The Plankton Lifeform Extraction Tool: a digital tool to increase the discoverability and usability of plankton time-series data

Publication history: Accepted - 25 October 2021; Published online - 6 December 2021.Plankton form the base of the marine food web and are sensitive indicators of environmental change. Plankton time series are therefore an essential part of monitoring progress towards global biodiversity goals, such as the Convention on Biological Diversity Aichi Targets, and for informing ecosystem-based policy, such as the EU Marine Strategy Framework Directive. Multiple plankton monitoring programmes exist in Europe, but differences in sampling and analysis methods prevent the integration of their data, constraining their utility over large spatio-temporal scales. The Plankton Lifeform Extraction Tool brings together disparate European plankton datasets into a central database from which it extracts abundance time series of plankton functional groups, called “lifeforms”, according to shared biological traits. This tool has been designed to make complex plankton datasets accessible and meaningful for policy, public interest, and scientific discovery. It allows examination of large-scale shifts in lifeform abundance or distribution (for example, holoplankton being partially replaced by meroplankton), providing clues to how the marine environment is changing. The lifeform method enables datasets with different plankton sampling and taxonomic analysis methodologies to be used together to provide insights into the response to multiple stressors and robust policy evidence for decision making. Lifeform time series generated with the Plankton Lifeform Extraction Tool currently inform plankton and food web indicators for the UK's Marine Strategy, the EU's Marine Strategy Framework Directive, and for the Convention for the Protection of the Marine Environment of the North-East Atlantic (OSPAR) biodiversity assessments. The Plankton Lifeform Extraction Tool currently integrates 155 000 samples, containing over 44 million plankton records, from nine different plankton datasets within UK and European seas, collected between 1924 and 2017. Additional datasets can be added, and time series can be updated. The Plankton Lifeform Extraction Tool is hosted by The Archive for Marine Species and Habitats Data (DASSH) at https://www.dassh.ac.uk/lifeforms/ (last access: 22 November 2021, Ostle et al., 2021). The lifeform outputs are linked to specific, DOI-ed, versions of the Plankton Lifeform Traits Master List and each underlying dataset.Funding that supports this work and the data collected has come from the European Commission, European Union (EU) grant no. 11.0661/2015/712630/SUB/ENVC.2 OSPAR; UK Natural Environment Research Council (grant nos. NE/R002738/1 and NE/M007855/1); EMFF, Climate Linked Atlantic Sector Science (grant no. NE/R015953/1), Department for Environment, Food and Rural Affairs, UK Government (grant nos. ME-5308 and ME-414135), NSF USA OCE-1657887, DFO CA F5955150026/001/HAL, Natural Environment Research Council UK (grant no. NC-R8/H12/100); Horizon 2020 (MISSION ATLANTIC (grant no. 862428)); iCPR (grant no. SBFF-2019-36526), IMR Norway; DTU Aqua Denmark; and the French Ministry of Environment, Energy, and the Sea (MEEM). Recent funding for the development of PLET and the Pelagic Habitats Indicator has been provided by HBDSEG/Defra and MMO/EMFF. The MSS Scottish Coastal Observatory data and analyses are funded and maintained by the Scottish Government Schedules of Service (grant nos. ST05a and ST02H), MSS Stonehaven Samplers, North Atlantic Fisheries College, Shetland, Orkney Islands Harbour Council, and Isle Ewe Shellfish

Large-scale geographic variations in copepod diversity in relation to environmental variability

Dans le contexte actuel du changement climatique, les études sur l influence des paramètres environnementaux et de leurs impacts sur la diversité sont essentielles dans le but d appréhender les altérations de cette diversité marine par le changement global. Les observations répétées des distributions latitudinales de la diversité, principalement en milieu terrestre, suggèrent que des mécanismes communs pourraient être responsables de leur formation et de leur maintien. Bien que de nombreuses hypothèses aient été proposées pour expliquer les distributions de la diversité terrestre et marine, les mécanismes sous-jacents restent encore à élucider dans de nombreux cas, en particulier dans le milieu océanique. Les copépodes planctoniques, maillon clé du réseau trophique en milieu marin, jouent un rôle majeur dans les fonctionnements des cycles biochimiques. Notre étude se focalise sur la manière dont la diversité des copépodes est influencée par l environnement, première étape vers la compréhension de leur distribution, et leur réponse aux changements hydroclimatiques. Les résultats obtenus montrent que la distribution latitudinale de la diversité ne diminue pas de façon symétrique de l Equateur aux Pôles, mais un large plateau au niveau de l Hémisphère Sud et à l inverse, un pic dans les latitudes subtropicales de l Hémisphère Nord. Cette asymétrie de la diversité des copépodes est susceptible d être influencée par la disponibilité en énergie pour les organismes, elle-même régulée par les forçages climatiques actuels dans la région équatoriale, à savoir la Zone de Convergence Inter-Tropicale. Notre étude montre que la température océanique peut expliquer 54% de la variation de la diversité et qu une forte corrélation avec les distributions à grande échelle des copépodes existe. Afin d étudier les relations entre descripteurs environnementaux et la diversité des copépodes, des analyses multivariées ont été appliquées et ont révélé que les régions à fortes diversités sont fréquemment associées à de fortes températures, des salinités élevées et de faibles concentrations en chlorophylle a et en nutriments. Les paramètres environnementaux les plus fortement corrélés à la diversité ont permis de modéliser les distributions et ainsi de prévoir à l échelle globale la diversité des copépodes et de mettre en évidence les zones nécessitant un effort d échantillonnage plus soutenu. Alors que la force de la relation entre la diversité et la température a été démontrée, les liens sous-jacents entre l'énergie disponible et la diversité restent insaisissables. Par conséquent, la Théorie Métabolique en Ecologie (MTE) a été testée afin d expliquer les possibles mécanismes de distributions des copépodes à l échelle mondiale. Les pentes de régression dévient des valeurs prévues par la théorie et cette différence quantitative met l'accent sur la nécessité d'amélioration de la MTE pour expliquer les motifs de la diversité à grande échelle. Enfin, nous avons examiné la variation spatio-temporelle dans les relations diversité - température au sein de biomes pouvant présenter une vulnérabilité régionale causée par le réchauffement climatique. Nous avons montré que malgré la relation positive entre la diversité annuelle et les températures de surface de l océan, la variabilité spatiale est moins évidente. Cela peut s expliquer par le fait que les relations entre le climat et la diversité, évidentes à grandes échelles, peuvent disparaître à plus petite échelle, substituées par les forçages des processus biologiques, mais également par le bruit introduit par l'effort d'échantillonnage inégal. En conclusion, nos résultats ont montré que les influences majeures du climat et de la disponibilité en énergie sont susceptibles de jouer un rôle important sur les variations géographiques à grande échelle de la diversité des copépodes, et que le rôle de la température sur la diversité reste un phénomène omniprésent et complexe.PARIS-BIUSJ-Sci.Terre recherche (751052114) / SudocSudocFranceF

Global latitudinal variations in marine copepod diversity and environmental factors

International audienc

Towards a better understanding of the life organisation in the sea

International audienceAim Latitudinal gradients in diversity intrigue scientists, and various hypotheses have been proposed to explain why the diversity of so many taxonomic groups increases from the poles to the equator. These hypotheses range from null models to environmental factors, and biotic interactions to those that include patterns of dispersal and speciation. Here, we formulate a new theory based upon the concept of the niche sensu Hutchinson and the principle of competitive exclusion, which shows that the latitudinal diversity gradient in the marine environment may result from an interaction between the thermal tolerances of species and climatic variability. Location The global ocean. Methods We design a bioclimatic model that creates pseudospecies from strict stenotherms to large eurytherms and subsequently allows them to colonize a global ocean provided they can tolerate fluctuations in temperature. We test 74 ecologically realistic scenarios that are then correlated with observed patterns of species richness for foraminifers and copepods, two important oceanic planktonic groups. Results We found that the model accounted for 96% of the latitudinal gradient in foraminifers and 85% for copepods. Our model both reveals how patterns of biodiversity may develop, and suggests why some taxonomic groups appear not to follow the general pattern. While climate ultimately selected species that could establish in any given habitat, we saw a strong mid-domain effect (MDE) in the niche space. We believe this negates some shortcomings of the MDE that is often assumed to occur in the geographical space. Main conclusions By showing the strong effect of temperature on biodiversity and revealing how it enables the development of a planetary gradient in marine biodiversity, our results offer a way to better understand why temperature is so often positively correlated with global patterns in species richness on a global scale

A multivariate approach to large-scale variation in marine planktonic copepod diversity and its environmental correlates

We have investigated the relationships between covariations in environmental variables and variations in distributions of marine copepod diversity over an extensive latitudinal range from 86.5 degrees N to 46.5 degrees S. For this purpose, 7 data sets (representing 13,713 samples) of copepod species composition data and 11 environmental data sets were assembled. Principal components analysis was applied to investigate the relationships among the mean and seasonal variations in environmental descriptors (ocean temperature, chlorophyll a [ Chl a], net primary production, and other physical and chemical properties of the ocean) and their relationships with spatial variations in copepod diversity. High copepod diversity corresponded to a combination of high ocean temperature and salinity and low Chl a and nutrient concentrations (nitrate, silicate, phosphate). To a lesser extent, high-diversity regions were also correlated to low seasonal variability in oxygen, ocean temperature, and mixed-layer depth. Regression on principal components provided a robust prediction of global copepod diversity (R-2 = 0.45, p < 0.001) as our subset of environmental data was representative of the full range of environmental variability that occurs globally

Evaluating marine ecosystem health : case studies of indicators using direct observations and modelling methods

International audienceA major challenge in ocean and coastal management is to find simple ways to evaluate the health of such complex ecosystems. This task may prove complicated as selection criteria needs to be established for choosing appropriate indicators and evaluation tools which do not mask or leave out inherent ecosystem properties and dynamics. Here, we review some empirical analyses and modelling techniques which can be used to derive environmental health indicators. With a series of case studies ranging from the combined use of structural and functional attributes of the system, to modelling outputs that integrate the biological and physical environments, we illustrate the usefulness and complementarities of these methods to assess ecosystem health. The choice of relevant indicators will depend on the ecological questions raised as well as the biological and habitat components considered which can range from a single level (individual or population) to multiple levels (community or ecosystem-based indicators) in the ecosystem. Each method has its own capabilities and limitations that may render it useful or insufficient in some cases. We suggest, however, that, whenever possible, the combination of ecological attributes and tools should be used to improve our knowledge and assessment of marine ecosystems for better management and conservation in the future

Evaluation of different topologies of integrated capillaries in effective structural health monitoring system produced by 3D printing

Over the last years the structural health monitoring (SHM) systems investigations have been focused on providing structures with similar functionality as the biological nervous system. There are numerous studies that have investigated this. In those studies a large number of sensors collects an extensive amount of data. In this study we demonstrate a novel effective SHM (eSHM) system which can monitor a structure with one single pressure sensor. The eSHM system can detect cracks by means of a system of capillaries integrated in a structure. This structure with the integrated capillaries can be produced by 3D printing, also known as additive manufacturing (AM). The principle of the eSHM system is monitoring the pressure variations in a network of capillaries. The effectiveness of this system is linked with the greatest strength of AM, which is the capability to create complex geometrical structures. Before the implementation in real structures, it is of crucial importance to be sure that the capillaries do not negatively influence the fatigue behaviour of the structures and the crack initiation. For this, the main objective of this study is to investigate different locations for a straight capillary incorporated into a four-point bending test specimen. The investigated titanium specimens with the integrated eSHM system are produced by AM. The capillary is located in the longitudinal dimension of the test specimen on the tension area of a four-point bending setup. We evaluate three different distances of the capillary to the outer surface of the test specimens. Furthermore, the results are also obtained by finite element simulations. We can conclude that -for the considered structure-the presence of the capillary does not influence the fatigue life negatively. On the other hand, cracks nucleate in the capillary region. Our future work will focus on the improvement of the capillary's robustness. Other parameters like roughness effect and residual stresses should be also taken into account

Tuberculosis-associated IFN-I induces Siglec-1 on tunneling nanotubes and favors HIV-1 spread in macrophages

International audienceWhile tuberculosis (TB) is a risk factor in HIV-1-infected individuals, the mechanisms by which Mycobacterium tuberculosis (Mtb) worsens HIV-1 pathogenesis remain scarce. We showed that HIV-1 infection is exacerbated in macrophages exposed to TB-associated microenvironments due to tunneling nanotube (TNT) formation. To identify molecular factors associated with TNT function, we performed a transcriptomic analysis in these macrophages, and revealed the upregulation of Siglec-1 receptor. Siglec-1 expression depends on Mtb-induced production of type I interferon (IFN-I). In co-infected non-human primates, Siglec-1 is highly expressed by alveolar macrophages, whose abundance correlates with pathology and activation of IFN-I/STAT1 pathway. Siglec-1 localizes mainly on microtubule-containing TNT that are long and carry HIV-1 cargo. Sigle