Compositional data analysis as a potential tool to study the (paleo)ecology of calcareous nannoplankton from the central portuguese submarine canyons (W off Portugal)

Submarine canyons are deep and steep incisions on the continental margins. The physical forcing mechanisms linked with these marine systems, such as the enhancement of upwelling and bottom sediment resuspension, are expected to provide a nutrient source that will increase phytoplankton density (Hickey, 1995, Kampf,2006). Coccolithophores are the predominant phytoplanktonic group within the calcareous nannoplankton and their sensitivity to a variety of surface water environmental parameters makes them important markers of oceanographic processes and proxies of sea surface water masses and temperatures, productivity and past climate changes (e.g. Ziveri et al., 2004; Silva et al., 2008). In the present work we propose to test compositional analysis (Buccianti & Esposito, 2004; Pawlowsky-Glahn & Egozcue, 2006) as a tool to: a) achieve a clearer distinction between opportunistic coastal-neritic species (r-strategists) and typical oceanic species (k-strategists) in the central Portuguese margin, and b) to identify a coccolith assemblage that might reflect favorable environmental conditions found in the vicinity of the canyon that promotes the productivity of calcareous nannoplankton. Our main difficulty will be in distinguishing the ecological signal from the effects of other environmental factors mentioned before (i.e. advection, dissolution, bottom resuspension). One way to infer the species’ ecological inter-relationships is by determining species relative percentages. The main concern is how the closure problem and the inconsistency of percentage determinations will affect our results. Compositional analysis was designed to provide more reliable and thus representative results, since the inference made on the coccolith assemblage features from which the data are drawn is correctly performed from a theoretical point of view (Buccianti & Esposito, 2004). Here, we present the first insights from applying compositional data analysis to coccolith assemblages from 85 surface sediment samples collected from the central Portuguese margin

Seasonal carbon cycling in a Greenlandic fjord: an integrated pelagic and benthic study

Climate change is expected to have a pronounced effect on biogeochemical cycling in Arctic fjords, but current insight on the biogeochemical functioning of these systems is limited. Here, we present seasonal data on primary production, export of particulate organic carbon (POC), and the coupling to benthic biogeochemistry in Kobbefjord (SW Greenland). Primary production and associated POC export from the photic zone showed marked seasonality, with annual integrated values of 7.2 and 19.9 mol C m-2 yr-1, respectively. This discrepancy, the isotopic signature, and C:N ratio of the sedimentating material suggested substantial import of marine POC from outside the fjord. At least 52% of the POC export reached the sediment, but the seasonality in pelagic productivity was not reflected in the sediment biogeochemistry, showing only moderate variation. Benthic mineralization and burial of organic carbon amounted to 3.2 and 5.3 mol C m-2 yr-1, respectively. Sulfate reduction was the most prominent mineralization pathway, accounting for 69% of the benthic mineralization, while denitrification accounted for 2%. Overall, the carbon mineralization and burial in Kobbefjord were significantly higher than previously observed in other more northerly Arctic fjords. Data compilation from Arctic fjords suggests proportional increases in surface production, POC export, benthic mineralization and burial of organic material with increasing duration of the ice-free period. Thus, the projected decline in ice coverage in higher Arctic Greenlandic fjords will, as a first approximation, entail proportional increases in productivity, mineralization, and burial of organic carbon in the fjords, which will thus become similar to present-day southerly systems

Coccolithophore fluxes in the open tropical North Atlantic: influence of thermocline depth, Amazon water, and Saharan dust

Coccolithophores are calcifying phytoplankton and major contributors to both the organic and inorganic oceanic carbon pumps. Their export fluxes, species composition, and seasonal patterns were determined in two sediment trap moorings (M4 at 12 degrees N, 49 degrees W and M2 at 14 degrees N, 37 degrees W) collecting settling particles synchronously from October 2012 to November 2013 at 1200 m of water depth in the open equatorial North Atlantic. The two trap locations showed a similar seasonal pattern in total coccolith export fluxes and a predominantly tropical coccolithophore settling assemblage. Species fluxes were dominated throughout the year by lower photic zone (LPZ) taxa (Florisphaera profunda, Gladiolithus flabellatus) but also included upper photic zone (UPZ) taxa (Umbellosphaera spp., Rhabdosphaera spp., Umbilicosphaera spp., Helicosphaera spp.). The LPZ flora was most abundant during fall 2012, whereas the UPZ flora was more important during summer. In spite of these similarities, the western part of the study area produced persistently higher fluxes, averaging 241 x 10(7) +/- 76 x 10(7) coccoliths m(-2) d(-1) at station M4 compared to only 66 x 10(7) +/- 31 x 10(7) coccoliths m(-2) d(-1) at station M2. Higher fluxes at M4 were mainly produced by the LPZ species, favoured by the westward deepening of the thermocline and nutricline. Still, most UPZ species also contributed to higher fluxes, reflecting enhanced productivity in the western equatorial North Atlantic. Such was the case of two marked flux peaks of the more opportunistic species Gephyrocapsa muellerae and Emiliania huxleyi in January and April 2013 at M4, indicating a fast response to the nutrient enrichment of the UPZ, probably by wind-forced mixing. Later, increased fluxes of G. oceanica and E. huxleyi in October-November 2013 coincided with the occurrence of Amazon-River-affected surface waters. Since the spring and fall events of 2013 were also accompanied by two dust flux peaks, we propose a scenario in which atmospheric dust also provided fertilizing nutrients to this area. Enhanced surface buoyancy associated with the river plume indicates that the Amazon acted not only as a nutrient source, but also as a surface density retainer for nutrients supplied from the atmosphere. Nevertheless, lower total coccolith fluxes during these events compared to the maxima recorded in November 2012 and July 2013 indicate that transient productivity by opportunistic species was less important than "background" tropical productivity in the equatorial North Atlantic. This study illustrates how two apparently similar sites in the tropical open ocean actually differ greatly in ecological and oceanographic terms. The results presented here provide valuable insights into the processes governing the ecological dynamics and the downward export of coccolithophores in the tropical North Atlantic.Netherlands Organization for Scientific Research (NWO) [822.01.008]; European Research Council (ERC) [311152]; University of Bremen; European Union [600411]info:eu-repo/semantics/publishedVersio

Alterações recentes nas razões isotópicas de Pb em sedimentos do Canhão Submarino de Cascais, Portugal

Temporal variations in lead concentrations and stable lead isotopic ratios in two sediment cores from the Cascais Canyon shows changes in sources of Pb during the last two centuries. The increase of total Pb contents wIth the evolution of Pb ratio recorded in both cores reveals the Increase of Pb from industrial sources. Nevertheless, this increase is lower in deeper core location (252-32) due to dilution and mixing with uncontaminated marine materials. An isotopic shift towards lower Pb/Pb in the shallower core (252-35) during the 1970s may reflect the increasing number of vehicles in the Lisboa area during that time

Equation of state for polymer liquid crystals: theory and experiment

The first part of this paper develops a theory for the free energy of lyotropic polymer nematic liquid crystals. We use a continuum model with macroscopic elastic moduli for a polymer nematic phase. By evaluating the partition function, considering only harmonic fluctuations, we derive an expression for the free energy of the system. We find that the configurational entropic part of the free energy enhances the effective repulsive interactions between the chains. This configurational contribution goes as the fourth root of the direct interactions. Enhancement originates from the coupling between bending fluctuations and the compressibility of the nematic array normal to the average director. In the second part of the paper we use osmotic stress to measure the equation of state for DNA liquid crystals in 0.1M to 1M NaCl solutions. These measurements cover 5 orders of magnitude in DNA osmotic pressure. At high osmotic pressures the equation of state, dominated by exponentially decaying hydration repulsion, is independent of the ionic strength. At lower pressures the equation of state is dominated by fluctuation enhanced electrostatic double layer repulsion. The measured equation of state for DNA fits well with our theory for all salt concentrations. We are able to extract the strength of the direct electrostatic double layer repulsion. This is a new and alternative way of measuring effective charge densities along semiflexible polyelectrolytes.Comment: text + 5 figures. Submitted to PR

Qualitative Evaluation of Common Quantitative Metrics for Clinical Acceptance of Automatic Segmentation:a Case Study on Heart Contouring from CT Images by Deep Learning Algorithms

Organs-at-risk contouring is time consuming and labour intensive. Automation by deep learning algorithms would decrease the workload of radiotherapists and technicians considerably. However, the variety of metrics used for the evaluation of deep learning algorithms make the results of many papers difficult to interpret and compare. In this paper, a qualitative evaluation is done on five established metrics to assess whether their values correlate with clinical usability. A total of 377 CT volumes with heart delineations were randomly selected for training and evaluation. A deep learning algorithm was used to predict the contours of the heart. A total of 101 CT slices from the validation set with the predicted contours were shown to three experienced radiologists. They examined each slice independently whether they would accept or adjust the prediction and if there were (small) mistakes. For each slice, the scores of this qualitative evaluation were then compared with the Sørensen-Dice coefficient (DC), the Hausdorff distance (HD), pixel-wise accuracy, sensitivity and precision. The statistical analysis of the qualitative evaluation and metrics showed a significant correlation. Of the slices with a DC over 0.96 (N = 20) or a 95% HD under 5 voxels (N = 25), no slices were rejected by the readers. Contours with lower DC or higher HD were seen in both rejected and accepted contours. Qualitative evaluation shows that it is difficult to use common quantification metrics as indicator for use in clinic. We might need to change the reporting of quantitative metrics to better reflect clinical acceptance

The Whittard Canyon - A case study of submarine canyon processes

Submarine canyons are large geomorphological features that incise continental shelves and slopes around the world. They are often suggested to be biodiversity and biomass hotspots, although there is no consensus about this in the literature. Nevertheless, many canyons do host diverse faunal communities but owing to our lack of understanding of the processes shaping and driving this diversity, appropriate management strategies have yet to be developed. Here, we integrate all the current knowledge of one single system, the Whittard Canyon (Celtic Margin, NE Atlantic), including the latest research on its geology, sedimentology, geomorphology, oceanography, ecology, and biodiversity in order to address this issue. The Whittard Canyon is an active system in terms of sediment transport. The net suspended sediment transport is mainly up-canyon causing sedimentary overflow in some upper canyon areas. Occasionally sediment gravity flow events do occur, some possibly the result of anthropogenic activity. However, the role of these intermittent gravity flows in transferring labile organic matter to the deeper regions of the canyon appears to be limited. More likely, any labile organic matter flushed downslope in this way becomes strongly diluted with bulk material and is therefore of little food value for benthic fauna. Instead, the fresh organic matter found in the Whittard Channel mainly arrives through vertical deposition and lateral transport of phytoplankton blooms that occur in the area during spring and summer. The response of the Whittard Canyon fauna to these processes is different in different groups. Foraminiferal abundances are higher in the upper parts of the canyon and on the slope than in the lower canyon. Meiofaunal abundances in the upper and middle part of the canyon are higher than on adjacent slopes, but lower in the deepest part. Mega- and macrofauna abundances are higher in the canyon compared with the adjacent slope and are higher in the eastern than the western branch. These faunal patterns reflect the fact that the Whittard Canyon encompasses considerable environmental heterogeneity, related to a combination of organic matter trapping, current regimes (due to focused internal tides) and different substrates. We conclude that coordinated observations of processes driving faunal patterns are needed at a fine scale in order to understand the functioning of communities in this and other submarine canyons

Assessing plume impacts caused by polymetallic nodule mining vehicles

Deep-sea mining may be just a few years away and yet society is struggling to assess the positive aspects, such as increasing the supply of metals for battery production to fuel the green revolution, versus the potentially large environmental impacts. Mining of polymetallic (manganese) nodules from the deep ocean is likely to be the first mineral resource targeted and will involve direct impacts to hundreds of km2 of seabed per mine per year. However, the mining activity will also cause the generation of large sediment plumes that will spread away from the mine site and have both immediate and long-term effects over much wider areas. We discuss what the impacts of plumes generated near the seabed by mining vehicles may be and how they might be measured in such challenging environments. Several different mining vehicles are under development around the world and depending on their design some may create larger plumes than others. We discuss how these vehicles could be compared so that better engineering designs could be selected and to encourage innovation in dealing with plume generation and spread. These considerations will aid the International Seabed Authority (ISA) that has the task of regulating mining activities in much of the deep sea in its commitment to promote the Best Available Technology (BAT) and Best Environmental Practice (BEP)