Francois Ribalet

Ferritin is used for iron storage in bloom-forming marine pennate diatoms

Primary productivity in 30–40% of the world’s oceans is limited by availability of the micronutrient iron. Regions with chronically low iron concentrations are sporadically pulsed with new iron inputs by way of dust or lateral advection from continental margins. Addition of iron to surface waters in these areas induces massive phytoplankton blooms dominated primarily by pennate diatoms. Here we provide evidence that the bloom-forming pennate diatoms Pseudo-nitzschia and Fragilariopsis use the iron-concentrating protein, ferritin, to safely store iron. Ferritin has not been reported previously in any member of the Stramenopiles, a diverse eukaryotic lineage that includes unicellular algae, macroalgae and plant parasites. Phylogenetic analyses suggest that ferritin may have arisen in this small subset of diatoms through a lateral gene transfer. The crystal structure and functional assays of recombinant ferritin derived from Pseudo-nitzschia multiseries reveal a maxi-ferritin that exhibits ferroxidase activity and binds iron. The protein is predicted to be targeted to the chloroplast to control the distribution and storage of iron for proper functioning of the photosynthetic machinery. Abundance of Pseudo-nitzschia ferritin transcripts is regulated by iron nutritional status, and is closely tied to the loss and recovery of photosynthetic competence. Enhanced iron storage with ferritin allows the oceanic diatom Pseudo-nitzschia granii to undergo several more cell divisions in the absence of iron than the comparably sized, oceanic centric diatom Thalassiosira oceanica. Ferritin in pennate diatoms probably contributes to their success in chronically low-iron regions that receive intermittent iron inputs, and provides an explanation for the importance of these organisms in regulating oceanic CO2 over geological timescales.

Unveiling a phytoplankton hotspot at a narrow boundary between coastal and offshore waters

In terrestrial ecosystems, transitional areas between different plant communities (ecotones) are formed by steep environmental gradients and are commonly characterized by high species diversity and primary productivity, which in turn influences the foodweb structure of these regions. Whether comparable zones of elevated diversity and productivity characterize ecotones in the oceans remains poorly understood. Here we describe a previously hidden hotspot of phytoplankton diversity and productivity in a narrow but seasonally persistent transition zone at the intersection of iron-poor, nitrate-rich offshore waters and iron-rich, nitrate-poor coastal waters of the Northeast Pacific Ocean. Novel continuous measurements of phytoplankton cell abundance and composition identified a complex succession of blooms of five distinct size classes of phytoplankton populations within a 100-km–wide transition zone. The blooms appear to be fueled by natural iron enrichment of offshore communities as they are transported toward the coast. The observed succession of phytoplankton populations is likely driven by spatial gradients in iron availability or time since iron enrichment. Regardless of the underlying mechanism, the resulting communities have a strong impact on the regional biogeochemistry as evidenced by the low partial pressure of CO2 and the nearly complete depletion of nutrients. Enhanced phytoplankton productivity and diversity associated with steep environmental gradients are expected wherever water masses with complementary nutrient compositions mix to create a region more favorable for phytoplankton growth. The ability to detect and track these important but poorly characterized marine ecotones is critical for understanding their impact on productivity and ecosystem structure in the oceans.

Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre

Significance The cyanobacterium Prochlorococcus is the most abundant photosynthetic organism in the oceans, driving marine food webs and biogeochemistry. Estimates of Prochlorococcus cell mortality and cell production are critical to determine how organic matter is transferred into the food web. Using novel high-resolution sampling methods on two winter-time cruises, we show that the daily production of Prochlorococcus cells in surface waters of the subtropical Pacific gyre is consistently balanced by their nightly consumption by other organisms. These synchronized loss processes suggest that Prochlorococcus-derived organic matter stabilizes multiple species interactions, from viruses to grazers. The observed resilience of this synchronized food web dynamic as temperature increased within the gyre suggests that ecosystem stability may persist in future warmer oceans. Theoretical studies predict that competition for limited resources reduces biodiversity to the point of ecological instability, whereas strong predator/prey interactions enhance the number of coexisting species and limit fluctuations in abundances. In open ocean ecosystems, competition for low availability of essential nutrients results in relatively few abundant microbial species. The remarkable stability in overall cell abundance of the dominant photosynthetic cyanobacterium Prochlorococcus is assumed to reflect a simple food web structure strongly controlled by grazers and/or viruses. This hypothesized link between stability and ecological interactions, however, has been difficult to test with open ocean microbes because sampling methods commonly have poor temporal and spatial resolution. Here we use continuous techniques on two different winter-time cruises to show that Prochlorococcus cell production and mortality rates are tightly synchronized to the day/night cycle across the subtropical Pacific Ocean. In warmer waters, we observed harmonic oscillations in cell production and mortality rates, with a peak in mortality rate consistently occurring ∼6 h after the peak in cell production. Essentially no cell mortality was observed during daylight. Our results are best explained as a synchronized two-component trophic interaction with the per-capita rates of Prochlorococcus consumption driven either directly by the day/night cycle or indirectly by Prochlorococcus cell production. Light-driven synchrony of food web dynamics in which most of the newly produced Prochlorococcus cells are consumed each night likely enforces ecosystem stability across vast expanses of the open ocean.

Two distinct pools of B12 analogs reveal community interdependencies in the ocean

Significance Cobalamin (vitamin B12)-dependent organisms span all domains of life, making procurement of the vitamin from the few prokaryotic producers an essential function in organismal interactions. Yet not all key producers of cobalamin have been identified in the ocean. We show that in the marine environment, select heterotrophic bacteria and Thaumarchaeota produce cobalamin, while Cyanobacteria, the most abundant phytoplankton on earth, supply and use pseudocobalamin. These chemically distinct cofactors support different members of the microbial community because they are not interchangeable as cofactors in enzymes. Our findings identify key organisms supporting cobalamin-based interdependencies that underpin primary production and microbial interactions in the ocean. Organisms within all domains of life require the cofactor cobalamin (vitamin B12), which is produced only by a subset of bacteria and archaea. On the basis of genomic analyses, cobalamin biosynthesis in marine systems has been inferred in three main groups: select heterotrophic Proteobacteria, chemoautotrophic Thaumarchaeota, and photoautotrophic Cyanobacteria. Culture work demonstrates that many Cyanobacteria do not synthesize cobalamin but rather produce pseudocobalamin, challenging the connection between the occurrence of cobalamin biosynthesis genes and production of the compound in marine ecosystems. Here we show that cobalamin and pseudocobalamin coexist in the surface ocean, have distinct microbial sources, and support different enzymatic demands. Even in the presence of cobalamin, Cyanobacteria synthesize pseudocobalamin—likely reflecting their retention of an oxygen-independent pathway to produce pseudocobalamin, which is used as a cofactor in their specialized methionine synthase (MetH). This contrasts a model diatom, Thalassiosira pseudonana, which transported pseudocobalamin into the cell but was unable to use pseudocobalamin in its homolog of MetH. Our genomic and culture analyses showed that marine Thaumarchaeota and select heterotrophic bacteria produce cobalamin. This indicates that cobalamin in the surface ocean is a result of de novo synthesis by heterotrophic bacteria or via modification of closely related compounds like cyanobacterially produced pseudocobalamin. Deeper in the water column, our study implicates Thaumarchaeota as major producers of cobalamin based on genomic potential, cobalamin cell quotas, and abundance. Together, these findings establish the distinctive roles played by abundant prokaryotes in cobalamin-based microbial interdependencies that sustain community structure and function in the ocean.

Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera

The temporal dynamics of phytoplankton growth and activity have large impacts on fluxes of matter and energy, yet obtaining in situ metabolic measurements of sufficient resolution for even dominant microorganisms remains a considerable challenge. We performed Lagrangian diel sampling with synoptic measurements of population abundances, dinitrogen (N2) fixation, mortality, productivity, export and transcription in a bloom of Crocosphaera over eight days in the North Pacific Subtropical Gyre (NPSG). Quantitative transcriptomic analyses revealed clear diel oscillations in transcript abundances for 34% of Crocosphaera genes identified, reflecting a systematic progression of gene expression in diverse metabolic pathways. Significant time-lagged correspondence was evident between nifH transcript abundance and maximal N2 fixation, as well as sepF transcript abundance and cell division, demonstrating the utility of transcriptomics to predict the occurrence and timing of physiological and biogeochemical processes in natural populations. Indirect estimates of carbon fixation by Crocosphaera were equivalent to 11% of net community production, suggesting that under bloom conditions this diazotroph has a considerable impact on the wider carbon cycle. Our cross-scale synthesis of molecular, population and community-wide data underscores the tightly coordinated in situ metabolism of the keystone N2-fixing cyanobacterium Crocosphaera, as well as the broader ecosystem-wide implications of its activities.

flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data

MOTIVATION Flow cytometry is a widely used technique among biologists to study the abundances of populations of microscopic algae living in aquatic environments. A new generation of high-frequency flow cytometers collects up to several hundred samples per day and can run continuously for several weeks. Automated computational methods are needed to analyze the different phytoplankton populations present in each sample. Software packages in the programming environment R provide powerful tools for conducting such analyses. RESULTS We introduce flowPhyto, an R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data. AVAILABILITY Freely accessible at http://www.bioconductor.org.

Collaborative Science Workflows in SQL

SQLShare is a Web-based application that emphasizes a simple upload-query-share protocol over conventional database design and uses ad hoc interactive query over general-purpose programming. Here, a case study examines the use of SQLShare as an alternative to script-based scientific workflows for a project in observational biological oceanography.

Scalable Clustering Algorithms for Continuous Environmental Flow Cytometry

MOTIVATION Recent technological innovations in flow cytometry now allow oceanographers to collect high-frequency flow cytometry data from particles in aquatic environments on a scale far surpassing conventional flow cytometers. The SeaFlow cytometer continuously profiles microbial phytoplankton populations across thousands of kilometers of the surface ocean. The data streams produced by instruments such as SeaFlow challenge the traditional sample-by-sample approach in cytometric analysis and highlight the need for scalable clustering algorithms to extract population information from these large-scale, high-frequency flow cytometers. RESULTS We explore how available algorithms commonly used for medical applications perform at classification of such a large-scale, environmental flow cytometry data. We apply large-scale Gaussian mixture models to massive datasets using Hadoop. This approach outperforms current state-of-the-art cytometry classification algorithms in accuracy and can be coupled with manual or automatic partitioning of data into homogeneous sections for further classification gains. We propose the Gaussian mixture model with partitioning approach for classification of large-scale, high-frequency flow cytometry data. AVAILABILITY AND IMPLEMENTATION Source code available for download at https://github.com/jhyrkas/seaflow_cluster, implemented in Java for use with Hadoop. CONTACT hyrkas@cs.washington.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Dynamics of Teleaulax-like cryptophytes during the decline of a red water bloom in the Columbia River Estuary

The mixotrophic ciliate, Mesodinium rubrum, is a globally distributed ciliate that relies on the acquisition and use of chloroplasts derived from its cryptophyte prey. The ecology and physiology of the cryptophytes is not well known, nor is it clear how their growth influences M. rubrum blooms. A 4-week survey was conducted in the Columbia River estuary in 2013 during the decline of the annual M. rubrum bloom to better understand how environmental factors influence the dynamics of the cryptophyte prey, Teleaulax amphioxeia. Abundances and division rates of freeliving Teleaulax-like cryptophytes were continuously monitored using flow cytometry. Cryptophyte division rates, estimated in situ for the first time using a size-structured division rate model, ranged from 0.2 to 1.5 d, with the highest rates observed in accordance with high abundances. These division rates were positively correlated with concentrations of dissolved inorganic nitrogen and phosphorus, suggesting nutrient availability limited the growth of Teleaulax-like cryptophytes at that time. Assuming a minimum ingestion rate of ~1 cryptophyte ciliate day, the growth of M. rubrum may have been limited by the low abundance of Teleaulax-like cryptophytes during the M. rubrum bloom decline. Our results highlight the importance of prey availability for understanding the dynamics of red water blooms.

Biological production, export efficiency, and phytoplankton communities across 8000 km of the South Atlantic

In situ oxygen tracers (triple oxygen isotope and oxygen/argon ratios) were used to evaluate meridional trends in surface biological production and export efficiency across ~8000 km of the tropical and subtropical South Atlantic in March-May 2013. We used observations of pico-, nano-, and microphytoplankton to evaluate community structure and diversity, and assessed the relationships of these characteristics with production, export efficiency, and particulate organic carbon (POC) fluxes. Rates of productivity were relatively uniform along most of the transect with net community production (NCP) between 0 and 10 mmol O2 m-2 d-1, gross primary production (GPP) between 40 and 100 mmol O2 m-2 d-1, and NCP/GPP, a measure of export efficiency, ranging from 0.1-0.2 (0.05-0.1 in carbon units). However, notable exceptions to this basin scale homogeneity included two locations with highly enhanced NCP and export efficiency compared to surrounding regions. Export of POC and particulate nitrogen, derived from sediment traps, correlated with GPP across the transect, over which the surface community was dominated numerically by picophytoplankton. NCP, however, did not correlate with POC flux; the mean difference between NCP and POC flux was similar to published estimates of DOC export from the surface ocean. The interrelated rates of production presented in this work contribute to the understanding, building on the framework of better-studied ocean basins, of how carbon is biologically transported between the atmosphere and the deep ocean.