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism.

Description: SS was supported by NSF grant OCE-1124272. This work was financed through the DFG Emmy Noether Grant BU 2606/1-1 to SB.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 560, doi:10.3389/fmicb.2018.00560.

Description: The observation of significant concentrations of soluble Mn(III) complexes in oxic, suboxic, and some anoxic waters has triggered a re-evaluation of the previous Mn paradigm which focused on the cycling between soluble Mn(II) and insoluble Mn(III,IV) species as operationally defined by filtration. Though Mn(II) oxidation in aquatic environments is primarily bacterially-mediated, little is known about the effect of Mn(III)-binding ligands on Mn(II) oxidation nor on the formation and removal of Mn(III). Pseudomonas putida GB-1 is one of the most extensively investigated of all Mn(II) oxidizing bacteria, encoding genes for three Mn oxidases (McoA, MnxG, and MopA). P. putida GB-1 and associated Mn oxidase mutants were tested alongside environmental isolates Pseudomonas hunanensis GSL-007 and Pseudomonas sp. GSL-010 for their ability to both directly oxidize weakly and strongly bound Mn(III), and to form these complexes through the oxidation of Mn(II). Using Mn(III)-citrate (weak complex) and Mn(III)-DFOB (strong complex), it was observed that P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 and mutants expressing only MnxG and McoA were able to directly oxidize both species at varying levels; however, no oxidation was detected in cultures of a P. putida mutant expressing only MopA. During cultivation in the presence of Mn(II) and citrate or DFOB, P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 formed Mn(III) complexes transiently as an intermediate before forming Mn(III/IV) oxides with the overall rates and extents of Mn(III,IV) oxide formation being greater for Mn(III)-citrate than for Mn(III)-DFOB. These data highlight the role of bacteria in the oxidative portion of the Mn cycle and suggest that the oxidation of strong Mn(III) complexes can occur through enzymatic mechanisms involving multicopper oxidases. The results support the observations from field studies and further emphasize the complexity of the geochemical cycling of manganese.

Description: This work was funded by grants from the Chemical Oceanography program of the National Science Foundation (OCE-1558738 and OCE-1558692).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 9 (2018): 886, doi:10.3389/fphys.2018.00886.

Description: Diving mammals have evolved a suite of physiological adaptations to manage respiratory gases during extended breath-hold dives. To test the hypothesis that offshore bottlenose dolphins have evolved physiological adaptations to improve their ability for extended deep dives and as protection for lung barotrauma, we investigated the lung function and respiratory physiology of four wild common bottlenose dolphins (Tursiops truncatus) near the island of Bermuda. We measured blood hematocrit (Hct, %), resting metabolic rate (RMR, l O2 ⋅ min-1), tidal volume (VT, l), respiratory frequency (fR, breaths ⋅ min-1), respiratory flow (l ⋅ min-1), and dynamic lung compliance (CL, l ⋅ cmH2O-1) in air and in water, and compared measurements with published results from coastal, shallow-diving dolphins. We found that offshore dolphins had greater Hct (56 ± 2%) compared to shallow-diving bottlenose dolphins (range: 30–49%), thus resulting in a greater O2 storage capacity and longer aerobic diving duration. Contrary to our hypothesis, the specific CL (sCL, 0.30 ± 0.12 cmH2O-1) was not different between populations. Neither the mass-specific RMR (3.0 ± 1.7 ml O2 ⋅ min-1 ⋅ kg-1) nor VT (23.0 ± 3.7 ml ⋅ kg-1) were different from coastal ecotype bottlenose dolphins, both in the wild and under managed care, suggesting that deep-diving dolphins do not have metabolic or respiratory adaptations that differ from the shallow-diving ecotypes. The lack of respiratory adaptations for deep diving further support the recently developed hypothesis that gas management in cetaceans is not entirely passive but governed by alteration in the ventilation-perfusion matching, which allows for selective gas exchange to protect against diving related problems such as decompression sickness.

Description: Funding for this project was provided by the Office of Naval Research (ONR YIP Award No. N000141410563, and Dolphin Quest, Inc. FHJ was supported by the Office of Naval Research (Award No. N00014-1410410) and an AIAS-COFUND fellowship from Aarhus Institute of Advanced Studies under the FP7 program of the EU (Agreement No. 609033).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 273, doi:10.3389/fmars.2018.00273.

Description: Mixotrophic flagellates can comprise significant proportions of plankton biomass in marine ecosystems. Despite the growing recognition of the importance of this ecological strategy, and the identification of major environmental factors controlling phagotrophic behavior (light and nutrients), the physiological and molecular mechanisms underlying mixotrophic behavior are still unclear. In this study, we performed RNA-Seq transcriptomic analysis for two mixotrophic prasinophytes, Micromonas polaris and Pyramimonas tychotreta, under dissolved nutrient regimes that altered their ingestion of bacteria prey. Though the strains examined were polar isolates, both belong to genera with widespread distribution. Our aim was to characterize the transcriptomes of these two non-model phytoflagellates, identify transcripts consistent with phagotrophic activity and assess their differential expression in response to nutrient stress. De novo assembly of the transcriptomes yielded large numbers of novel coding transcripts with no known match within public databases. A summary of the transcripts by Gene Ontology terms showed many expected expression patterns, including genes involved in photosynthetic pathways and enzymes implicated in nutrient uptake pathways. Searches of KEGG databases identified several genes associated with intra-cellular digestive pathways actively transcribed in both prasinophytes. Differential expression analysis showed a larger response in P. tychotreta, where 23,373 genes were up-regulated and 1,752 were down-regulated in the low nutrient treatment when phagotrophy was enhanced. In contrast, in M. polaris, low nutrient treatments resulted in up-regulation of 314 transcripts while down-regulating 371. With respect to phagotrophic-related expression, 37 genes were co-expressed in both P. tychotreta and M. polaris, and although the response was less pronounced in M. polaris, it is consistent with differences in observed ingestion behavior. This study presents the first genomic data for Pyramimonas tychotreta, and also contributes to the limited available data for Micromonas polaris. Furthermore, it provides insight into the presence of genes associated with phagocytosis within the Prasinophyceae and contributes to the understanding of potential target genes required for the construction of a complete model of gene regulation of phagocytic behavior in algae.

Description: The Owlsnest Super-Computing Cluster at Temple University is funded by a National Science Foundation Grant CNS-09-58854. The CUNY HPCC is operated by the College of Staten Island and funded, in part, by grants from the City of New York, State of New York, CUNY Research Foundation, and National Science Foundation Grants CNS-0958379, CNS-0855217, and ACI 1126113. Support for this work was also supplied by National Science Foundation grants PLR-1341362 (RG), PLR-1603538 (RS), and PLR-1603833 (RG).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Environmental Science 6 (2018): 100, doi:10.3389/fenvs.2018.00100.

Description: Determining how microbial communities organize and function at the ecosystem level is essential to understanding and predicting how they will respond to environmental change. Mathematical models can be used to describe these communities, but properly representing all the biological interactions in extremely diverse natural microbial ecosystems in a mathematical model is challenging. We examine a complementary approach based on the maximum entropy production (MEP) principle, which proposes that systems with many degrees of freedom will likely organize to maximize the rate of free energy dissipation. In this study, we develop an MEP model to describe biogeochemistry observed in Siders Pond, a phosphate limited meromictic system located in Falmouth, MA that exhibits steep chemical gradients due to density-driven stratification that supports anaerobic photosynthesis as well as microbial communities that catalyze redox cycles involving O, N, S, Fe, and Mn. The MEP model uses a metabolic network to represent microbial redox reactions, where biomass allocation and reaction rates are determined by solving an optimization problem that maximizes entropy production over time, and a 1D vertical profile constrained by an advection-dispersion-reaction model. We introduce a new approach for modeling phototrophy and explicitly represent oxygenic photoautotrophs, photoheterotrophs and anoxygenic photoautotrophs. The metabolic network also includes reactions for aerobic organoheterotrophic bacteria, sulfate reducing bacteria, sulfide oxidizing bacteria and aerobic and anaerobic grazers. Model results were compared to observations of biogeochemical constituents collected over a 24 h period at 8 depths at a single 15 m deep station in Siders Pond. Maximizing entropy production over long (3 day) intervals produced results more similar to field observations than short (0.25 day) interval optimizations, which support the importance of temporal strategies for maximizing entropy production over time. Furthermore, we found that entropy production must be maximized locally instead of globally where energy potentials are degraded quickly by abiotic processes, such as light absorption by water. This combination of field observations and modeling results indicate that natural microbial systems can be modeled by using the maximum entropy production principle applied over time and space using many fewer parameters than conventional models.

Description: Primary funding for this project was from NSF GG grant EAR-1451356 to JV and JH, with additional support from Gordon and Betty Moore Foundation grant GBMF 3297. JV also received support from NSF Grants OCE-1637630 and OCE-1558710 and Simons Foundation grant 549941. The NSF Center for Dark Energy Biosphere Investigations (C-DEBI; OCE-0939564) also supported the participation of JH.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Earth Science 6 (2018): 88, doi:10.3389/feart.2018.00088.

Description: Shallow seamounts at ocean island hotspots and in other settings may record emergence histories in the form of submarine erosional terraces. Exposure histories are valuable for constraining paleo-elevations and sea levels in the absence of more traditional markers, such as drowned coral reefs. However, similar features can also be produced through primary volcanic processes, which complicate the use of terraced seamounts as an indicator of paleo-shorelines. In the western Galápagos Archipelago, we utilize newly collected bathymetry along with seafloor observations from human-occupied submersibles to document the location and depth of erosional terraces on seamounts near the islands of Santiago, Santa Cruz, Floreana, Isabela, and Fernandina. We directly observed erosional features on 22 seamounts with terraces. We use these observations and bathymetric analysis to develop a framework to identify terrace-like morphologic features and classify them as either erosional or volcanic in origin. From this framework we identify 79 erosional terraces on 30 seamounts that are presently found at depths of 30 to 300 m. Although intermittent subaerial connectivity between the islands has been hypothesized, the depths of these erosional terraces in the Santiago region are the first direct evidence of paleo-connectivity in the modern archipelago. Collectively, the terraces have non-randomly distributed depths. We suggest that peaks in the distribution of terrace depths likely represent long durations of exposure (i.e., sea-level still or lowstands). By comparing these peaks to those of subsidence adjusted sea-level curves, we identify the average subsidence rate that best reproduces the observed terrace distributions. These rates are 0.2–0.4 m/ka for this portion of the central Galápagos, since the formation of the seamounts, consistent with previous independent estimates. Using these subsidence rates and evidence for erosional terraces at depths up to 300 m, we conclude that all islands in the central archipelago have been intermittently connected starting between 435 and 900 ka. Individual island pairs have likely been repeatedly subaerially connected for short intervals since that time.

Description: This project was carried out with financial support from the NSF (OCE-1634685 to SS and OCE-1634952 to VW) and the Dalio Explore Fund.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Molecular Neuroscience 11 (2018): 427, doi:10.3389/fnmol.2018.00427.

Description: Electrical signaling is a cardinal feature of the nervous system and endows it with the capability of quickly reacting to changes in the environment. Although synaptic communication between nerve cells is perceived to be mainly chemically mediated, electrical synaptic interactions also occur. Two different strategies are responsible for electrical communication between neurons. One is the consequence of low resistance intercellular pathways, called “gap junctions”, for the spread of electrical currents between the interior of two cells. The second occurs in the absence of cell-to-cell contacts and is a consequence of the extracellular electrical fields generated by the electrical activity of neurons. Here, we place present notions about electrical transmission in a historical perspective and contrast the contributions of the two different forms of electrical communication to brain function.

Description: This research was supported by National Institutes of Health grants DC03186, DC011099, NS055726, NS085772 and NS0552827 to AP.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Benson, A., Brooks, C. M., Canonico, G., Duffy, E., Muller-Karger, F., Sosik, H. M., Miloslavich, P., & Klein, E.. Integrated observations and informatics improve understanding of changing marine ecosystems. Frontiers in Marine Science, 5, (2018):428, doi:10.3389/fmars.2018.00428.

Description: Marine ecosystems have numerous benefits for human societies around the world and many policy initiatives now seek to maintain the health of these ecosystems. To enable wise decisions, up to date and accurate information on marine species and the state of the environment they live in is required. Moreover, this information needs to be openly accessible to build indicators and conduct timely assessments that decision makers can use. The questions and problems being addressed demand global-scale investigations, transdisciplinary science, and mechanisms to integrate and distribute data that otherwise would appear to be disparate. Essential Ocean Variables (EOVs) and marine Essential Biodiversity Variables (EBVs), conceptualized by the Global Ocean Observing System (GOOS) and the Marine Biodiversity Observation Network (MBON), respectively, guide observation of the ocean. Additionally, significant progress has been made to coordinate efforts between existing programs, such as the GOOS, MBON, and Ocean Biogeographic Information System collaboration agreement. Globally and nationally relevant indicators and assessments require increased sharing of data and analytical methods, sustained long-term and large-scale observations, and resources to dedicated to these tasks. We propose a vision and key tenets as a guiding framework for building a global integrated system for understanding marine biological diversity and processes to address policy and resource management needs. This framework includes: using EOVs and EBVs and implementing the guiding principles of Findable, Accessible, Interoperable, Reusable (FAIR) data and action ecology. In doing so, we can encourage relevant, rapid, and integrative scientific advancement that can be implemented by decision makers to maintain marine ecosystem health.

Description: We thank T.Malone and A. Knap for the invitation to contribute our ideas to this topic. We also thank the two reviewers and editor for their comments, which strengthened our manuscript.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, M. D., Beaudoin, D. J., Frada, M. J., Brownlee, E. F., & Stoecker, D. K. High grazing rates on cryptophyte algae in Chesapeake Bay. Frontiers in Marine Science, 5, (2018): 241. doi:10.3389/fmars.2018.00241.

Description: Cryptophyte algae are globally distributed photosynthetic flagellates found in freshwater, estuarine, and neritic ecosystems. While cryptophytes can be highly abundant and are consumed by a wide variety of protistan predators, few studies have sought to quantify in situ grazing rates on their populations. Here we show that autumnal grazing rates on in situ communities of cryptophyte algae in Chesapeake Bay are high throughout the system, while growth rates, particularly in the lower bay, were low. Analysis of the genetic diversity of cryptophyte populations within dilution experiments suggests that microzooplankton may be selectively grazing the fastest-growing members of the population, which were generally Teleaulax spp. We also demonstrate that potential grazing rates of ciliates and dinoflagellates on fluorescently labeled (FL) Rhodomonas salina, Storeatula major, and Teleaulax amphioxeia can be high (up to 149 prey predator−1 d−1), and that a Gyrodinium sp. and Mesodinium rubrum could be selective grazers. Potential grazing was highest for heterotrophic dinoflagellates, but due to its abundance, M. rubrum also had a high overall impact. This study reveals that cryptophyte algae in Chesapeake Bay can experience extremely high grazing pressure from phagotrophic protists, and that this grazing likely shapes their community diversity.

Description: The authors thank the National Science Foundation (OCE 1031718 and 1436169) for providing support for this research.

Description: The Protocol on Environmental Protection of the Antarctic Treaty stipulates that the protection of the Antarctic environment and associated ecosystems be fundamentally considered in the planning and conducting of all activities in the Antarctic Treaty area. One of the key pollutants created by human activities in the Antarctic is noise, which is primarily caused by ship traffic (from tourism, fisheries, and research), but also by geophysical research (e.g., seismic surveys) and by research station support activities (including construction). Arguably, amongst the species most vulnerable to noise are marine mammals since they specialize in using sound for communication, navigation and foraging, and therefore have evolved the highest auditory sensitivity among marine organisms. Reported effects of noise on marine mammals in lower-latitude oceans include stress, behavioral changes such as avoidance, auditory masking, hearing threshold shifts, and—in extreme cases—death. Eight mysticete species, 10 odontocete species, and six pinniped species occur south of 60�S (i.e., in the Southern or Antarctic Ocean). For many of these, the Southern Ocean is a key area for foraging and reproduction. Yet, little is known about how these species are affected by noise. We review the current prevalence of anthropogenic noise and the distribution of marine mammals in the Southern Ocean, and the current research gaps that prevent us from accurately assessing noise impacts on Antarctic marine mammals. A questionnaire given to 29 international experts on marine mammals revealed a variety of research needs. Those that received the highest rankings were (1) improved data on abundance and distribution of Antarctic marine mammals, (2) hearing data for Antarctic marine mammals, in particular a mysticete audiogram, and (3) an assessment of the effectiveness of various noise mitigation options. The management need with the highest score was a refinement of noise exposure criteria. Environmental evaluations are a requirement before conducting activities in the Antarctic. Because of a lack of scientific data on impacts, requirements and noise thresholds often vary between countries that conduct these evaluations, leading to different standards across countries. Addressing the identified research needs will help to implement informed and reasonable thresholds for noise production in the Antarctic and help to protect the Antarctic environment.

Description: The heat imbalance is the fundamental driver for the atmospheric circulation. Therefore, it is crucially important to understand how it responds to global warming. In this study, the role of the ocean in reshaping the atmospheric meridional heat imbalance is explored based on observations and climate simulations. We found that ocean tends to strengthen the meridional heat imbalance over the mid-latitudes. This is primarily because of the uneven ocean heat uptake between the subtropical and subpolar oceans. Under global warming, the subtropical ocean absorbs relatively less heat as the water there is well stratified. In contrast, the subpolar ocean is the primary region where the ocean heat uptake takes place, because the subpolar ocean is dominated by upwelling, strong mixing, and overturning circulation. We propose that the enhanced meridional heat imbalance may potentially contribute to strengthening the water cycle, westerlies, jet stream, and mid-latitude storms.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Braun, C. D., Skomal, G. B., & Thorrold, S. R. (2018). Integrating archival tag data and a high-resolution oceanographic model to estimate basking shark (Cetorhinus maximus) movements in the western Atlantic. Frontiers in Marine Science, 5, (2018):25, doi:10.3389/fmars.2018.00025.

Description: Basking shark (Cetorhinus maximus) populations are considered “vulnerable” globally and “endangered” in the northeast Atlantic by the International Union for the Conservation of Nature (IUCN). Much of our knowledge of this species comes from surface observations in coastal waters, yet recent evidence suggests the majority of their lives may be spent in the deep ocean. Depth preferences of basking sharks have significantly limited movement studies that used pop-up satellite archival transmitting (PSAT) tags as conventional light-based geolocation is impossible for tagged animals that spend significant time below the photic zone. We tagged 57 basking sharks with PSAT tags in the NW Atlantic from 2004 to 2011. Many individuals spent several months at meso- and bathy-pelagic depths where accurate light-level geolocation was impossible during fall, winter and spring. We applied a newly-developed geolocation approach for the PSAT data by comparing three-dimensional depth-temperature profile data recorded by the tags to modeled in situ oceanographic data from the high-resolution HYbrid Coordinate Ocean Model (HYCOM). Observation-based likelihoods were leveraged within a state-space hidden Markov model (HMM). The combined tracks revealed that basking sharks moved from waters around Cape Cod, MA to as far as the SE coast of Brazil (20°S), a total distance of over 17,000 km. Moreover, 59% of tagged individuals with sufficient deployment durations (〉250 days) demonstrated seasonal fidelity to Cape Cod and the Gulf of Maine, with one individual returning to within 60 km of its tagging location 1 year later. Tagged sharks spent most of their time at epipelagic depths during summer months around Cape Cod and in the Gulf of Maine. During winter months, sharks spent extended periods at depths of at least 600 m while moving south to the Sargasso Sea, the Caribbean Sea, or the western tropical Atlantic. Our work demonstrates the utility of applying advances in oceanographic modeling to understanding habitat use of highly migratory, often meso- and bathy-pelagic, ocean megafauna. The large-scale movement patterns of tagged sharks highlight the need for international cooperation when designing and implementing conservation strategies to ensure that the species recovers from the historical effects of over-fishing throughout the North Atlantic Ocean.

Description: We thank B. Galuardi and C. H. Lam for contributing analysis code, and H. Dewar, U. Thygesen and I. Jonsen for valuable feedback on the manuscript. We gratefully acknowledge funding from the US National Science Foundation (OCE 0825148), the National Aeronautics and Space Administration (NNS06AA96G), the Massachusetts Environmental Trust, and the Federal Aid in Sport Fish Restoration Program. Computational support was provided by the AWS Cloud Credits for Research program. CB was funded by the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology, the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution, and the NASA Earth and Space Science Fellowship. Funding for the development of HYCOM has been provided by the National Ocean Partnership Program and the Office of Naval Research. Data assimilative products using HYCOM are funded by the U.S. Navy. Computer time for HYCOM was made available by the DoD High Performance Computing Modernization Program.

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in DeCarlo, T. M., Hen, H., & Farfan, G. A. (2018). The origin and role of organic matrix in coral calcification: Insights from comparing coral skeleton and abiogenic aragonite. Frontiers in Marine Science, 5, (2018): 170. doi:10.3389/fmars.2018.00170.

Description: Understanding the mechanisms of coral calcification is critical for accurately projecting coral reef futures under ocean acidification and warming. Recent suggestions that calcification is primarily controlled by organic molecules and the biological activity of the coral polyp imply that ocean acidification may not affect skeletal accretion. The basis for these suggestions relies heavily on correlating the presence of organic matter with the orientation and disorder of aragonite crystals in the skeleton, carrying the assumption that organic matter observed in the skeleton was produced by the polyp to control calcification. Here we use Raman spectroscopy to test whether there are differences in organic matter content between coral skeleton and abiogenic aragonites precipitated from seawater, both before and after thermal annealing (heating). We measured the background fluxorescence and intensity of C-H bonding signals in the Raman spectra, which are commonly attributed to coral polyp-derived skeletal organic matrix (SOM) and have been used to map its distribution. Surprisingly, we found no differences in either fluorescence or C-H bonding between abiogenic aragonite and coral skeleton. Annealing reduced the molecular disorder in coral skeleton, potentially due to removal of organic matter, but the same effect was also observed in the abiogenic aragonites. The presence of organic molecules in the abiogenic aragonites is further supported by measurements of N content and δ15N. Together, our data suggest that some of what has been interpreted in previous studies as polyp-derived SOM may actually be seawater-sourced organic matter or some other signal not unique to biogenic aragonite. Finally, we create a high-resolution Raman map of a Pocillopora skeleton to demonstrate how patterns of fluorescence and elevated calcifying fluid aragonite saturation state (ΩAr) along centers of calcification are consistent with both biological and physico-chemical controls. Our aim is to advance discussion on biological mediation of calcification and the implications for coral resilience in a high-CO2 world.

Description: This study was supported by an ARC Laureate Fellowship (FL120100049) awarded to Professor Malcolm McCulloch and the ARC Centre of Excellence for Coral Reef Studies (CE140100020).

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bundy, R. M., Boiteau, R. M., McLean, C., Turk-Kubo, K. A., Mcllvin, M. R., Saito, M. A., Van Mooy, B. A. S., & Repeta, D. J.. Distinct siderophores contribute to iron cycling in the mesopelagic at station ALOHA. Frontiers in Marine Science, 5, (2018): 61. doi:10.3389/fmars.2018.00061.

Description: The distribution of dissolved iron (Fe), total organic Fe-binding ligands, and siderophores were measured between the surface and 400 m at Station ALOHA, a long term ecological study site in the North Pacific Subtropical Gyre. Dissolved Fe concentrations were low throughout the water column and strong organic Fe-binding ligands exceeded dissolved Fe at all depths; varying from 0.9 nmol L−1 in the surface to 1.6 nmol L−1 below 150 m. Although Fe does not appear to limit microbial production, we nevertheless found siderophores at nearly all depths, indicating some populations of microbes were responding to Fe stress. Ferrioxamine siderophores were most abundant in the upper water column, with concentrations between 0.1 and 2 pmol L−1, while a suite of amphibactins were found below 200 m with concentrations between 0.8 and 11 pmol L−1. The distinct vertical distribution of ferrioxamines and amphibactins may indicate disparate strategies for acquiring Fe from dust in the upper water column and recycled organic matter in the lower water column. Amphibactins were found to have conditional stability constants (log KcondFeL1,Fe′) ranging from 12.0 to 12.5, while ferrioxamines had much stronger conditional stability constants ranging from 14.0 to 14.4, within the range of observed L1 ligands by voltammetry. We used our data to calculate equilibrium Fe speciation at Station ALOHA to compare the relative concentration of inorganic and siderophore complexed Fe. The results indicate that the concentration of Fe bound to siderophores was up to two orders of magnitude higher than inorganic Fe, suggesting that even if less bioavailable, siderophores were nevertheless a viable pathway for Fe acquisition by microbes at our study site. Finally, we observed rapid production of ferrioxamine E by particle-associated bacteria during incubation of freshly collected sinking organic matter. Fe-limitation may therefore be a factor in regulating carbon metabolism and nutrient regeneration in the mesopelagic.

Description: We thank Chief Scientists Tara Clemente and Sam Wilson for leading the SCOPE Diel cruises. We also thank the Captain and crew of the R/V Ka'imikai-O-Kanaloa, as well as Paul Henderson in the Woods Hole Oceanographic Nutrient Analytical Facility for nutrient analyses. This work was funded by the Woods Hole Oceanographic Postdoctoral Fellowship for RaB, the Simons Foundation (Award 329108), and the National Science Foundation (OCE-1356747). We also thank two reviewers for helpful comments on the manuscript.

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 358, doi:10.3389/fmicb.2015.00358.

Description: Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for 4 months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540 Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n = 2), Rhodanobacter (n = 5), Acidobacteria (n = 2), Sporolactobacillus (n = 2, novel nitrogen fixing taxon), Ktedonobacter (n = 1, second representative of the family Ktedonobacteraceae), Streptomyces (n = 3, novel polyketide synthase modules), and Burkholderia (n = 2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9 Mb, with relative abundances ranging from rare (〈0.0001%) to relatively abundant (〉0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.

Description: This research was supported by the French National Research Agency (Agence National de Recherche) project Metasoil (Projet ANR-08-GENM-025). TOD was funded by the Rhone-Alpes Région. LM was supported with a PhD fellowship from the Région Rhône-Alpes.

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 564, doi:10.3389/fmicb.2016.00564.

Description: Dental plaque is a bacterial biofilm composed of a characteristic set of organisms. Relatively little information from cultivation-independent, high-throughput analyses has been published on the temporal dynamics of the dental plaque microbiome. We used Minimum Entropy Decomposition, an information theory-based approach similar to oligotyping that provides single-nucleotide resolution, to analyze a previously published time series data set and investigate the dynamics of the plaque microbiome at various analytic and taxonomic levels. At both the genus and 97% Operational Taxonomic Unit (OTU) levels of resolution, the range of variation within each individual overlapped that of other individuals in the data set. When analyzed at the oligotype level, however, the overlap largely disappeared, showing that single-nucleotide resolution enables differentiation of individuals from one another without ambiguity. The overwhelming majority of the plaque community in all samples was made up of bacteria from a moderate number of plaque-typical genera, indicating that the overall community framework is shared among individuals. Each of these genera fluctuated in abundance around a stable mean that varied between individuals, with some genera having higher inter-individual variability than others. Thus, at the genus level, differences between individuals lay not in the identity of the major genera but in consistently differing proportions of these genera from mouth to mouth. However, at the oligotype level, we detected oligotype “fingerprints,” a highly individual-specific set of persistently abundant oligotypes fluctuating around a stable mean over time. For example, within the genus Corynebacterium, more than a dozen oligotypes were detectable in each individual, of which a different subset reached high abundance in any given person. This pattern suggests that each mouth contains a subtly different community of organisms. We also compared the Chinese plaque community characterized here to previously characterized Western plaque communities, as represented by analyses of data emerging from the Human Microbiome Project, and found no major differences between Chinese and Western supragingival plaque. In conclusion, we found the plaque microbiome to be highly individualized at the oligotype level and characterized by stability of community membership, with variability in the relative abundance of community members between individuals and over time.

Description: Our work was supported by National Institutes of Health (NIH) National Institute of Dental and Craniofacial Research Grant DE022586 (to GGB). Additional support was provided by Harvard University's Department of Organismic and Evolutionary Biology graduate program (to DRU).

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 75, doi:10.3389/fmicb.2016.00075.

Description: The hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region.

Description: AT acknowledges a W. Reynolds research leave from UNC, Guaymas-relevant support from the Center for Dark Energy Biosphere Investigations (C-DEBI) at the University of Southern California

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 163, doi:10.3389/fmicb.2016.00163.

Description: Some benthic foraminiferal species are reportedly capable of nitrate storage and denitrification, however, little is known about nitrate incorporation and subsequent utilization of nitrate within their cell. In this study, we investigated where and how much 15N or 34S were assimilated into foraminiferal cells or possible endobionts after incubation with isotopically labeled nitrate and sulfate in dysoxic or anoxic conditions. After 2 weeks of incubation, foraminiferal specimens were fixed and prepared for Transmission Electron Microscopy (TEM) and correlative nanometer-scale secondary ion mass spectrometry (NanoSIMS) analyses. TEM observations revealed that there were characteristic ultrastructural features typically near the cell periphery in the youngest two or three chambers of the foraminifera exposed to anoxic conditions. These structures, which are electron dense and ~200–500 nm in diameter and co-occurred with possible endobionts, were labeled with 15N originated from 15N-labeled nitrate under anoxia and were labeled with both 15N and 34S under dysoxia. The labeling with 15N was more apparent in specimens from the dysoxic incubation, suggesting higher foraminiferal activity or increased availability of the label during exposure to oxygen depletion than to anoxia. Our results suggest that the electron dense bodies in Ammonia sp. play a significant role in nitrate incorporation and/or subsequent nitrogen assimilation during exposure to dysoxic to anoxic conditions.

Description: This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (Young Scientists B No. 22740340 and Scientific Research C No. 24540504 to HN), an Invitation Fellowship for Research in Japan to JB by Japan Society for the Promotion of Science (JSPS), the Robert W. Morse Chair for Excellence in Oceanography at WHOI to JB, and The Investment in Science Fund at WHOI to JB.

Description: The sedimentary dynamics and geological evolution of the Naples canyons during the Late Quaternary have been studied based on sedimentological and seismo-stratigraphic data. Several factors, including the sedimentary environments, tectonic setting, and volcanic eruptions, have controlled the geological evolution of the coastal and marine areas of the Bay of Naples. The main data and methods include the sedimentological data analysis, the seismo-stratigraphic techniques applied in the geological interpretation of seismic profiles, and the integrated analysis of core data that were previously published. The formation of the Dohrn canyon is controlled by fluvial processes, active in correspondence with the palaeo-Schiazzano River system and by the main eruptive events involving the submarine portion of Naples Bay, including the Campanian Ignimbrite (CI; 39 ky B.P.) and the Neapolitan Yellow Tuff (NYT; 15 ky B.P.). The formation of the Magnaghi canyon is controlled by erosional processes on the continental slope of Procida Island, which was active during the last eruptive phases of the island (Solchiaro Formation; 18 ky B.P.), triggering high rates of volcaniclastic supply.

Description: Published

Description: 226

Description: 1T. Struttura della Terra

Description: JCR Journal

Description: The chemical composition of rainwater was studied in two highly-industrialised areas in Sicily (southern Italy), between June 2018 and July 2019. The study areas were characterised by large oil refining plants and other industrial hubs whose processes contribute to the release of large amounts of gaseous species that can affect the chemical composition of atmospheric deposition As in most of the Mediterranean area, rainwater acidity (ranging in the study area between 3.9 and 8.3) was buffered by the dissolution of abundant geogenic carbonate aerosol. In particular, calcium and magnesium cations showed the highest pH-neutralizing factor, with ~92% of the acidity brought by SO42- and NO3- neutralized by alkaline dust. The lowest pH values were observed in samples collected after abundant rain periods, characterised by a less significant dry deposition of alkaline materials. Electrical Conductivity (ranging between 7 µS cm-1 and 396 µS cm-1) was inversely correlated with the amount of rainfall measured in the two areas. Concentrations of major ionic species followed the sequence Cl- 〉 Na+ 〉 SO42- ≃ HCO3- 〉 ≃ Ca2+ 〉 NO3- 〉 Mg2+ 〉 K+ 〉 F-. High loads of Na+ and Cl- (with a calculated R2 = 0.99) reflected proximity to the sea. Calcium, potassium, and non-sea-salt magnesium had a prevalent crustal origin. Non-sea salt sulphate, nitrate, and fluoride can be attributed mainly to anthropogenic sources. Mt. Etna, during eruptive periods, may be also considered, on a regional scale, a significant source for fluoride, non-sea salt sulphate, and even chloride.

Description: Published

Description: 3898

Description: 6A. Geochimica per l'ambiente e geologia medica

Description: JCR Journal