Diatomées biodiversité mondiale : une évaluation utilisant une approche metabarcoding

Diatoms (Stramenopiles, Bacillariophyceae) are an ecologically important and one of the most diverse phytoplanktonic groups, with an estimated ~1,800 marine planktonic species. Although widely studied, their diversity and biogeographic distribution patterns are not well known. The advent of high-throughput DNA sequencing has revolutionized molecular biodiversity studies facilitating the understanding of biogeography, community assembly and ecological processes. The two major goals of this thesis are (1) to investigate global biodiversity patterns and structure of marine planktonic diatom communities across the world’s oceans, and (2) to understand the mechanisms and processes determining their community structure and assembly. This thesis also presents an initial attempt to discern the distribution of rare species in protist communities. The study was conducted using the metabarcoding data generated from the biological samples and associated environmental data collected during the Tara Oceans (2009-2013) global circumnavigation covering all major oceanic provinces. A total of ~12 million diatom V9-18S rDNA tags from 46 sampling stations, constituting 293 size fractionated samples represent the study material for the thesis. Using 63,371 unique diatom metabarcodes, this study presents an in-depth evaluation of global diatom distribution and diversity. The analyses study draw a number of revelations related to diatom biogeography, e.g. a new estimate of the total number of planktonic diatom species, a considerable unknown diversity, exceptionally high diversity in the open ocean, complex diversity patterns across oceanic provinces. The thesis then looks into the factors determining the beta-diversity patterns. The results suggest that diatoms represent biogeographically structured ecological communities regulated by both environmental heterogeneity and spatial processes. Nonetheless, the majority of the total variation in community composition remained unexplained by either the examined measured environmental factors or spatial distances, which warrants future analyses focusing on biological interactions, historical events, and other factors that are not considered. The thesis further outlines an approach to characterize significantly associated clusters of co-occurring ribotypes. Finally, a preliminary study of size-fractionated protistan communities reveals that the tail (of their rank-abundance distributions) appears to follow a power-law behavior in almost all protistan communities. This observation may indicate a potential universal mechanism which can explain the organization of marine planktonic communities. In general, this work has presented a global comprehensive perspective on diatom distribution and diversity in the world’s oceans. The thesis offers an overall framework for metabarcoding-based global diversity assessments which in turn can be employed to study distribution and diversity of other taxonomic lineages. Consequently, this work provides a reference point to explore how microbial communities will respond/change in response to environmental conditions.Les diatomées (Stramenopiles, Bacillariophyceae) jouent un rôle important sur le plan écologique et sont l'un des groupes phytoplanctoniques les plus divers, avec environ 1800 espèces planctoniques estimées. Bien que largement étudiées, leurs modèles de diversité et de distribution biogéographique ne sont pas bien connus. L'avènement du séquençage de l'ADN à haut débit a révolutionné les études de biodiversité moléculaire facilitant la compréhension de la biogéographie, de la structure des communautés et des processus écologiques. Les deux principaux objectifs de cette thèse sont (1) d'enquêter sur les modèles de la biodiversité mondiale et la structure des communautés de diatomées planctoniques à travers les océans du monde, et (2) de comprendre les mécanismes et processus déterminants la structure de la communauté. Cette thèse présente également une première tentative de discerner la répartition des espèces rares dans les communautés de protistes. L'étude a été réalisée en utilisant les données de metabarcoding générées à partir des échantillons biologiques et des données environnementales associées recueillies au cours de la campagne Tara Oceans (2009-2013), une circumnavigation globale couvrant toutes les principales provinces océaniques. Le matériel d’étude pour cette thèse est constitué d’un total de 12 millions de séquences de la sous unité V9 du 18S ribosomal (barcode), récoltées à partir de 46 stations soit 293 échantillons. Basée sur 63371 metabarcodes de diatomées uniques, cette étude présente une évaluation approfondie de la distribution mondiale des diatomées et de leur diversité. Les analyses révèlent des faits marquants liées à la biogéographie des diatomées, par exemple une nouvelle estimation du nombre total d'espèces de diatomées planctoniques, une diversité considérable inconnue, une diversité exceptionnellement élevée en haute mer, et des patrons de diversité complexes entre les provinces océaniques. La thèse examine ensuite les facteurs qui déterminent les modèles de bêta-diversité. Les résultats suggèrent que les diatomées sont des communautés structurées et réglementées par l'hétérogénéité de l'environnement et des processus spatiaux. Néanmoins, la majorité de la variation totale dans la composition de la communauté ne peut être expliquée ni par les facteurs environnementaux, ni par les distances spatiales, ce qui justifie les analyses futures se concentrant sur les interactions biologiques, les événements historiques, et d'autres facteurs qui ne sont pas considérés. La thèse décrit en outre une approche pour caractériser les clusters significativement associés de ribotypes concomitants. Enfin, une étude préliminaire de communautés de protistes fractionnées par taille révèle que la queue (de leurs distributions rang abondance) semble suivre un comportement en loi de puissance dans presque toutes les communautés de protistes. Cette observation peut indiquer un mécanisme universel potentiel qui peut expliquer l'organisation de communautés planctoniques marines. De façon générale, ce travail présent une perspective globale et complète de la distribution et de la diversité des diatomées dans les océans du monde. La thèse propose un cadre global pour l'évaluation de la diversité mondiale basée sur le metabarcoding, qui pourra être utilisé pour étudier la distribution et la diversité des autres lignées taxonomiques. Par conséquent, ce travail fournit un point de référence pour explorer comment les communautés microbiennes feront face à la variation des conditions environnementales

Plankton networks driving carbon export in the oligotrophic ocean

The biological carbon pump is the process by which CO 2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions

Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment

Tackling technology and social ties: the stressful implications of organizational videoconferencing on employees during COVID-19

The outbreak of the Coronavirus Disease (COVID-19) across the world in the first quarter of 2020 impelled organizations to drastically move their workforce to a remote working or a Work from Home (WFH) setup, where physical interaction was ceased indefinitely. Videoconferencing soon became the predominant mode of organizational communication. However, extensive use of videoconferencing led to repercussions among remote working employees such as technostress, both in terms of the stress experienced from the technology of videoconferencing as well as from the employees’ estranged relationships such as family, roommates, friends, and colleagues and managers. There has been a gap in the research on stress, strain, and coping from videoconferencing in an organizational context, especially among employees of different hierarchies, and its repercussions from a socio-relational perspective. With technostress as the theoretical framework, this study explored the techno and socio-relational stressors of videoconferencing, the strains incurred, and the coping measures adapted by employees to counter the stress from videoconferencing in Singapore. Through interviews with 30 fulltime WFH employees in Singapore across various industries, and 7 diary studies from the interviewees, and by using qualitative data analysis, the study examined how employees experience socio-relational stress more than technostress as they switched to videoconferencing during the pandemic and what coping strategies they employ to manage the strains they experienced. This study suggested a relook at the existing concepts of videoconferencing and technostress which are applicable to the incumbent working scenario and provided a perspective into employees’ changing relationship dynamics from remote videoconferencing, especially employees across different hierarchies.Master of Communication Studie

Minidiscus-Minutocellus-V9_data.xlsx

<b>Tara Oceans </b><b>V9-</b><b>18S rDNA metabarcodes</b><b> </b>-<b> </b>We used the global metabarcoding data set generated from the biological samples collected from 146 sampling locations during the <i>Tara</i> Oceans expedition. We extracted ribotypes that were assigned to <i>Minidiscus </i>and <i>Minutocellus </i>from the three depths - surface (SRF), deep chlorophyll maximum (DCM) and mesopelagic (MESO)- within the different size class filters (ranging from 0.8 - 2,000 µm, with the smallest fraction being 0.8 to 5 µm). The taxonomic assignations was done using PR2 reference database which has six reference sequences from <i>Minidiscus</i> <i>trioculatus</i>, 2 from <i>Minidiscus</i> sp., and one is environmental sequence. Relative abundance was calculated with respect to total diatom reads and to total phytosynthetic reads, which comprised reads assigned to major phytoplanktonic groups, namely Bacillariophyta, Chlorophyceae, Cryptophyta, Dictyochophyceae, Dinophyceae, Haptophyta, Mamiellophyceae, Pelagophyceae and Raphidophyceae. Exponentiated Shannon-Weiner H’ diversity index was used as the estimates of diversity at each station. All the analyses were conducted using open source R version 3.3.1.<p><br></p

Videoconferencing and work-family conflict: exploring the role of videoconference fatigue

Videoconferencing has become an essential communication tool for employees to engage in virtual meetings with their colleagues and complete work tasks remotely. However, there have been reports of a phenomenon termed videoconference fatigue. Concurrently, there has been an increase in work-family conflict among individuals working from home, due to an imbalance from role demands and expectations between work and family. With the rise of videoconferencing that has come to characterize work-from-home setups, it is important to explore the role videoconferencing plays on work-family conflict. We propose a model where the increase in use of videoconferencing as a result of working from home may lead to higher levels of videoconference fatigue, which will in turn result in greater work-family conflict. An online nationwide survey was conducted in Singapore with 590 respondents to test the proposed hypotheses. Results of serial mediation analyses conducted using PROCESS macro supported all hypotheses and indicated support for serial mediation. Emotional and occupational videoconference fatigue were further found to be significantly related to work-family conflict, whereas physical videoconference was not. Our results suggest that as videoconferencing continues to become the default mode of work-related communication, sustained investigation on its implications on work-family conflict is crucial.Nanyang Technological UniversityThis work was supported by the Centre for Information Integrity and the Internet (IN- Cube), Nanyang Technological University, Singapore

Clade-specific diversification dynamics of marine diatoms since the Jurassic

International audienceDiatoms are one of the most abundant and diverse groups of phytoplankton and play a major role in marine ecosystems and Earth's biogeochemical cycles. Here we combine DNA metabarcoding data from the Tara Oceans Expedition with palaeoenvironmental data and phylogenetic models of diversification to analyse the diversity dynamics of marine diatoms. We reveal a primary effect of pCO 2 variation on early diatom diversification, followed by a major burst of diversification in the late Eocene, after which diversification is chiefly affected by sea level, an influx of silica availability, and competition with other planktonic groups. Our results demonstrate a remarkable heterogeneity of diversification dynamics across diatoms and suggest that a changing climate will favor some clades at the expense of others

Ubiquitous abundance distribution of non-dominant plankton across the global ocean

International audienceMarine plankton populate 70% of Earth's surface, providing the energy that fuels ocean food webs and contributing to global biogeochemical cycles. Plankton communities are extremely diverse and geographically variable, and are overwhelmingly composed of low-abundance species. The role of this rare biosphere and its ecological underpinnings are however still unclear. Here, we analyse the extensive dataset generated by the Tara Oceans expedition for marine microbial eukaryotes (protists) and use an adaptive algorithm to explore how metabarcoding-based abundance distributions vary across plankton communities in the global ocean. We show that the decay in abundance of non-dominant operational taxonomic units, which comprise over 99% of local richness, is commonly governed by a power-law. Despite the high spatial turnover in species composition, the power-law exponent varies by less than 10% across locations and shows no biogeographical signature, but is weakly modulated by cell size. Such striking regularity suggests that the assembly of plankton communities in the dynamic and highly variable ocean environment is governed by large-scale ubiquitous processes. Understanding their origin and impact on plankton ecology will be important for evaluating the resilience of marine biodiversity in a changing ocean

Insights into global diatom distribution and diversity in the world's ocean

International audienceDiatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of similar to 12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered