Syndiniales are a parasitic order within the eukaryotic lineage Dinophyceae (Alveolata). Here, we analysed the taxonomy of this group using 43655 18S rRNA gene sequences obtained either from environmental data sets or cultures, including 6874 environmental sequences from this study derived from Atlantic and Mediterranean waters. A total of 5571 out of the 43655 sequences analysed fell within the Dinophyceae. Both bayesian and maximum likelihood phylogenies placed Syndiniales in five main groups (I-V), as a monophyletic lineage at the base of 'core' dinoflagellates (all Dinophyceae except Syndiniales), although the latter placement was not bootstrap supported. Thus, the two uncultured novel marine alveolate groups I and II, which have been highlighted previously, are confirmed to belong to the Syndiniales. These groups were the most diverse and highly represented in environmental studies. Within each, 8 and 44 clades were identified respectively. Co-evolutionary trends between parasitic Syndiniales and their putative hosts were not clear, suggesting they may be relatively 'general' parasitoids. Based on the overall distribution patterns of the Syndiniales-affiliated sequences, we propose that Syndiniales are exclusively marine. Interestingly, sequences belonging to groups II, III and V were largely retrieved from the photic zone, while Group I dominated samples from anoxic and suboxic ecosystems. Nevertheless, both groups I and II contained specific clades preferentially, or exclusively, retrieved from these latter ecosystems. Given the broad distribution of Syndiniales, our work indicates that parasitism may be a major force in ocean food webs, a force that is neglected in current conceptualizations of the marine carbon cycle.

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A central goal in ecology is to understand the factors affecting the temporal dynamics and spatial distribution of microorganisms and the underlying processes causing differences in community structure and composition. However, little is known in this respect for photosynthetic picoeukaryotes (PPEs), algae that are now recognised as major players in marine CO 2 fixation. Here, we analysed dot blot hybridisation and cloning-sequencing data, using the plastid-encoded 16S rRNA gene, from seven research cruises that encompassed all four ocean biomes. We provide insights into global abundance, a-and b-diversity distribution and the environmental factors shaping PPE community structure and composition. At the class level, the most commonly encountered PPEs were Prymnesiophyceae and Chrysophyceae. These taxa displayed complementary distribution patterns, with peak abundances of Prymnesiophyceae and Chrysophyceae in waters of high (25:1) or low (12:1) nitrogen:phosphorus (N:P) ratio, respectively. Significant differences in phylogenetic composition of PPEs were demonstrated for higher taxonomic levels between ocean basins, using Unifrac analyses of clone library sequence data. Differences in composition were generally greater between basins (interbasins) than within a basin (intrabasin). These differences were primarily linked to taxonomic variation in the composition of Prymnesiophyceae and Prasinophyceae whereas Chrysophyceae were phylogenetically similar in all libraries. These data provide better knowledge of PPE community structure across the world ocean and are crucial in assessing their evolution and contribution to CO 2 fixation, especially in the context of global climate change.

Varved lake sediments provide opportunities for high-resolution paleolimnological investigations that may extend monitoring surveys in order to target priority management actions under climate warming. This paper provides the synthesis of an international research program relying on >150 years-long, varved records for three managed perialpine lakes in Europe (Lakes Geneva, Annecy, and Bourget). The dynamics of the dominant, local human pressures, as well as the ecological responses in the pelagic, benthic, and littoral habitats were reconstructed using classical and newly developed paleo-proxies. Statistical modeling achieved the hierarchization of the drivers of their ecological trajectories. All three lakes underwent different levels of eutrophication in the first half of the XXth century, followed by re-oligotrophication. Climate warming came along with a 2 • C increase in air temperature over the last century, to which lakes were unequally thermally vulnerable. Unsurprisingly, phosphorous concentration has been the dominant ecological driver over the last century. Yet, other human-influenced, local environmental drivers (fisheries management practices, river regulations) have also significantly inflected ecological trajectories. Climate change has been impacting all habitats at rates that, in some cases, exceeded those of local factors. The amplitude and ecological responses to similar climate change varied between lakes, but, at least for pelagic habitats, rather depended on the intensity of local human pressures than on the thermal effect of climate change. Deep habitats yet showed higher sensitivity to climate change but substantial influence of river flows. As a consequence, adapted local management strategies, fully integrating nutrient inputs, fisheries management, and hydrological regulations, may enable mitigating the deleterious consequences of ongoing climate change on these ecosystems.

Photosynthetic picoeukaryotes (PPEs) of a size < 3 µm play a crucial role in oceanic primary production. However, little is known of the structure of the PPE community over large spatial scales. Here, we investigated the distribution of various PPE classes along an Atlantic Meridional Transect sampled in boreal autumn 2004 that encompasses a range of ocean provinces (gyres, upwelling, temperate regions), using dot blot hybridization technology targeting plastid 16S rRNA gene amplicons. Two algal classes, Prymnesiophyceae and Chrysophyceae, dominated the PPE community throughout the Atlantic Ocean, over a range of water masses presenting different trophic profiles. However, these classes showed strongly complementary distributions with Chrysophyceae dominating northern temperate waters, the southern gyre and equatorial regions, while prymnesiophytes dominated the northern gyre. Phylogenetic analyses using both plastid and nuclear rRNA genes revealed a high diversity among members of both classes, including sequences contained in lineages with no close cultured counterpart. Other PPE classes were less prevalent along the transect, with members of the Cryptophyceae, Pelagophyceae and Eustigmatophyceae essentially restricted to specific regions. Multivariate statistical analyses revealed strong relationships between the distribution patterns of some of these latter PPE classes and temperature, light intensity and nutrient concentrations. Cryptophyceae, for example, were mostly found in the upwelling region and associated with higher nutrient concentrations. However, the key classes of Prymnesiophyceae and Chrysophyceae were not strongly influenced by the variables measured. Although there appeared to be a positive relationship between Chrysophyceae distribution and light intensity, the complementary distributions of these classes could not be explained by the variables recorded and this requires further explanation.

1. Decennial changes in Planktothrix rubescens diversity and dynamics were reconstructed by applying molecular tools to analyse DNA and RNA extracted from lake sediments. The sediments studied were sampled from a deep peri-alpine lake that has experienced both dramatic shifts in trophic conditions and large-scale climatic changes. Palaeolimnological proxies were combined with statistical modelling to investigate the relative influence of phosphorus concentrations and temperature changes on the extent of Planktothrix blooms over the last century. 2. Phylogenetic analysis revealed that the overall composition of the cyanobacterial community changed over the transition from oligotrophic to eutrophic conditions. When the relative abundance of Planktothrix decreased in the 1970s, concomitant with eutrophication, total cyanobacterial abundance remained high and more Anabaena and Microcystis sequences were detected. In spite of such drastic environmental changes, the lake provided a constant niche for one particular Planktothrix species, which was consistently present from the 1920s to the present day. 3. Phosphorus concentration was found to be the dominant driver of the relative abundance of P. rubescens, with the highest abundances observed during mesotrophic conditions. The relative role of climate was nutrient-dependent, with warmer springs having a positive effect on P. rubescens abundance only during mesotrophic periods. 4. Overall, this study confirms that analysis of genetic signatures preserved in sediment archives allows assessment of key palaeoenvironmental indicator species that have no diagnostic microscopic cellular features in the sediment record. In the case of cyanobacteria, palaeogenetics offer unique opportunities to anticipate how future climate change might affect the response of P. rubescens to phosphorus concentration.

Diatoms contribute 20% of global primary production and form the basis of many marine food webs. Although their species diversity correlates with broad diversity in cell size, there is also an intraspecific cell-size plasticity owing to sexual reproduction and varying environmental conditions. However, despite the ecological significance of the diatom cell size for food-web structure and global biogeochemical cycles, our knowledge about genes underpinning the size of diatom cells remains elusive. Here, a combination of reverse genetics, experimental evolution and comparative RNA-sequencing analyses enabled us to identify a previously unknown genetic control of cell size in the diatom Thalassiosira pseudonana. In particular, the targeted deregulation of the expression of the cell-wall protein silacidin caused a significant increase in valve diameter. Remarkably, the natural downregulation of the silacidin gene transcript due to experimental evolution under low temperature also correlated with cell-size increase. Our data give first evidence for a genetically controlled regulation of cell size in T. pseudonana and possibly other centric diatoms as they also encode the silacidin gene in their genomes.

The application of genomic approaches to marine biota has profoundly altered our understanding of life in the oceans, especially regarding concepts of adaptation, speciation and evolution. The avalanche of genomic data has provided an unbiased view of marine biology that has never been seen before. In particular, comparative and metagenomic approaches with microbes from different biogeochemical marine provinces provided the first insights into how they acquire and discard genes as needed, even across kingdom boundaries, in response to their environment. These data clearly reveal that marine microbes have remarkable abilities to change their genomes according to both environmental stresses and biotic interactions. Thus, it is most likely that the flux of energy and matter in the marine system is reflected by the presence or absence of genes and proteins in marine organisms, which could provide novel tools to understand biogeochemical processes of global significance. However, the challenge is to put the reductionistic knowledge gained by genomics and metagenomics into the larger contexts of cellular systems and ecosystems to identify emergent properties that could not have been predicted by breaking down the whole into its individual parts