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Aurelien Dommergue, Pierre Amato, Romie Tignat-Perrier, Olivier Magand, Alban Thollot, Muriel Joly, Laetitia Bouvier, Karine Sellegri, Timothy Vogel, Jeroen E. Sonke, Jean-Luc Jaffrezo, Marcos Andrade, Isabel Moreno, Casper Labuschagne, Lynwill Martin, Qianggong Zhang, Catherine Larose. (2019). Methods to Investigate the Global Atmospheric Microbiome (Vol. 10).
Abstract: The interplay between microbes and atmospheric physical and chemical conditions is an open field of research that can only be fully addressed using multidisciplinary approaches. The lack of coordinated efforts to gather data at representative temporal and spatial scales limits aerobiology to help understand large scale patterns of global microbial biodiversity and its causal relationships with the environmental context. This paper presents the sampling strategy and analytical protocols developed in order to integrate different fields of research such as microbiology, –omics biology, atmospheric chemistry, physics and meteorology to characterize atmospheric microbial life. These include control of chemical and microbial contaminations from sampling to analysis and identification of experimental procedures for characterizing airborne microbial biodiversity and its functioning from the atmospheric samples collected at remote sites from low cell density environments. We used high-volume sampling strategy to address both chemical and microbial composition of the atmosphere, because it can help overcome low aerosol and microbial cell concentrations. To account for contaminations, exposed and unexposed control filters were processed along with the samples. We present a method that allows for the extraction of chemical and biological data from the same quartz filters. We tested different sampling times, extraction kits and methods to optimize DNA yield from filters. Based on our results, we recommend supplementary sterilization steps to reduce filter contamination induced by handling and transport. These include manipulation under laminar flow hoods and UV sterilization. In terms of DNA extraction, we recommend a vortex step and a heating step to reduce binding to the quartz fibers of the filters. These steps have led to a 10-fold increase in DNA yield, allowing for downstream omics analysis of air samples. Based on our results, our method can be integrated into pre-existing long-term monitoring field protocols for the atmosphere both in terms of atmospheric chemistry and biology. We recommend using standardized air volumes and to develop standard operating protocols for field users to better control the operational quality.
Keywords: aerobiology Aerosols Atmosphere Biodiversity biogeography methods microorganisms Protocols
Programme: 1028
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Pearce, D.A., Alekhina, I.A., Terauds, A., Wilmotte, A., Quesada, A., Edwards, A., Dommergue, A., Sattler, B., Adams, B., Magalhães, C.M., Chu, W.-L., Lau, M., Cary, S.C., Smith, D.J., Wall, D.H., Eguren, G., Matcher, G., Bradley, J., De Vera, J.-P.P., Elster, J., Hughes, K.A., Benning, L.G., Gunde - Cimerman, N., Convey, P., Hong, S.G., Pointing, S.B., Pellizari, V.H., Vincent, W.F., 2016. . (2016). Aerobiology over Antarctica – a new initiative for atmospheric ecology. 1664-302X, 7.
Abstract: The role of aerial dispersal in shaping patterns of biodiversity remains poorly understood, mainly due to a lack of coordinated efforts in gathering data at appropriate temporal and spatial scales. It has been long known that the rate of dispersal to an ecosystem can significantly influence ecosystem dynamics, and that aerial transport has been identified as an important source of biological input to remote locations. With the considerable effort devoted in recent decades to understanding atmospheric circulation in the south polar region, a unique opportunity has emerged to investigate the atmospheric ecology of Antarctica, from local to continental scales. This concept note identifies key questions in Antarctic microbial biogeography and the need for standardized sampling and analysis protocols to address such questions. A consortium of polar aerobiologists is established to bring together researchers with a common interest in the airborne dispersion of microbes and other propagules in the Antarctic, with opportunities for comparative studies in the Arctic.
Programme: 1028
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Maccario Lorrie, Vogel Timothy, Larose Catherine, . (2014). Potential drivers of microbial community structure and function in Arctic snow
. Frontiers in Microbiology , 5 ( ).
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Loïc Le Ster, Hervé Claustre, Francesco d’Ovidio, David Nerini, Baptiste Picard, Christophe Guinet. (2023). Improved accuracy and spatial resolution for bio-logging-derived chlorophyll a fluorescence measurements in the Southern Ocean (Vol. 10).
Abstract: The ocean’s meso- and submeso-scales (1-100 km, days to weeks) host features like filaments and eddies that have a key structuring effect on phytoplankton distribution, but that due to their ephemeral nature, are challenging to observe. This problem is exacerbated in regions with heavy cloud coverage and/or difficult access like the Southern Ocean, where observations of phytoplankton distribution by satellite are sparse, manned campaigns costly, and automated devices limited by power consumption. Here, we address this issue by considering high-resolution in-situ data from 18 bio-logging devices deployed on southern elephant seals (Mirounga leonina) in the Kerguelen Islands between 2018 and 2020. These devices have submesoscale-resolving capabilities of light profiles due to the high spatio-temporal frequency of the animals’ dives (on average 1.1 +-0.6 km between consecutive dives, up to 60 dives per day), but observations of fluorescence are much coarser due to power constraints. Furthermore, the chlorophyll a concentrations derived from the (uncalibrated) bio-logging devices’ fluorescence sensors lack a common benchmark to properly qualify the data and allow comparisons of observations. By proposing a method based on functional data analysis, we show that a reliable predictor of chlorophyll a concentration can be constructed from light profiles (14 686 in our study). The combined use of light profiles and matchups with satellite ocean-color data enable effective (1) homogenization then calibration of the bio-logging devices’ fluorescence data and (2) filling of the spatial gaps in coarse-grained fluorescence sampling. The developed method improves the spatial resolution of the chlorophyll a field description from ~30 km to ~12 km. These results open the way to empirical study of the coupling between physical forcing and biological response at submesoscale in the Southern Ocean, especially useful in the context of upcoming high-resolution ocean-circulation satellite missions.
Keywords: bio-logging tag chla fluorescence Sensor calibration Southern elephant seal Southern Ocean Submesoscale
Programme: 1201
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Clive R. McMahon, Fabien Roquet, Sophie Baudel, Mathieu Belbeoch, Sophie Bestley, Clint Blight, Lars Boehme, Fiona Carse, Daniel P. Costa, Michael A. Fedak, Christophe Guinet, Robert Harcourt, Emma Heslop, Mark A. Hindell, Xavier Hoenner, Kim Holland, Mellinda Holland, Fabrice R. A. Jaine, Tiphaine Jeanniard du Dot, Ian Jonsen, Theresa R. Keates, Kit M. Kovacs, Sara Labrousse, Philip Lovell, Christian Lydersen, David March, Matthew Mazloff, Megan K. McKinzie, Mônica M. C. Muelbert, Kevin O’Brien, Lachlan Phillips, Esther Portela, Jonathan Pye, Stephen Rintoul, Katsufumi Sato, Ana M. M. Sequeira, Samantha E. Simmons, Vardis M. Tsontos, Victor Turpin, Esmee van Wijk, Danny Vo, Mia Wege, Frederick Gilbert Whoriskey, Kenady Wilson, Bill Woodward. (2021). Animal Borne Ocean Sensors – AniBOS – An Essential Component of the Global Ocean Observing System (Vol. 8).
Abstract: Marine animals equipped with biological and physical electronic sensors have produced long-term data streams on key marine environmental variables, hydrography, animal behavior and ecology. These data are an essential component of the Global Ocean Observing System (GOOS). The Animal Borne Ocean Sensors (AniBOS) network aims to coordinate the long-term collection and delivery of marine data streams, providing a complementary capability to other GOOS networks that monitor Essential Ocean Variables (EOVs), essential climate variables (ECVs) and essential biodiversity variables (EBVs). AniBOS augments observations of temperature and salinity within the upper ocean, in areas that are under-sampled, providing information that is urgently needed for an improved understanding of climate and ocean variability and for forecasting. Additionally, measurements of chlorophyll fluorescence and dissolved oxygen concentrations are emerging. The observations AniBOS provides are used widely across the research, modeling and operational oceanographic communities. High latitude, shallow coastal shelves and tropical seas have historically been sampled poorly with traditional observing platforms for many reasons including sea ice presence, limited satellite coverage and logistical costs. Animal-borne sensors are helping to fill that gap by collecting and transmitting in near real time an average of 500 temperature-salinity-depth profiles per animal annually and, when instruments are recovered (∼30% of instruments deployed annually, n = 103 ± 34), up to 1,000 profiles per month in these regions. Increased observations from under-sampled regions greatly improve the accuracy and confidence in estimates of ocean state and improve studies of climate variability by delivering data that refine climate prediction estimates at regional and global scales. The GOOS Observations Coordination Group (OCG) reviews, advises on and coordinates activities across the global ocean observing networks to strengthen the effective implementation of the system. AniBOS was formally recognized in 2020 as a GOOS network. This improves our ability to observe the ocean’s structure and animals that live in them more comprehensively, concomitantly improving our understanding of global ocean and climate processes for societal benefit consistent with the UN Sustainability Goals 13 and 14: Climate and Life below Water. Working within the GOOS OCG framework ensures that AniBOS is an essential component of an integrated Global Ocean Observing System.
Programme: 1201
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Rob Harcourt, Mark A. Hindell, Clive R. McMahon, Kimberly T. Goetz, Jean-Benoit Charrassin, Karine Heerah, Rachel Holser, Ian D. Jonsen, Michelle R. Shero, Xavier Hoenner, Rose Foster, Baukje Lenting, Esther Tarszisz, Matthew Harry Pinkerton. (2021). Regional Variation in Winter Foraging Strategies by Weddell Seals in Eastern Antarctica and the Ross Sea (Vol. 8).
Abstract: The relative importance of intrinsic and extrinsic determinants of animal foraging is often difficult to quantify. The most southerly breeding mammal, the Weddell seal, remains in the Antarctic pack-ice year-round. We compared Weddell seals tagged at three geographically and hydrographically distinct locations in East Antarctica (Prydz Bay, Terre Adélie, and the Ross Sea) to quantify the role of individual variability and habitat structure in winter foraging behaviour. Most Weddell seals remained in relatively small areas close to the coast throughout the winter, but some dispersed widely. Individual utilisation distributions (UDi, a measure of the total area used by an individual seal) ranged from 125 to 20,825 km2. This variability was not due to size or sex but may be due to other intrinsic states for example reproductive condition or personality. The type of foraging (benthic vs. pelagic) varied from 56.6 ± 14.9% benthic dives in Prydz Bay through 42.1 ± 9.4% Terre Adélie to only 25.1 ± 8.7% in the Ross Sea reflecting regional hydrographic structure. The probability of benthic diving was less likely the deeper the ocean. Ocean topography was also influential at the population level; seals from Terre Adélie, with its relatively narrow continental shelf, had a core (50%) UD of only 200 km2, considerably smaller than the Ross Sea (1650 km2) and Prydz Bay (1700 km2). Sea ice concentration had little influence on the time the seals spent in shallow coastal waters, but in deeper offshore water they used areas of higher ice concentration. Marine Protected Areas (MPAs) in the Ross Sea encompass all the observed Weddell seal habitat, and future MPAs that include the Antarctic continental shelf are likely to effectively protect key Weddell seal habitat.
Programme: 1182
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Angus F. Henderson, Clive R. McMahon, Rob Harcourt, Christophe Guinet, Baptiste Picard, Simon Wotherspoon, Mark A. Hindell. (2020). Inferring Variation in Southern Elephant Seal At-Sea Mortality by Modelling Tag Failure (Vol. 7).
Abstract: Identifying factors influencing survivorship is key to understanding population persistence. Although satellite telemetry is a powerful tool for studying remote animal ecology and behaviour it is rarely used for demographic studies because distinguishing the death of the animal (individual mortality) from failure of the tag (mechanical tag failure) has proven difficult. Southern elephant seals present an opportunity to separate tag failure from animal mortality thanks to the availability of large tracking datasets, broad knowledge of demographic rates, and because for these large animals, satellite tags are known not to influence mortality rates. A key rationale for investigating satellite telemetry to estimate mortality as compared to using traditional Capture-Mark-Recapture methods is the potential for obtaining spatially and temporally specific information, particularly while the animals are at sea and largely unobservable. We used satellite tag data from 182 seals from Isles Kerguelen, deployed between 2004 and 2018. Of these, 76 (42%) tags transmitted for the full post-moult foraging trip (max. 265 days for females and max. 305 days for sub-adult males) with the remaining 107 tags (58%) ceasing transmission at sea. We found that contrary to expectations, behavioural choices seem not to influence tag failure rates by mechanical means, rather the signals we detected seemed to align with previously described variation in mortality between groups. There was evidence, albeit limited, for an increase in tag failure for adult females in years with negative Southern Annular Mode (lower Southern Ocean productivity). We speculate that this increase in failure may suggest higher mortality in these years. Also, males using the Kerguelen Plateau had higher tag failure rates than those in the sea-ice zone, perhaps indicative of higher mortality. We suspect that these differences in tag failure rates between groups reflect variation in predator exposure and foraging success. This suggests satellite telemetry could be used to infer mortality events for southern elephant seals while they are at sea.
Programme: 1201
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Morgan Godard, Claude Manté, Christophe Guinet, Baptiste Picard, David Nerini. (2020). Diving Behavior of Mirounga leonina: A Functional Data Analysis Approach (Vol. 7).
Abstract: The diving behavior of southern elephant seals, Mirounga leonina, is investigated through the analysis of time-depth dive profiles. The originality of this work is to consider dive profiles as continuous curves. For this purpose, a Functional Data Analysis (FDA) approach is proposed for the shape analysis of a collection of dive profiles. Complexity of dive shapes is characterized by a mixture of three main shape variations accounting for about 80% of the entire variability: U or V shape, vertical depth variability during the bottom time, and skewed left or right. Model-based clustering allows the identification of eight dive shape clusters in a quick and automated way. Connection between shape patterns and classical descriptors, as well as the number of prey capture events, is achieved, showing that the clusters are coherent to specific foraging behaviors previously identified in the literature labeled as drift, exploratory and active dives. Finally, FDA is compared to classical methods relying on the computation of discrete dive descriptors. Results show that taking the shape of the dive as a whole is more resilient to corrupted or incomplete sampled data. FDA is, therefore, an efficient tool adapted for processing and comparing dive data with different sampling frequencies and for improving the quality and the accuracy of transmitted data.
Programme: 1201
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Sanne Muis, Maialen Irazoqui Apecechea, Job Dullaart, Joao de Lima Rego, Kristine Skovgaard Madsen, Jian Su, Kun Yan, Martin Verlaan. (2020). A High-Resolution Global Dataset of Extreme Sea Levels, Tides, and Storm Surges, Including Future Projections (Vol. 7).
Abstract: The world’s coastal areas are increasingly at risk of coastal flooding due to sea-level rise (SLR). We present a novel global dataset of extreme sea levels, the Coastal Dataset for the Evaluation of Climate Impact (CoDEC), which can be used to accurately map the impact of climate change on coastal regions around the world. The third generation Global Tide and Surge Model (GTSM), with a coastal resolution of 2.5 km (1.25 km in Europe), was used to simulate extreme sea levels for the ERA5 climate reanalysis from 1979 to 2017, as well as for future climate scenarios from 2040 to 2100. The validation against observed sea levels demonstrated a good performance, and the annual maxima had a mean bias (MB) of -0.04 m, which is 50% lower than the MB of the previous GTSR dataset. By the end of the century (2071–2100), it is projected that the 1 in 10-year water levels will have increased 0.34 m on average for RCP4.5, while some locations may experience increases of up to 0.5 m. The change in return levels is largely driven by SLR, although at some locations changes in storms surges and interaction with tides amplify the impact of SLR with changes up to 0.2 m. By presenting an application of the CoDEC dataset to the city of Copenhagen, we demonstrate how climate impact indicators derived from simulation can contribute to an understanding of climate impact on a local scale. Moreover, the CoDEC output locations are designed to be used as boundary conditions for regional models, and we envisage that they will be used for dynamic downscaling.
Programme: 688
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Lisa C. Matthes, C. J. Mundy, S. L.-Girard, M. Babin, G. Verin, J. K. Ehn. (2020). Spatial Heterogeneity as a Key Variable Influencing Spring-Summer Progression in UVR and PAR Transmission Through Arctic Sea Ice (Vol. 7).
Abstract: The transmission of ultraviolet (UVR) and photosynthetically available radiation (PAR) through sea ice is a key factor controlling under-ice phytoplankton growth in seasonally ice-covered waters. The increase toward sufficient light levels for positive net photosynthesis occurs concurrently with the sea ice melt progression in late spring when ice surface conditions shift from a relatively homogeneous high-albedo snow cover to a less reflective mosaic of bare ice and melt ponds. Here, we present a detailed dataset on the spatial and temporal progression of transmitted UVR and PAR in relation to changing quantities of snow, sea ice and melt ponds. Data were collected with a remotely operated vehicle (ROV) during the GreenEdge landfast sea ice campaign in June–July 2016 in southwestern Baffin Bay. Over the course of melt progression, there was a 10-fold increase in spatially averaged UVR and PAR transmission through the sea ice cover, reaching a maximum transmission of 31% for PAR, 7% for UVB, and 26% for UVA radiation. The depth under the sea ice experiencing spatial variability in light levels due to the influence of surface heterogeneity in snow, white ice and melt pond distributions increased from 7 ± 4 to 20 ± 6 m over our study. Phytoplankton drifting in under-ice surface waters were thus exposed to variations in PAR availability of up to 43%, highlighting the importance to account for spatial heterogeneity in light transmission through melting sea ice. Consequently, we demonstrate that spatial averages of PAR transmission provided more representative light availability estimates to explain under-ice bloom progression relative to single point irradiance measurements during the sea ice melt season. Encouragingly, the strong dichotomy between white ice and melt pond PAR transmittance and surface albedo permitted a very good estimate of spatially averaged light transmission from drone imagery of the surface and point transmittance measurements beneath different ice surface types.
Programme: 1164
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