Classification of Southern Ocean krill and icefish echoes using random forests

Acknowledgements The authors thank the crews, fishers, and scientists who conducted the various surveys from which data were obtained. This work was supported by the Government of South Georgia and South Sandwich Islands. Additional logistical support provided by The South Atlantic Environmental Research Institute, with thanks to Paul Brickle. PF receives funding from the MASTS pooling initiative (TheMarine Alliance for Science and Technology for Scotland), and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. SF is funded by the Natural Environment Research Council, and data were provided from the British Antarctic Survey Ecosystems Long-term Monitoring and Surveys programme as part of the BAS Polar Science for Planet Earth Programme. The authors also thank the anonymous referees for their helpful suggestions on an earlier version of this manuscript.Peer reviewedPostprin

Restricted regions of enhanced growth of Antarctic krill in the circumpolar Southern Ocean

Food webs in high-latitude oceans are dominated by relatively few species. Future ocean and sea-ice changes affecting the distribution of such species will impact the structure and functioning of whole ecosystems. Antarctic krill (Euphausia superba) is a key species in Southern Ocean food webs, but there is little understanding of the factors influencing its success throughout much of the ocean. The capacity of a habitat to maintain growth will be crucial and here we use an empirical relationship of growth rate to assess seasonal spatial variability. Over much of the ocean, potential for growth is limited, with three restricted oceanic regions where seasonal conditions permit high growth rates, and only a few areas around the Scotia Sea and Antarctic Peninsula suitable for growth of the largest krill (>60 mm). Our study demonstrates that projections of impacts of future change need to account for spatial and seasonal variability of key ecological processes within ocean ecosystems

The contribution of zooplankton faecal pellets to deep carbon transport in the Scotia Sea (Southern Ocean)

The northern Scotia Sea contains the largest seasonal uptake of atmospheric carbon dioxide yet measured in the Southern Ocean. This study examines one of the main routes by which this carbon fluxes to the deep ocean, through the production of faecal pellets (FPs) by the zooplankton community. Deep sediment traps were deployed in two sites with contrasting ocean productivity regimes (P3, naturally iron-fertilized and P2, iron-limited), within the same water mass. The magnitude and seasonal pattern of particulate organic carbon (POC) and FPs in the traps was markedly different between the two sites. Maximum fluxes at P3 (22.91 mg C m−2 d−1; 2534 × 10 FP m−2 d−1) were an order of magnitude higher than at P2 (4.01 mg C m−2 d−1; 915 × 10 FP m−2 d−1), with flux at P3 exhibiting a double seasonal peak, compared to a single flatter peak at P2. The maximum contribution of FP carbon to the total amount of POC was twice as high at P3 (91%) compared to P2 (40%). The dominant FP category at P3 varied between round, ovoidal, cylindrical and tabular over the course of the year while, at P2, ovoidal FPs were consistently dominant, always making up more than 60% of the FP assemblage. There was also a difference in the FP state between the two sites, with FPs being relatively intact at P3, while FPs were often fragmented with broken peritrophic membranes at P2. The exception was ovoidal FPs, which were relatively intact at both sites. Our observations suggest that there was community shift from an herbivorous to an omnivorous diet from spring through to autumn at P3 while detritivores had a higher relative importance over the year at P2. Furthermore, the flux was mainly a product of the vertically migrating zooplankton community at P3 while the FP flux was more likely to be generated by deeper-dwelling zooplankton feeding on recycled material at P2. The results demonstrate that the feeding behavior and vertical distribution of the zooplankton community plays a critical role in controlling the magnitude of carbon export to the deep ocean in this region

TB Fast Track patient cost data

A tabular dataset containing information provided by 99 HIV-positive individuals – men and women aged 18 or above who had a low CD4 count and were not yet on TB or HIV treatment - enrolled in the TB FastTrack trial, a cluster randomised trial to establish the direct and indirect costs of illness incurred at the patient/household level. Data was collected through patient interviews conducted at the health facility where they were receiving treatment in North West Limpopo and Gauteng provinces between June 2014 and March 2015. The dataset contains 450+ variables, including details on quantity of visits, time spent in seeking care, direct medical and non-medical costs incurred, and individual and estimated household income. Household income was established using 4 approaches: (1) self-reported (detail), (2) self-reported (brackets), (3) by matching through an asset index, and (4) national average income

Ocean processes at the Antarctic continental slope

The Antarctic continental shelves and slopes occupy relatively small areas, but, nevertheless, are important for global climate, biogeochemical cycling and ecosystem functioning. Processes of water mass transformation through sea ice formation/melting and ocean-atmosphere interaction are key to the formation of deep and bottom waters as well as determining the heat flux beneath ice shelves. Climate models, however, struggle to capture these physical processes and are unable to reproduce water mass properties of the region. Dynamics at the continental slope are key for correctly modelling climate, yet their small spatial scale presents challenges both for ocean modelling and for observational studies. Cross-slope exchange processes are also vital for the flux of nutrients such as iron from the continental shelf into the mixed layer of the Southern Ocean. An © 2014 The Authors

Assessing the potential of autonomous submarine gliders for ecosystem monitoring across multiple trophic levels (plankton to cetaceans) and pollutants in shallow shelf seas

A combination of scientific, economic, technological and policy drivers is behind a recent upsurge in the use of marine autonomous systems (and accompanying miniaturized sensors) for environmental mapping and monitoring. Increased spatial–temporal resolution and coverage of data, at reduced cost, is particularly vital for effective spatial management of highly dynamic and heterogeneous shelf environments. This proof-of-concept study involves integration of a novel combination of sensors onto buoyancy-driven submarine gliders, in order to assess their suitability for ecosystem monitoring in shelf waters at a variety of trophic levels. Two shallow-water Slocum gliders were equipped with CTD and fluorometer to measure physical properties and chlorophyll, respectively. One glider was also equipped with a single-frequency echosounder to collect information on zooplankton and fish distribution. The other glider carried a Passive Acoustic Monitoring system to detect and record cetacean vocalizations, and a passive sampler to detect chemical contaminants in the water column. The two gliders were deployed together off southwest UK in autumn 2013, and targeted a known tidal-mixing front west of the Isles of Scilly. The gliders’ mission took about 40 days, with each glider travelling distances of >1000 km and undertaking >2500 dives to depths of up to 100 m. Controlling glider flight and alignment of the two glider trajectories proved to be particularly challenging due to strong tidal flows. However, the gliders continued to collect data in poor weather when an accompanying research vessel was unable to operate. In addition, all glider sensors generated useful data, with particularly interesting initial results relating to subsurface chlorophyll maxima and numerous fish/cetacean detections within the water column. The broader implications of this study for marine ecosystem monitoring with submarine gliders are discussed

Dissolution dominating calcification process in polar pteropods close to the point of aragonite undersaturation

Thecosome pteropods are abundant upper-ocean zooplankton that build aragonite shells. Ocean acidification results in the lowering of aragonite saturation levels in the surface layers, and several incubation studies have shown that rates of calcification in these organisms decrease as a result. This study provides a weight-specific net calcification rate function for thecosome pteropods that includes both rates of dissolution and calcification over a range of plausible future aragonite saturation states (Omega_Ar). We measured gross dissolution in the pteropod Limacina helicina antarctica in the Scotia Sea (Southern Ocean) by incubating living specimens across a range of aragonite saturation states for a maximum of 14 days. Specimens started dissolving almost immediately upon exposure to undersaturated conditions (Omega_Ar,0.8), losing 1.4% of shell mass per day. The observed rate of gross dissolution was different from that predicted by rate law kinetics of aragonite dissolution, in being higher at Var levels slightly above 1 and lower at Omega_Ar levels of between 1 and 0.8. This indicates that shell mass is affected by even transitional levels of saturation, but there is, nevertheless, some partial means of protection for shells when in undersaturated conditions. A function for gross dissolution against Var derived from the present observations was compared to a function for gross calcification derived by a different study, and showed that dissolution became the dominating process even at Omega_Ar levels close to 1, with net shell growth ceasing at an Omega_Ar of 1.03. Gross dissolution increasingly dominated net change in shell mass as saturation levels decreased below 1. As well as influencing their viability, such dissolution of pteropod shells in the surface layers will result in slower sinking velocities and decreased carbon and carbonate fluxes to the deep ocean

Colour maps for fisheries acoustic echograms

Echograms are used to visualize fisheries acoustic data, but choice of colour map has a significant effect on appearance. Quantitative echograms should use colour maps, which are colourful (have a perceived variety and intensity of colours), sequential (have monotonic lightness), and perceptually uniform (have consistency of perceived colour contrast over their range). We measure whether colour maps are colourful (⁠Mˆ(3)>0⁠), sequential (⁠rs=±1⁠), and perceptually uniform (ρ = 1) using an approximately perceptually uniform colour space (CIELAB). Whilst all the fisheries acoustic colour maps tested are colourful, none is sequential or perceptually uniform. The widely used EK500 colour map is extremely colourful (⁠Mˆ(3)=186⁠), not sequential (⁠rs=0.06⁠), and has highly uneven perceptual contrast over its range (⁠ρ=0.26⁠). Of the fisheries acoustic colour maps tested, the Large Scale Survey System default colour map is least colourful (⁠Mˆ(3)=79⁠), but comes closest to being sequential (⁠rs=−0.94⁠), and perceptually uniform (⁠ρ=0.95⁠). Modern colour maps have been specifically designed for colour contrast consistency, accessibility for viewers with red-green colour-blindness, and legibility when printed in monochrome, and may be better suited to the presentation and interpretation of quantitative fisheries acoustic echograms

Zooplankton and micronekton respond to climate fluctuations in the Amundsen Sea polynya, Antarctica

The vertical migration of zooplankton and micronekton (hereafter 'zooplankton') has ramifications throughout the food web. Here, we present the first evidence that climate fluctuations affect the vertical migration of zooplankton in the Southern Ocean, based on multi-year acoustic backscatter data from one of the deep troughs in the Amundsen Sea, Antarctica. High net primary productivity (NPP) and the annual variation in seasonal ice cover make the Amundsen Sea coastal polynya an ideal site in which to examine how zooplankton behavior responds to climate fluctuations. Our observations show that the timing of the seasonal vertical migration and abundance of zooplankton in the seasonally varying sea ice is correlated with the Southern Annular Mode (SAM) and El Nino Southern Oscillation (ENSO). Zooplankton in this region migrate seasonally and overwinter at depth, returning to the surface in spring. During +SAM/La Nina periods, the at-depth overwintering period is shorter compared to -SAM/El Nino periods, and return to the surface layers starts earlier in the year. These differences may result from the higher sea ice cover and decreased NPP during +SAM/La Nina periods. This observation points to a new link between global climate fluctuations and the polar marine food web