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The petB gene has been proposed as a high-resolution marker gene to access the diversity of marine Synechococcus populations. A systematic metabarcoding approach based on the petB gene would improve the characterization/assessment of the Synechococcus community structure in marine planktonic ecosystems.

We present annual cycles of chlorophyll a, phytoplankton carbon, nitrate and oxygen for Subtropical (STW), Subantarctic (SAW), and Subantarctic Mode (SAMW) waters near Aotearoa New Zealand from data collected by two Biogeochemical (BGC) Argo floats. We develop two simple models of depth-integrated net primary production (NPP), tuned against 14C-uptake measurements, to compare with Vertically-Generalised Production Model (VGPM) satellite-based estimates of NPP. One model is the simplest possible, and assumes production is proportional to light multiplied by chlorophyll a concentration. The second model modifies the light response profile to account for photoacclimation. In STW at 30–35°S, enhanced production is initiated in austral autumn when the mixed layer deepens to entrain nutrients into the photic zone. For about half the year, there is substantial production within a deep chlorophyll maximum that sits below the mixed layer. Consequently, depth-integrated NPP is only loosely related to surface biomass as imaged from satellite remote-sensing, and BGC Argo-based model estimates of depth-integrated NPP are about double VGPM estimates. In SAW at 45–55°S, production is initiated when vertical mixing decreases in austral spring. Production is largely within the mixed layer, and depth-integrated phytoplankton biomass and depth-integrated NPP follow surface phytoplankton biomass. Model estimates of depth-integrated NPP based on BGC Argo float profiles are comparable with VGPM estimates for the southern water masses., SI

Planktonic protists are an essential component of marine pelagic ecosystems where they mediate important trophic and biogeochemical functions. Although these functions are largely influenced by their taxonomic affiliation, the composition and spatial variability of planktonic protist communities remain poorly characterized in vast areas of the ocean. Here, we investigated the diversity of these communities in contrasting oceanographic conditions of the southwest Pacific (33–58 °S) using DNA metabarcoding of the 18S rRNA gene. Seawater samples collected during twelve cruises ( = 482, 0–3100 m) conducted east of New Zealand were used to characterize protist communities in Subtropical (STW) and Subantarctic (SAW) surface water masses and the Subtropical Front (STF) that separates them. Diversity decreased with increasing latitude and increasing temperature but tended to be lowest in the STF. Sample ordination resulting from the abundance of amplicon single variants (ASVs) corresponded to the different water masses. Overall, Dinoflagellata (Syndiniales, 27%; Dinophyceae, 24% of standardized number of reads) dominated the euphotic zone followed by Chlorophyta (20%), but their relative abundance and composition at class and lower taxonomic levels varied consistently between water masses. Among Chlorophyta, several picoplanktonic algae species of the Mamiellophyceae class including Ostreococcus lucimarinus dominated in STW, while the Chloropicophyceae species Chloroparvula pacifica was most abundant in SAW. Bacillariophyta (5%), Prymnesiophyceae (5%), and Pelagophyceae (2%) classes were less abundant but showed analogous water mass specificity at class and finer taxonomic levels. Protist community composition in the STF had mixed characteristics and showed regional differences with the southern STF (50 °S) having more resemblance with subantarctic communities than the STF over the Chatham Rise region (42–44 °S). Below the euphotic zone, Syndiniales sequences (40%) dominated the dataset followed by Radiolaria (31%), Dinophyceae (14%) and other heterotrophic groups like Marine Stramenopiles and ciliates (1–1.5%). Among Radiolaria, several unidentified ASVs assigned to Spumellaria were most abundant, but showed significantly different distributions between STW and SAW highlighting the need to further investigate the taxonomy and ecology of this group. The present study represents a significant step forward towards characterizing protistan communities composition in relation to major physical oceanographic features in the southwest Pacific providing new insights about the biogeography and ecological preferences of different planktonic protist taxa from class to species and genotypic level., SI

Spiny-surfaced species of Prorocentrum form harmful algal blooms, and its taxonomic identity is obscure due to the size and shape variability. Molecular phylogenies reveal two major clades: one for P. cordatum with sequences mainly retrieved as P. minimum, and the other for P. shikokuense with sequences also retrieved as P. dentatum and P. donghaiense. Several closely related clades still need to be characterized. Here, we provide nuclear SSU and LSU rRNA genes, and nuclear ITS region (ITS1-5.8S gene-ITS2) sequences of the strain CCMP3122 isolated from Florida (initially named P. donghaiense) and strains Prorocentrum sp. RCC6871-2 from the Ross Sea, Antarctica. We describe Prorocentrum thermophilum sp. nov. based on the strain CCMP3122, a species also distributed in the open waters of the Gulf of Mexico, New Zealand, and the Arabian Gulf; and Prorocentrum criophilum sp. nov. based on the strain RCC6872, which is distributed in the Antarctic Ocean and Arctic Sea. Prorocentrum thermophilum is roundish (~14 μm long, ~12 μm wide), with an inconspicuous anterior spine-like prolongation under light microscopy, valves with tiny, short knobs (5-7 per μm

23 pages, 10 figures, 5 tables, supplementary material https://doi.org/10.1016/j.pocean.2021.102737, A detailed study of phytoplankton composition and dynamics was carried out during three contrasting situations (cruises F1, F2, and F3) in the northwestern (NW) Mediterranean Sea. Haptophytes, diatoms, and green algae dominated in F1, during the spring bloom, with high nutrients and high phytoplankton biomass. In F2, the post-bloom situation with a still weak stratification and lower nutrient concentrations, we found a high spatial variability. Stations were clearly dominated by either Synechococcus, haptophytes or cryptophytes; with Synechococcus reaching the highest abundance (4 × 105 cells mL−1, 60% of the integrated chlorophyll a) reported to date for the open Mediterranean Sea. Cryptophytes accumulated close to the surface in very shallow mixed layer stations. In late summer, F3 revealed a fully developed stratification with low nutrients and a marked deep chlorophyll maximum (DCM). Prochlorococcus was present only during this cruise, mainly in deep layers together with haptophytes and pelagophytes, while haptophytes and Synechococcus dominated the upper mixed layer. Flow cytometry (FCM) and pigment-based abundance estimates for Prochlorococcus, Synechococcus and cryptophytes were well correlated, as happened also between small picoeukaryotes (FCM) and green algae (pigments), and between large picoeukaryotes (FCM) and haptophytes (pigments). Dinoflagellate abundance by microscopy and by pigments did not agree well, probably due to the presence of heterotrophic forms or because they contained pigments other than peridinin, the standard dinoflagellate marker. The decrease in size of the FCM large picoeukaryotes group with depth was presumably related to the increasing contribution of pelagophytes, with smaller cells than haptophytes, the other main component of this fraction. Cell size increase of Prochlorococcus and Synechococcus with depth suggests vertical segregation of genotypes or photoadaptation. The groups' ecological preferences are presented with respect to depth and nutrient concentrations. Synechococcus and cryptophytes occupied shallow layers; diatoms, green algae and Prochlorococcus showed a tendency for deep layers and pelagophytes for even deeper layers, while haptophyte and dinoflagellate allocations were less clear. As for nutrients, the maximum relative contributions of green algae and especially diatoms occurred when dissolved inorganic phosphorus (DIP) concentrations were highest, of Prochlorococcus, dinoflagellates and pelagophytes when lowest, and of Synechococcus and cryptophytes when DIP concentrations were low but not minimal. The contribution of haptophytes did not show a relationship with DIP concentration. These results from individual groups stand as significant exceptions to the general relationship between phytoplankton cell size and nutrient availability, This work was funded by Spanish Government, Ministerio de Ciencia e Innovación (project FAMOSO, grant CTM2008-06261-C03/MAR). AGR was also supported by the Generalitat de Catalunya (Grup de Recerca 2061), With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

Polar marine ecosystems are particularly vulnerable to the effects of climate change. Warming temperatures, freshening seawater, and disruption to sea-ice formation potentially all have cascading effects on food webs. New approaches are needed to better understand spatiotemporal interactions among biogeochemical processes at the base of Southern Ocean food webs. In marine systems, isoscapes (models of the spatial variation in the stable isotopic composition) of carbon and nitrogen have proven useful in identifying spatial variation in a range of biogeochemical processes, such as nutrient utilization by phytoplankton. Isoscapes provide a baseline for interpreting stable isotope compositions of higher trophic level animals in movement, migration, and diet research. Here, we produce carbon and nitrogen isoscapes across the entire Southern Ocean (>40°S) using surface particulate organic matter isotope data, collected over the past 50 years. We use Integrated Nested Laplace Approximation-based approaches to predict mean annual isoscapes and four seasonal isoscapes using a suite of environmental data as predictor variables. Clear spatial gradients in δ13C and δ15N values were predicted across the Southern Ocean, consistent with previous statistical and mechanistic views of isotopic variability in this region. We identify strong seasonal variability in both carbon and nitrogen isoscapes, with key implications for the use of static or annual average isoscape baselines in animal studies attempting to document seasonal migratory or foraging behaviors.

Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells. Extensive examination of a wide variety of phagotrophic, parasitic, and phototrophic microeukaryotes demonstrates that a catabolic process that converts chlorophylls into nonphotosensitive 13(2),17(3)-cyclopheophorbide enols (CPEs) is phylogenetically ubiquitous among extant eukaryotes. The accumulation of CPEs is identified in phagotrophic algivores belonging to virtually all major eukaryotic assemblages with the exception of Archaeplastida, in which no algivorous species have been reported. In addition, accumulation of CPEs is revealed to be common among phototrophic microeukaryotes (i.e., microalgae) along with dismantling of their secondary chloroplasts. Thus, we infer that CPE-accumulating chlorophyll catabolism (CACC) primarily evolved among algivorous microeukaryotes to detoxify chlorophylls in an early stage of their evolution. Subsequently, it also underpinned photosynthetic endosymbiosis by securing close interactions with photosynthetic machinery containing abundant chlorophylls, which led to the acquisition of secondary chloroplasts. Our results strongly suggest that CACC, which allowed the consumption of oxygenic primary producers, ultimately permitted the successful radiation of the eukaryotes throughout and after the late Proterozoic global oxygenation.

We examined biogenic silica production and elementary composition (biogenic Si, particulate organic carbon and particulate organic nitrogen) of Rhizaria and diatoms in the upper 200 m along a transect in the Southwest Pacific sector of the Southern Ocean during austral summer (January–February 2019). From incubations using the 32Si radioisotope, silicic acid uptake rates were measured at 15 stations distributed in the Polar Front Zone, the Southern Antarctic Circumpolar Current and the Ross Sea Gyre. Rhizaria cells are heavily silicified (up to 7.6 nmol Si cell−1), displaying higher biogenic Si content than similar size specimens found in other areas of the global ocean, suggesting a higher degree of silicification of these organisms in the silicic acid rich Southern Ocean. Despite their high biogenic Si and carbon content, the Si/C molar ratio (average of 0.05 ± 0.03) is quite low compared to that of diatoms and relatively constant regardless of the environmental conditions. The direct measurements of Rhizaria's biogenic Si production (0.8–36.8 μmol Si m−2 d−1) are of the same order of magnitude than previous indirect estimations, confirming the importance of the Southern Ocean for the global Rhizaria silica production. However, diatoms largely dominated the biogenic Si standing stock and production of the euphotic layer, with low rhizarians' abundances and biogenic Si production (no more than 1%). In this manuscript, we discuss the Antarctic paradox of Rhizaria, that is, the potential high accumulation rates of biogenic Si due to Rhizaria in siliceous sediments despite their low production rates in surface waters., SI

Polar marine ecosystems are particularly vulnerable to the effects of climate change. Warming temperatures, freshening seawater and disruption to sea ice formation potentially all have detrimental ...

Symbiosis with micro-algae (photosymbiosis) is a common feature among marine planktonic protists, but very little is known about the physiology and ecological significance of these associations. High concentrations of dimethylsulfoniopropionate (DMSP), a metabolite produced by marine microalgae, are commonly observed in coral-microalgae symbiosis, where DMS(P) is involved in multiple physiological functions. Knowledge on concentration and role of DMSP in analogous photosymbiosis in plankton is lacking. Here, we assess the total DMSP (DMSPt = DMSP + DMS) concentration and natural stable isotopes of sulfur across ecologically relevant symbiotic plankton groups, the Radiolaria and Foraminifera. We found that intracellular DMSPt concentrations in microalgal symbionts were among the highest recorded (range = 170–702 mmol L−1), while lower concentrations (range = 0.1–23 mmol L−1) were characteristic of the holobiont (i.e., host-microalgae). The contribution of symbiotic Radiolaria to the water column particulate DMSPt concentration ranged 0.1–8%. Sulfur isotopic composition (34S) of DMSPt in the Collodaria holobionts was significantly higher than their symbiotic microalgae isolated in culture. Despite their high intracellular DMSPt content, math formula uptake in these holobionts throughout 3-d incubations was not detected. We observed a systematic 34S depletion (∼ 1.5‰) of DMS relative to DMSP in experimental incubations containing filtered seawater, which we hypothesize is related to the bacterial preference for the uptake of 34S-depleted DMS. Overall, the results indicate that plankton symbiosis can, at times, represent a potentially important source of DMS(P). Specific differences in 34S provided new insights into sulfur isotopic fractionation associated with DMS(P) biotransformation processes, with potential implications for current interpretations of isotopically tracked biogenic sources of marine aerosols.

Passive sinking of particulate organic matter (POM) is the main mechanism through which the biological pump transports surface primary production to the ocean interior. However, the contribution and variability of different biological sources to vertical export is not fully understood. Here, we use DNA metabarcoding of the 18S rRNA gene and particle interceptor traps (PITs) to characterize the taxonomic composition of particles sinking out of the photic layer in the California Current Ecosystem (CCE), a productive system with high export potential. The PITs included formalin-fixed and ‘live’ traps to investigate eukaryotic communities involved in the export and remineralization of sinking particles. Sequences affiliated with Radiolaria dominated the eukaryotic assemblage in fixed traps (90%), with Dinophyta and Metazoa making minor contributions. The prominence of Radiolaria decreased drastically in live traps, possibly due to selective consumption by copepods, heterotrophic nanoflagellates, and phaeodarians that were heavily enriched in these traps. These patterns were consistent across the water masses surveyed extending from the coast to offshore, despite major differences in productivity and trophic st, Sí

Special volume: Planet Ocean. Scientia Marina 80(Suppl.1) 2016.-- 6 pages, 1 figure, 1 table, [EN] Ecological traits of phytoplankton are being incorporated into models to better understand the dynamics of marine ecosystems and to predict their response to global change. We have compared the distribution of major phytoplankton groups in two different systems: in surface waters of the NW Mediterranean during key ecological periods, and in the DCM (deep chlorophyll maximum) formed in summer in the temperate NE Atlantic. This comparison disentangled the influence of light and nutrients on the relative position of diatoms, dinoflagellates, prymnesiophytes, pelagophytes, chlorophytes, Synechococcus and Prochlorococcus in these environments. Three clusters formed according to their affinity for nutrients: diatoms, chlorophytes and dinoflagellates as the most eutrophic groups; Synechococcus, pelagophytes and prymnesiophytes as mesotrophic groups; and Prochlorococcus as an oligotrophic group. In terms of irradiance, the phytoplankton groups did not cluster clearly. Comparing the nutrient and light preferences of the groups with their distribution in the DCM, dinoflagellates and chlorophytes appear as the most stressed, i.e. their position was most distant from their optimal light and nutrient conditions. Diatoms stayed in deeper than optimal irradiance layers, probably to meet their high nutrient requirements. On the opposite side, low nutrient requirements allowed Prochlorococcus to remain in the uppermost part of the DCM layer. The slight sub-optimal position of Synechococcus and prymnesiophytes with regard to their nutrient requirements suggests that their need for high irradiance plays a significant role in their location within the DCM. Finally, pelagophytes remained in deep layers without an apparent need for the high nutrient concentrations at those depths, [ES] Las características ecológicas del fitoplancton se están incorporando en modelos con el fin de comprender mejor la dinámica de los ecosistemas marinos y para predecir su respuesta al cambio global. En este trabajo, hemos comparado la distribución de los principales grupos del fitoplancton en dos sistemas diferentes: en las aguas superficiales del Mediterráneo noroccidental durante períodos ecológicos clave, y en el Máximo Profundo de Clorofila (MPC) que se forma en verano en el Atlántico NE templado. Esta comparación permitió diferenciar la influencia de la luz y los nutrientes en la posición relativa de diatomeas, dinoflagelados, primnesiofitas, pelagofitas, clorofitas, Synechococcus y Prochlorococcus en estos ambientes. Se pudieron diferenciar tres agrupaciones de acuerdo con su afinidad por los nutrientes: diatomeas, clorofitas y dinoflagelados como los grupos más eutróficos; Synechococcus, pelagofitas y primnesiofitas como grupos mesotróficos; y Prochlorococcus como el grupo más oligotrófico. En términos de irradiancia los grupos de fitoplancton no se agruparon de una manera clara. La comparación de las preferencias por nutrientes y luz con su distribución en el MPC permite distinguir que dinoflagelados y clorofitas aparecen como los más estresados en su posición en el MPC, es decir, su posición era la más distante de sus condiciones óptimas de irradiancia y nutrientes. Las diatomeas permanecieron por debajo de su irradiancia óptima probablemente para satisfacer sus altos requisitos de nutrientes, que se encuentran en las capas más profundas. En el lado opuesto, los bajos requerimientos de nutrientes de Prochlorococcus les permitieron permanecer en la parte más superior de la capa del MPC. La ligera posición subóptima de Synechococcus y primnesiofitas con respecto a sus requerimientos de nutrientes sugiere que su necesidad de condiciones relativamente altas de irradiancia juega un papel significativo en su ubicación dentro del MPC. Por último, las pelagofitas permanecieron en capas profundas sin que aparentemente necesitaran las altas concentraciones de nutrientes que se encuentran en esas profundidades, The databases used for this study derive from work performed under the framework of the Spanish-funded projects EFLUBIO (REN2002-04151-C02/MAR) and FAMOSO (CTM2008-06261-C03-01/MAR) and the EU-funded project LIFE-INDEMARES

We investigated phytoplankton production rates and grazing fates in the Costa Rica Dome (CRD) during summer 2010 based on dilution depth profiles analyzed by flow cytometry and pigments and mesozooplankton grazing assessed by gut fluorescence. Three community production estimates, from ^(14)C uptake (1025 ± 113 mg C m^(−2) day^(−1)) and from dilution experiments analyzed for total Chla (990 ± 106 mg C m^(−2) day^(−1)) and flow cytometry populations (862 ± 71 mg C m^(−2) day^(−1)), exceeded regional ship-based values by 2–3-fold. Picophytoplankton accounted for 56% of community biomass and 39% of production. Production profiles extended deeper for Prochlorococcus (PRO) and picoeukaryotes than for Synechococcus (SYN) and larger eukaryotes, but 93% of total production occurred above 40 m. Microzooplankton consumed all PRO and SYN growth and two-third of total production. Positive net growth of larger eukaryotes in the upper 40 m was balanced by independently measured consumption by mesozooplankton. Among larger eukaryotes, diatoms contributed ∼3% to production. On the basis of this analysis, the CRD region is characterized by high production and grazing turnover, comparable with or higher than estimates for the eastern equatorial Pacific. The region nonetheless displays characteristics atypical of high productivity, such as picophytoplankton dominance and suppressed diatom roles.

We investigated biomass, size-structure, composition, depth distributions and spatial variability of the phytoplankton community in the Costa Rica Dome (CRD) in June–July 2010. Euphotic zone profiles were sampled daily during Lagrangian experiments in and out of the dome region, and the community was analyzed using a combination of digital epifluorescence microscopy, flow cytometry and HPLC pigments. The mean depth-integrated biomass of phytoplankton ranged 2-fold, from 1089 to 1858 mg C m−2 (mean ± SE = 1378 ± 112 mg C m−2), among 4 water parcels tracked for 4 days. Corresponding mean (±SE) integrated values for total chlorophyll a (Chl a) and the ratio of autotrophic carbon to Chl a were 24.1 ± 1.5 mg Chl a m−2 and 57.5 ± 3.4, respectively. Absolute and relative contributions of picophytoplankton (∼60%), Synechococcus (>33%) and Prochlorococcus (17%) to phytoplankton community biomass were highest in the central dome region, while >20 µm phytoplankton accounted for ≤10%, and diatoms

The Costa Rica Dome (CRD) represents a classic case of the bloom-forming capacity of small phytoplankton. Unlike other upwelling systems, autotrophic biomass in the CRD is dominated by picocyanobacteria and small eukaryotes that outcompete larger diatoms and reach extremely high biomass levels. We investigated responses of the subsurface phytoplankton community of the CRD to changes associated with vertical displacement of water masses, coupling in situ transplanted dilution experiments with flow cytometry and epifluorescence microscopy to assess group-specific dynamics. Growth rates of Synechococcus (SYN) and photosynthetic picoeukaryotes (PEUK) were positively correlated with light (Rpearson_SYN = 0.602 and Rpearson_PEUK = 0.588, P < 0.001). Growth rates of Prochlorococcus (PRO), likely affected by photoinhibition, were not light correlated (Rpearson_PRO = 0.101, P = 0.601). Overall, grazing and growth rates were closely coupled in all picophytoplankton groups (Rspearman_PRO = 0.572, Rspearman_SYN = 0.588, Rspearman_PEUK = 0.624), and net growth rates remained close to zero. Conversely, the abundance and biomass of larger phytoplankton, mainly diatoms, increased more than 10-fold in shallower transplant incubations indicating that, in addition to trace-metal chemistry, light also plays a significant role in controlling microphytoplankton populations in the CRD.

During summer 2010, we investigated phytoplankton production and growth rates at 19 stations in the eastern tropical Pacific, where winds and strong opposing currents generate the Costa Rica Dome (CRD), an open-ocean upwelling feature. Primary production (14C-incorporation) and group-specific growth and net growth rates (two-treatment seawater dilution method) were estimated from samples incubated in situ at eight depths. Our cruise coincided with a mild El Niño event, and only weak upwelling was observed in the CRD. Nevertheless, the highest phytoplankton abundances were found near the dome center. However, mixed-layer growth rates were lowest in the dome center (∼0.5–0.9 day−1), but higher on the edge of the dome (∼0.9–1.0 day−1) and in adjacent coastal waters (0.9–1.3 day−1). We found good agreement between independent methods to estimate growth rates. Mixed-layer growth rates of Prochlorococcus and Synechococcus were largely balanced by mortality, whereas eukaryotic phytoplankton showed positive net growth (∼0.5–0.6 day−1), that is, growth available to support larger (mesozooplankton) consumer biomass. These are the first group-specific phytoplankton rate estimates in this region, and they demonstrate that integrated primary production is high, exceeding 1 g C m−2 day−1 on average, even during a period of reduced upwelling.

Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins involved in toxin biosynthesis pathways (e.g. sxtA1-4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56% and 57% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.

We investigated the spatial variability of picocyanobacterial community structure across the Costa Rica Dome (CRD), an offshore upwelling system characterized by high seasonal abundance of Synechococcus spp. We constructed clone libraries of the rpoC1 gene to survey picocyanobacterial diversity and developed specific real-time quantitative polymerase chain reaction assays to assess the distribution of genetically distinct Synechococcus (SYN) and Prochlorococcus (PRO) populations across vertical and horizontal physicochemical gradients. Flow cytometry data showed that cell abundances for both SYN and PRO were highest near the dome center. Phylogenetic analysis of rpoC1 sequences revealed a remarkably high and distinctive picocyanobacterial diversity (FLU1-3, CRD1, Clade II, XV, XVI) that included ‘‘novel’’ SYN and PRO genotypes. Furthermore, genetically different populations exhibited vertical and horizontal spatial partitioning. Abundances of distinct SYN genotypes peaked at subsequent depth horizons, leading to a fine vertical structure with at least three populations stacked within the upper 30–40 m at the dome. Clade II and FLU1A peaked in surface waters, while maximum concentrations of CRD1, FLU1B, and Clade XVI occurred in the upper and lower thermocline, respectively. Horizontally, Clade II abundance in surface waters remained high across the entire region, while SYN genotypes CRD1 and FLU1A increased with shoaling of the thermo- and nutricline toward the center of the dome to become the dominant genotypes of the SYN assemblage in the dome. Below the mixed layer, Clade XVI and PRO genotype FLU2, virtually absent outside the dome, became abundant components of the picocyanobacterial assemblage. Despite their phylogenetic relatedness, FLU1A and FLU1B subclades followed different distributional patterns, suggesting ecological significance of the microdiversity within the clade. The unprecedented fine vertical structure demonstrated for SYN genotypes is driven by sharp physicochemical gradients (e.g., density, nutrient, oxygen, and trace metals) created by the dome and the presence of a shallow oxycline that enhances habitat diversification. Marine picocyanobacteria of the genera Synechococcus (SYN) and Prochlorococcus (PRO) dominate photosynthetic biomass and productivity across vast regions of the oceans and constitute a major component of the global carbon cycle (Li 1994; Jardillier et al. 2010). Despite their phylogenetic proximity, SYN and PRO follow different spatial distributions, both horizontally and vertically, that reflect their distinct ecophysiological preferences (Ferris and Palenik

Collodaria are heterotrophic marine protists that exist either as large colonies composed of hundreds of cells or as large solitary cells. All described species so far harbour intracellular microalgae as photosymbionts. Although recent environmental diversity surveys based on molecular methods demonstrated their consistently high contribution to planktonic communities and their worldwide occurrence, our understanding of their diversity and biogeography is still very limited. Here we estimated the 18S ribosomal DNA (rDNA) gene copies per collodarian cell for solitary (5770 +/- 1960 small subunit (SSU) rDNA copies) and colonial specimens (37 474 +/- 17 799 SSU rDNA copies, for each individual cell within a colony) using single-specimen quantitative PCR. We then investigated the environmental diversity of Collodaria within the photic zone through the metabarcoding survey from the Tara Oceans expedition and found that the two collodarian families Collosphaeridae and Sphaerozoidae contributed the most to the collodarian diversity and encompassed mostly cosmopolitan taxa. Although the biogeographical patterns were homogeneous within each biogeochemical biome considered, we observed that coastal biomes were consistently less diverse than oceanic biomes and were dominated by the Sphaerozoidae while the Collosphaeridae were dominant in the open oceans. The significant relationships with six environmental variables suggest that collodarian diversity is influenced by the trophic status of oceanic provinces and increased towards more oligotrophic regions.

9 pages, 6 figures, 1 tables, 2 appendices, Phytoplankton distribution is relatively constant in large areas of the surface ocean. In order to maintain this apparent stability, phytoplankton production and losses have to be balanced. Indeed, growth (μo) and grazing (g) rates obtained simultaneously with the dilution technique are often tightly coupled. One problem with this approach is that growth and grazing are not independent in the ecological model on which the method is based (net growth rate = μo – g). We evaluated to which extent this methodological artefact may influence the correlation between μo and g estimated using the dilution technique. Following a Monte-Carlo approach, we show that the methodological correlation can be substantial depending on: (1) the % error in the measurement of the state variable ND (e.g. chlorophyll a) and (2) the range (± SD) of the μo and g considered. As long as the error of ND is small (< 10%), the measured correlation between growth and grazing closely reflects a true ecological relationship. For large errors, the dilution technique can yield a substantial correlation between both variables, regardless of their ecological relation. The influence of this methodological correlation decreases as the range of growth and grazing rate values increases. We developed a procedure to evaluate the ecological versus the methodological nature of the correlation observed between μo and g. The application of this procedure to a data set obtained from a coastal site revealed that the high correlation observed (rS = 0.881, p < 0.0001) reflected a true ecological relationship, This work was supported by the research project Eflubio (REN2002-04151-C02-01), funded by the Spanish Ministry of Education and Science. Financial support was provided by a PhD fellowship from the Spanish goverment to A.G.R. Different projects sustaining the Blanes Bay Microbial Observatory provided sampling facilities

The Costa Rica Dome (CRD) represents a classic case of the bloom-forming capacity of small phytoplankton. Unlike other upwelling systems, autotrophic biomass in the CRD is dominated by picocyanobacteria and small eukaryotes that outcompete larger diatoms and reach extremely high biomass levels. We investigated responses of the subsurface phytoplankton community of the CRD to changes associated with vertical displacement of water masses, coupling in situ transplanted dilution experiments with flow cytometry and epifluorescence microscopy to assess group-specific dynamics. Growth rates of Synechococcus (SYN) and photosynthetic picoeukaryotes (PEUK) were positively correlated with light (Rpearson_SYN = 0.602 and Rpearson_PEUK = 0.588, P < 0.001). Growth rates of Prochlorococcus (PRO), likely affected by photoinhibition, were not light correlated (Rpearson_PRO = 0.101, P = 0.601). Overall, grazing and growth rates were closely coupled in all picophytoplankton groups (Rspearman_PRO = 0.572, Rspearman_SYN = 0.588, Rspearman_PEUK = 0.624), and net growth rates remained close to zero. Conversely, the abundance and biomass of larger phytoplankton, mainly diatoms, increased more than 10-fold in shallower transplant incubations indicating that, in addition to trace-metal chemistry, light also plays a significant role in controlling microphytoplankton populations in the CRD.

17 pages, 12 figures, 3 tables, The phytoplankton bloom in the Liguro-Provençal deep convection region represents one of the main fertilization mechanisms in the Mediterranean. This communication examines nano- and microphytoplankton observations, and measurements of primary production and chlorophyll a concentration (Chl a) in the southwestern part of the deep convection region, where such information is scarce. Data were obtained from four cruises, carried out in 2005 (EFLUBIO project) and 2009 (FAMOSO project), covering the seasonality between mid-March and September in the region. Our aims were to constrain primary production estimates and to ascertain the importance of short-term variability on the photosynthetic response of phytoplankton assemblages during bloom, post-bloom and late-summer stratification periods in the area. Overall, the initial slope of the P-E relationship (αB) increased and the Chl a-normalized photosynthetic rate (PmB) decreased with increasing optical depth of sample origin, but there were exceptions. In general, there were marked seasonal trends, with stratification increasing and Chl a concentration, primary production and dissolved inorganic nitrogen and phosphate fluxes decreasing from winter to late summer. Chl a at 5m depth reached a maximum of 7mgm-3 on 25 March 2005, one of the highest values measured in the region. Average surface values (±SD) ranged from respectively 2.4±2.3mgm-3 and 2±0.7mgm-3 in the March 2005 and March 2009 cruises to 0.12±0.01mgm-3 in the September 2009 cruise. Vertically integrated (0-80m) primary production (PPint) attained 1800mgCm-2d-1 in March 2009, with an average of 1024±523mgCm-2d-1, and decreased to a mean of 141±0.43mgCm-2d-1 in September 2009. Superimposed to the seasonal trends, there was a considerable within-cruise variability of biomass and primary production, especially during the spring-winter bloom and post-bloom periods, when PPint could change more than threefold within a few days. These differences were mainly associated with the intense hydrographic mesoscale and sub-mesoscale heterogeneity in the region and with the differences in the physiological and ecological history of the phytoplankton communities inhabiting the different water bodies. In late summer, most PPint variability could be explained by fluctuations in surface incident irradiance. © 2014 Elsevier Ltd., This work was supported by the Spanish Projects EFLUBIOREN2002-04151-C02, FAMOSO (CTM2008-06261-C03) and TURBIMOC (CTM2009-06712-E/MAR), and partially by the Grup de Recerca of the (2009 SGR 588). B.F.-C. holds a FPU fellowship of the Spanish Government

According to modern oceanographic perspectives that emphasize microbial pathways, phagotrophic protists comprise one to several levels of intermediate consumers between phytoplankton and larger metazooplankton (copepods and krill). However, recent attempts to quantify pelagic trophic structure in the open ocean using nitrogen stable isotope techniques have brought into question whether such measurements adequately account for protistan trophic steps. Here, we use a two-stage chemostat system, with Dunaliella tertiolecta andOxyrrhis marina as a predator-prey model, to address this question experimentally. To investigate15N trophic discrimination under different conditions of nitrogen availability and recycling, Oxyrrhis was fed in the light and in the dark on phytoplankton provided with high and low nutrient ratios of N: P. We used both bulk and amino acids-compound specific isotopic analysis (AA-CSIA) to distinguish trophic fractionation from changes in the δ15N values of phytoplankton (isotopic baseline). Results demonstrate that protistan consumers are not, in fact, significantly enriched in 15N relative to their prey, a marked departure from the general findings for metazoan consumers. In addition, we show that changes in the isotopic baseline propagate rapidly through the protistan food chain, highlighting the need to account for this variability at ecologically relevant time scales. If protistan trophic steps are largely invisible or significantly underestimated using nitrogen isotope measurements, research that utilize such measurements in ecological, fisheries, and climate change studies may miss a large part of the ocean's variability in food-web structure and ecosystem function. © 2014, by the Association for the Sciences of Limnology and Oceanography, Inc.

Physical processes forced by tidal dynamics, such as bores and internal waves, have a high influence on biological patterns in the main channel of the Strait of Gibraltar. To analyse this connection in the case of photosynthetic processes, a set of high resolution profiles of physical (temperature, salinity, and light) and chemical (nutrients and chlorophyll) variables was acquired during a tidal cycle, together with high resolution profiles of physiological parameters (photosynthetic efficiency Fv/Fm and functional cross section of photosystem II, σPSII) quantified by in situ fast repetition rate (FRR) fluorometry. Vertical profiles of variable fluorescence revealed two different chlorophyll maxima that had been previously described in the neighborhood of the Strait; Atlantic Maximum (AM) and Deep Maximum (DM). AM was present in the photic zone throughout the whole sampling period and the phytoplankton community associated to this maximum was responsible of the main production in the site until the arrival of the internal bore. DM only appeared after high water at 44. m depth, at the lower end of the photic zone and was associated to the Atlantic Mediterranean Interface (AMI). Phytoplankton associated to this maximum showed very low productivity values. FRR profiles revealed that the arrival of the internal bore happened concomitant with the appearance of a unique, deep and broad chlorophyll maximum associated to a water mass with different physico-chemical and optical characteristics. This maximum ascended quickly to the surface waters in the order of a few minutes. The internal bore's passage becomes a mechanism that supplies phytoplankton to the incoming Atlantic water and a transient increase of primary production in the site was then detected. In addition, FRR derived primary production profiles revealed a significant daily variability. © 2011 Elsevier B.V., This work was funded by the Spanish National Research program through the projects — CTM2005-08142-CO3-01 and CTM2008-06124. D.M. was supported by a JAE-doc contract (# X0SC000087) funded by the Spanish CSIC.

11 pages, 5 figures, 3 tables, supplementary material in https://doi.org/10.1016/j.ecss.2011.08.008, There has been more attention to phytoplankton dynamics in nutrient-rich waters than in oligotrophic ones thus requiring the need to study the dynamics and responses in oligotrophic waters. Accordingly, phytoplankton community in Blanes Bay was overall dominated by Prymnesiophyceae, remarkably constant throughout the year (31 ± 13% Total chlorophyll a, Tchl a) and Bacillariophyta with a more episodic appearance (20 ± 23% Tchl a). Prasinophyceae and Synechococcus contribution became substantial in winter (Prasinophyceae = 30% Tchl a) and summer (Synechococcus = 35% Tchl a). Phytoplankton growth and grazing mortality rates for major groups were estimated by dilution experiments in combination with high pressure liquid chromatography and flow cytometry carried out monthly over two years. Growth rates of total phytoplankton (range = 0.30–1.91 d−1) were significantly higher in spring and summer (μ > 1.3 d−1) than in autumn and winter (μ ∼ 0.65 d−1) and showed a weak dependence on temperature but a significant positive correlation with day length. Microzooplankton grazing (range = 0.03–1.4 d−1) was closely coupled to phytoplankton growth. Grazing represented the main process for loss of phytoplankton, removing 60 ± 34% (±SD) of daily primary production and 70 ± 48% of Tchl a stock. Chla synthesis was highest during the Bacillarophyceae-dominated spring bloom (Chl asynt = 2.3 ± 1.6 μg Chl a L−1 d−1) and lowest during the following post-bloom conditions dominated by Prymnesiophyceae (Chl asynt = 0.23 ± 0.08 μg Chl a L−1 d−1). This variability was smoothed when expressed in carbon equivalents mainly due to the opposite dynamics of C:chl a (range = 11–135) and chl a concentration (range = 0.07–2.0 μg chl a L−1). Bacillariophyta and Synechococcus contribution to C fluxes was higher than to biomass because of their fast-growth rate. The opposite was true for Prymnesiophyceae, This is a contribution of the Microbial Observatory of Blanes Bay. Research was supported by Spanish research grant EFLUBIO (REN2002-04151-C02-01/MAR) and EU project BASICS (EVK3-CT-2002-00078). Financial support was provided by a Ph.D fellowship from the Spanish Ministry of Education and Science to A.G.R.

15 pages, 8 figures, 7 tables, The relation between trophic regime and phytoplankton composition and function in oceanic systems is well accepted in oceanography. However, the relative dynamics and carbon cycling contributions of different phytoplankton groups across gradients of ocean richness are not fully understood. In this work we investigated phytoplankton dynamics along two transects from the NW African coastal upwelling to open-ocean waters of the north Atlantic subtropical gyre. We adopted a pigment-based approach to characterize community structure and to quantify group-specific growth and grazing rates and associated carbon fluxes. Changes in pigment cell concentration during the incubation experiments due to photoadaptation were corrected to obtain reliable rates. The oceanic region was dominated by Prochlorococcus (PRO) (45±7% of total chlorophyll a) while diatoms dominated in upwelling waters (40±37%). Phytoplankton grew faster (μ=0.78±0.26 d−1) and free of nutrient limitation (μ/μn=0.98±0.42) in the coastal upwelling region, with all groups growing at similar rates. In oceanic waters, the growth rate of bulk phytoplankton was lower (μ=0.52±0.16 d−1) and nutrient limited (μ/μn=0.68±0.19 d−1). Diatoms (0.80±0.39 d−1) and Synechococcus (SYN) (0.72±0.25 d−1) grew faster than Prymnesiophyceae (PRYMN) (0.62±0.26 d−1) and PRO (0.46±0.18 d−1). The growth rates of PRO and SYN were moderately nutrient limited (μ/μn=0.81 and 0.91, respectively), while the limitation for diatoms (μ/μn=0.71) and PRYMN (μ/μn=0.37) was more severe. Microzooplankton grazing rate was higher in upwelling (0.68±0.32 d−1) than in oceanic waters (0.37±0.19 d−1), but represented the main loss pathway for phytoplankton in both systems (m/μ=0.90±0.32 and 0.69±0.24, respectively). Carbon flux through phytoplankton, produced and grazed, increased from offshore to coastal (∼2 to ∼200 μg C L−1 d−1), with diatoms dominating the flux in the upwelling region (52%) while PRYMN (40%) and PRO (30%) dominated in the open ocean, This study was supported by the project COCA(REN2000-1471-C02-01/MAR) and EFLUBIO (REN2002-04151-C02-01/MAR). Financial support was provided by a Ph.D. fellowship from the Spanish Ministry of Education and Science to A.G.R.

15 pages, 7 figures, 6 tables, The carbon flux through major phytoplankton groups, defined by their pigment markers, was estimated in two contrasting conditions of the Northwestern Mediterranean open ocean ecosystem: the spring bloom and post-bloom situations (hereafter Bloom and Post-bloom, respectively). During Bloom, surface chlorophyll a (Chl a) concentration was higher and dominated by diatoms (53% of Chl a), while during Post-bloom Synechococcus (42%) and Prymnesiophyceae (29%) became dominant. The seawater dilution technique, coupled to high pressure liquid chromatography (HPLC) analysis of pigments and flow cytometry (FCM), was used to estimate growth and grazing rates of major phytoplankton groups in surface waters. Estimated growth rates were corrected for photoacclimation based on FCM-detected changes in red fluorescence per cell. Given the 30% average decrease in the pigment content per cell between the beginning and the end of the incubations, overlooking photoacclimation would have resulted in a 0.40 d-1 underestimation of phytoplankton growth rates. Corrected average growth rates (μo) were 0.90±0.20 (SD) and 0.40±0.14 d-1 for Bloom and Post-bloom phytoplankton, respectively. Diatoms, Cryptophyceae and Synechococcus were identified as fast-growing groups and Prymnesiophyceae and Prasinophyceae as slow-growing groups across Bloom and Post-bloom conditions. The higher growth rate during Bloom was due to dominance of phytoplankton groups with higher growth rates than those dominating in Post-bloom. Average grazing rates (m) were 0.58±0.20 d-1 (SD) and 0.31±0.07 d-1. The proportion of phytoplankton growth consumed by microzooplankton grazing (m/μo) tended to be lower in Bloom (0.69±0.34) than in Post-bloom (0.80±0.08). The intensity of nutrient limitation experienced by phytoplankton indicated by μo/μn (where μn is the nutrient-amended growth rate), was similar during Bloom (0.78) and Post-bloom (0.73). Primary production from surface water (PP) was estimated with 14C incubations. A combination of PP and Chl a synthesis rate yielded C/Chl a ratios of 34±21 and 168±75 (g:g) for Bloom and Post-bloom, respectively. Transformation of group-specific Chl a fluxes into carbon equivalents confirmed the dominant role of diatoms during Bloom and Synechococcus and Prymnesiophyceae during Post-bloom, This study was supported by the project EFLUBIO (REN2002-04151-C02-01, former Ministry of Science and Technology, Spanish Government) and associated pre-doctoral grant (BES-2003 0895) both funded by the Spanish Ministry of Education and Science

16 pages, 6 figures, 4 tables, We examined the preferences of phytoplankton groups for waters of different trophic status by comparing the distribution of 8 main phytoplankton groups during the spring bloom, postbloom, and late stratification periods in the northwestern Mediterranean. Pigment chemotaxonomy (using the CHEMTAX computer program) was applied to estimate the contribution of Prymnesiophyceae, Pelagophyceae, Synechococcus spp., Prochlorococcus spp., Prasinophyceae, Cryptophyceae, Dinophyceae, and Bacillariophyceae to the chlorophyll a (chl a) stock. Particulate organic nitrogen (PON) concentration was used as an indicator of trophic status. PON at the surface was 1.7 ± 1.4, 0.57 ± 0.02, and 0.37 ± 0.04 μmol l-1 in the bloom, post-bloom, and stratification periods, respectively. During the bloom period, there was a weak stratification and a large chl a biomass. Bacillariophyceae dominated during the bloom period, with a substantial contribution of Prasinophyceae. Prymnesiophyceae and Synechococcus spp. dominated during post-bloom and stratification periods, and Prochlorococcus spp. was a major contributor to biomass in the deep chlorophyll maximum (DCM) during the stratification period. Vertical segregation was also evident for Pelagophyceae, Prymnesiophyceae, and Cryptophyceae, which preferred the DCM to surface layers in non-bloom conditions. The relative distribution of each group combined with PON concentrations in these 3 periods allowed us to calculate a group-specific trophic preference index, which showed its highest values (more eutrophic) for Bacillariophyceae, Prasinophyceae, Cryptophyceae, and Dinophyceae; medium values (mesotrophic) for Prymnesiophyceae, Pelagophyceae, and Synechococcus spp.; and a very low value (oligotrophic) for Prochlorococcus spp. The pigment-group diversity (Shannon index) and evenness were lower during the bloom period, Funding for this study was provided by research grants from the Spanish Ministry of Education and Science (REN2002-04151-C02-01/MAR, REN2002-10809-E/MAR, and REN-2002-10718-E/MAR) and Generalitat of Catalunya (2002PIRA00297). [...] This work has been carried out under the framework of the Convenio de Colaboración between the IEO and the ICM-CSIC