Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are important contributors to global primary production occupying a key position at the base of marine food webs. The genetically diverse nature of each genus is likely an important reason for their successful colonization of vast tracts of the world's oceans, a feature that has led to detailed analysis of the distribution of these genetic lineages at the local and ocean basin scale. Here, we extend these analyses to the global dimension, using new data from cruises in the Pacific, Indian and Arctic Oceans in combination with data from previous studies in the Atlantic Ocean, Arabian Sea, Red Sea and a circumnavigation of the southern hemisphere to form a data set which comprises most of the world's major ocean systems. We show that the distribution patterns of Prochlorococcus and Synechococcus lineages are remarkably similar in different ocean systems with comparable environmental conditions, but producing a strikingly different 'signature' in the four major ocean domains or biomes (the Polar Domain, Coastal Boundary Domain, Trade Winds Domain and Westerly Winds Domain). This clearly reiterates the idea of spatial partitioning of individual cyanobacterial lineages, but at the global scale.

Global estimates indicate the oceans are responsible for approximately half of the carbon dioxide fixed on Earth. Organisms p5 lm in size dominate open ocean phytoplankton communities in terms of abundance and CO 2 fixation, with the cyanobacterial genera Prochlorococcus and Synechococcus numerically the most abundant and more extensively studied compared with small eukaryotes. However, the contribution of specific taxonomic groups to marine CO 2 fixation is still poorly known. In this study, we show that among the phytoplankton, small eukaryotes contribute significantly to CO 2 fixation (44%) because of their larger cell volume and thereby higher cell-specific CO 2 fixation rates. Within the eukaryotes, two groups, herein called Euk-A and Euk-B, were distinguished based on their flow cytometric signature. Euk-A, the most abundant group, contained cells 1.8±0.1 lm in size while Euk-B was the least abundant but cells were larger (2.8±0.2 lm). The Euk-B group comprising prymnesiophytes (73±13%) belonging largely to lineages with no close cultured counterparts accounted for up to 38% of the total primary production in the subtropical and tropical northeast Atlantic Ocean, suggesting a key role of this group in oceanic CO 2 fixation.

BackgroundPhotosynthetic picoeukaryotes (PPE) with a cell size less than 3 µm play a critical role in oceanic primary production. In recent years, the composition of marine picoeukaryote communities has been intensively investigated by molecular approaches, but their photosynthetic fraction remains poorly characterized. This is largely because the classical approach that relies on constructing 18S rRNA gene clone libraries from filtered seawater samples using universal eukaryotic primers is heavily biased toward heterotrophs, especially alveolates and stramenopiles, despite the fact that autotrophic cells in general outnumber heterotrophic ones in the euphotic zone.Methodology/Principal FindingsIn order to better assess the composition of the eukaryotic picophytoplankton in the South East Pacific Ocean, encompassing the most oligotrophic oceanic regions on earth, we used a novel approach based on flow cytometry sorting followed by construction of 18S rRNA gene clone libraries. This strategy dramatically increased the recovery of sequences from putative autotrophic groups. The composition of the PPE community appeared highly variable both vertically down the water column and horizontally across the South East Pacific Ocean. In the central gyre, uncultivated lineages dominated: a recently discovered clade of Prasinophyceae (IX), clades of marine Chrysophyceae and Haptophyta, the latter division containing a potentially new class besides Prymnesiophyceae and Pavlophyceae. In contrast, on the edge of the gyre and in the coastal Chilean upwelling, groups with cultivated representatives (Prasinophyceae clade VII and Mamiellales) dominated.Conclusions/SignificanceOur data demonstrate that a very large fraction of the eukaryotic picophytoplankton still escapes cultivation. The use of flow cytometry sorting should prove very useful to better characterize specific plankton populations by molecular approaches such as gene cloning or metagenomics, and also to obtain into culture strains representative of these novel groups.

Small eukaryotes have key roles in aquatic ecosystems, influencing their local environment, global biogeochemical cycles and climate. Their impact depends on community structure, which varies along time. However, very few studies take into account temporal variation. This is especially true for small, shallow freshwater systems, which remain largely understudied despite their wide variety, global surface and intense microbial activity. We have monthly followed changes in the community structure of small microbial eukaryotes (0.2-5 μm cell diameter) for 2 years in four ponds and one brook located in North-Western France based on massive 18S rDNA amplicon 454 pyrosequencing. We detected a total of 3742 stringently defined operational taxonomic units (OTUs) encompassing all recognized eukaryotic supergroups and lineages of uncertain affiliation. Although geographically close, protist communities in the five ecosystems were contrasting, with very few shared OTUs, suggesting that environmental selection mainly drives community structure. The temporal dynamics of different high-rank taxa appeared complex and rapid at monthly scales. Despite this, a clear and reproducible seasonality was observed. As expected, low-abundance OTUs dominated the community. Although some of them appeared sporadically or remained at low frequencies during the survey, others occasionally reached relatively high abundances, sometimes recurrently. This shows that at least a fraction of low-abundance eukaryotes constitutes a seed bank. The annual proportion of primary producers, free-living heterotrophs and parasites appeared remarkably constant among the different ecosystems, suggesting underlying trends of ecosystem carrying capacity for these functional groups.

The structure and dynamics of small eukaryotes (cells with a diameter less than 5 m) were studied over two consecutive years in an oligomesotrophic lake (Lake Pavin in France). Water samples were collected at 5 and 30 m below the surface; when the lake was stratified, these depths corresponded to the epilimnion and hypolimnion. Changes in small-eukaryote structure were analyzed using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of the 18S rRNA genes. Terminal restriction fragments from clones were used to reveal the dominant taxa in T-RFLP profiles of the environmental samples. Spumellalike cells (Chrysophyceae) did not dominate the small eukaryote community identified by molecular techniques in lacustrine ecosystems. Small eukaryotes appeared to be dominated by heterotrophic cells, particularly Cercozoa, which represented nearly half of the identified phylotypes, followed by the Fungi-LKM11 group (25%), choanoflagellates (10.3%) and Chrysophyceae (8.9%). Bicosoecida, Cryptophyta, and ciliates represented less than 9% of the community studied. No seasonal reproducibility in temporal evolution of the small-eukaryote community was observed from 1 year to the next. The T-RFLP patterns were related to bottom-up (resources) and top-down (grazing) variables using canonical correspondence analysis. The results showed a strong top-down regulation of small eukaryotes by zooplankton, more exactly, by cladocerans at 5 m and copepods at 30 m. Among bottom-up factors, temperature had a significant effect at both depths. The concentrations of nitrogenous nutrients and total phosphorus also had an effect on small-eukaryote dynamics at 5 m, whereas bacterial abundance and dissolved oxygen played a more important structuring role in the deeper zone.Small phototrophic and heterotrophic eukaryotes (Ͻ5 m) are found throughout the world's oceans and lakes at concentrations between 10 2 and 10 4 cells ml Ϫ1 in the photic zone (11). Small eukaryotes are known to be essential components in marine trophic food webs (20). The small-eukaryote assemblage is formed by picoalgae, which participate in primary production (55), by colorless heterotrophic cells, mostly flagellates, which are considered to be important grazers of prokaryotic and eukaryotic cells (11) and also play a significant role in the mineralization of organic matter, and finally by some small eukaryotes which can be mixotrophs. Despite the ecological importance of small eukaryotes and the general lack of distinct morphological features of these small cells, they have only recently been studied from a molecular perspective (20, 37). Thanks to these techniques, recent studies, conducted in various environments, have revealed a surprisingly high diversity of small eukaryotes and the existence of novel lineages (39). For example, the genetic diversity of small eukaryotes from coastal waters showed the dominance of novel alveolates (from 36% to 62% of total sequences obtained in their libraries) and the importance of novel stramenopiles, ...

SummaryAlthough inland water bodies are more heterogeneous and sensitive to environmental variation than oceans, the diversity of small protists in these ecosystems is much less well-known. Some molecular surveys of lakes exist, but little information is available from smaller, shallower and often ephemeral freshwater systems, despite their global distribution and ecological importance. We carried out a comparative study based on massive pyrosequencing of amplified 18S rRNA gene fragments of protists in the 0.2-5 μm-size range in one brook and four shallow ponds located in the Natural Regional Park of the Chevreuse Valley, France. Our study revealed a wide diversity of small protists, with 812 stringently defined operational taxonomic units (OTUs) belonging to the recognized eukaryotic supergroups (SAR -Stramenopiles, Alveolata, Rhizaria-, Archaeplastida, Excavata, Amoebozoa, Opisthokonta) and to groups of unresolved phylogenetic position (Cryptophyta, Haptophyta, Centrohelida, Katablepharida, Telonemida, Apusozoa). Some OTUs represented deep-branching lineages (Cryptomycota, Aphelida, Colpodellida, Tremulida, clade-10 Cercozoa, HAP-1 Haptophyta). We identified several lineages previously thought to be marine including, in addition to MAST-2 and MAST-12, already detected in freshwater, MAST-3 and possibly MAST-6. Protist community structures were different in the five ecosystems. These differences did not correlate with geographical distances, but seemed to be influenced by environmental parameters.

M Microbial life has adapted to various individual extreme conditions; yet, organisms simultaneously adapted to very low pH, high salt and high temperature are unknown. We combined environmental 16S/18S rRNAgene metabarcoding, cultural approaches, fluorescence-activated cell sorting, scanning electron microscopy and chemical analyses to study samples along such unique polyextreme gradients in the Dallol-Danakil area (Ethiopia). We identify two physicochemical barriers to life in the presence of surface liquid water defined by: i) high chaotropicity-low water activity in Mg 2+ /Ca 2+-dominated brines and ii) hyperacidity-salt combinations (pH~0/ NaCl-dominated salt-saturation). When detected, life was dominated by highly diverse ultrasmall archaea widely distributed across phyla with and without previously known halophilic members. We hypothesize that high cytoplasmic K +-level was an original archaeal adaptation to hyperthermophily, subsequently exapted during multiple transitions to extreme halophily. W We detect active silica encrustment/fossilization of cells but also abiotic biomorphs of varied chemistry. Our work helps circumscribing habitability and calls for cautionary interpretations of morphological biosignatures on Earth and beyond. Belilla et al. 3 Microbial life has adapted to so-called extreme values of temperature, pH or salinity, but also to several polyextreme, e.g. hot acidic or salty alkaline, ecosystems 1,2. Various microbial lineages have been identified in acidic brines in the pH range 1.5-4.5, e.g. in Western Australia 3,4 and Chile 3. However, although some acidophilic archaea thrive at pH~0 (Picrophilus oshimae grows at an optimal pH of 0.7) 5 and many halophilic archaea live in hypersaline systems (>30%; NaCl-saturation conditions), organisms adapted simultaneously to very low pH (<1) and high salt, and eventually also high temperature, are not known among cultured prokaryotic species 1. Are molecular adaptations to these combinations incompatible or (hot) hyperacidic hypersaline environments simply rare and unexplored? The Dallol geothermal dome and its surroundings (Danakil Depression, Afar, Ethiopia) allow to address this question by offering unique polyextreme gradients combining high salt content (33 to >50%; either Mg 2+ /Ca 2+ or Na + (/Fe 2+/3+)-rich), high temperature (25-110°C) and low pH (≤-1.5 to 6). Dallol is an uplifted (~40 m) dome structure located in the North of the Danakil depression (~120 m below-sea-level), a 200 km-long basin within the Afar rift, at the triple junction between the Nubian, Somalian and Arabian Plates 6. Lying only 30 km north of the hypersaline, hydrothermally-influenced, Lake Assale (Karum) and the Erta Ale volcanic range, Dallol does not display volcanic outcrops but intense degassing and hydrothermalism. These activities are observed on the salt dome and the adjacent Black Mountain and Yellow Lake (Gaet'Ale) areas 6,7 (Fig. 1a-b). Gas and fluid isotopic measurements indicate that meteoritic waters, notably infiltrating from the high Ethiopian plat...

Although they are widespread, diverse and involved in biogeochemical cycles, microbial eukaryotes attract less attention than their prokaryotic counterparts in environmental microbiology. In this study, we used publicly available 18S barcoding data to define biases that may limit such analyses and to gain an overview of the planktonic microbial eukaryotic diversity in freshwater ecosystems. The richness of the microbial eukaryotes was estimated to 100 798 operational taxonomic units (OTUs) delineating 1267 clusters or phylogenetic units (PUs, i.e. monophyletic groups of OTUs that are phylogenetically close). By summing the richness found in aquatic environments, we can predict the microbial eukaryotic richness to be around 200 000-250 000 species. The molecular diversity of protists in freshwater environments is generally higher than that of the morphospecies and cultivated species catalogued in public databases. Amoebozoa, Viridiplantae, Ichthyosporea, and Cryptophyta are the most phylogenetically diverse taxa, and characterisation of these groups is still needed. A network analysis showed that Fungi, Stramenopiles and Viridiplantae play central role in lake ecosystems. Finally, this work provides guidance for compiling metabarcoding data and identifies missing data that should be obtained to increase our knowledge on microbial eukaryote diversity.