Lee Karp-Boss

Plankton networks driving carbon export in the oligotrophic ocean.

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Spectral backscattering properties of marine phytoplankton cultures.

The backscattering properties of marine phytoplankton, which are assumed to vary widely with differences in size, shape, morphology and internal structure, have been directly measured in the laboratory on a very limited basis. This work presents results from laboratory analysis of the backscattering properties of thirteen phytoplankton species from five major taxa. Optical measurements include portions of the volume scattering function (VSF) and the absorption and attenuation coefficients at nine wavelengths. The VSF was used to obtain the backscattering coefficient for each species, and we focus on intra- and interspecific variability in spectral backscattering in this work. Ancillary measurements included chlorophyll-a concentration, cell concentration, and cell size, shape and morphology via microscopy for each culture. We found that the spectral backscattering properties of phytoplankton deviate from theory at wavelengths where pigment absorption is significant. We were unable to detect an effect of cell size on the spectral shape of backscattering, but we did find a relationship between cell size and both the backscattering ratio and backscattering cross-section. While particulate backscattering at 555 nm was well correlated to chlorophyll-a concentration for any given species, the relationship was highly variable between species. Results from this work indicate that phytoplankton cells may backscatter light at significantly higher efficiencies than what is predicted by Mie theory, which has important implications for closing the underwater and remotely sensed light budget.

Sexual reproduction in the marine centric diatom Ditylum brightwellii (Bacillariophyta)

Ditylum brightwellii (T. West) Grunow in Van Heurck is now a model organism for population genetic studies of marine phytoplankton, but observations of sexual reproduction in this species are sparse and there are controversial aspects to the identification of its gametes. Culture studies and field observations of D. brightwellii from Wadsworth Cove (Castine), Maine (USA) showed that it was homothallic, producing and releasing two naked, spherical eggs from each oogonium and 64 uniflagellate sperm per spermatogonangium. Eggs and sperm were produced by larger and smaller cells, respectively, and were formed in nutrient-replete medium, without special procedures for induction. Size regeneration was achieved from a putatively fertilized egg via a true auxospore. Vegetative cell enlargement occurred in senescent cultures and resulted in intermediate-sized cells. The size structure of natural populations of D. brightwellii was monitored weekly in autumn 2004 and was unimodal throughout, with slight shifts in size accompanying low levels of gametogenesis and auxosporulation. Gametogenesis and size reduction ceased with the onset of winter. Previous reports concerning gametogenesis and auxosporulation in Ditylum are reinterpreted on the basis of our studies.

Nutrient transport and acquisition by diatom chains in a moving fluid

A computational model of the flexible diatom chains and nutrient dynamics in a moving fluid is presented in our dissertation. The chain is modelled as a collection of neutrally-buoyant cylinders connected by filaments. The motion of the fluid is governed by the incompressible Navier-Stokes equations. We use the immersed boundary method to couple the interaction of non-motile diatom chains with the viscous, incompressible, moving fluid, and with the nutrient that is advected by and diffusing in the fluid and also consumed by the cells. We apply our model to study the impact of length and flexibility of chains on nutrient uptake and transport in a turbulent environment. In those studies we consider two types of distributions of nutrient. One, where nutrient is introduced into the medium through point sources randomly distributed in space and time. Other, where initial nutrient concentration is uniform. The presented results suggest that the nutrient uptake per cell in a chain and nutrient fluxes towards cells increase with decreasing flexibility of the chain. The numerical experiments further suggest that the cells on the exterior of chains experience larger enhancement of nutrient flux due to flow than the cells on the interior. Our numerical solutions for nutrient mass transfer to diatom cells fall within the bounds of the known analytic solutions for limiting cases. These results confirm intuitive predictions, and open the door to possible experimental work to measure the nutrient transport and acquisition for chains with different elasticities.

Distributions and Variability of Particulate Organic Matter in a Coastal Upwelling System

[1] In this study we examined the spatial and temporal variability of particulate organic material (POM) off Oregon during the upwelling season. High-resolution vertical profiling of beam attenuation was conducted along two cross-shelf transects. One transect was located in a region where the shelf is relatively uniform and narrow (off Cascade Head (CH)); the second transect was located in a region where the shelf is shallow and wide (off Cape Perpetua (CP)). In addition, water samples were collected for direct analysis of chlorophyll, particulate organic carbon (POC), and particulate organic nitrogen (PON). Beam attenuation was highly correlated with POC and PON. Striking differences in distribution patterns and characteristics of POM were observed between CH and CP. Off CH, elevated concentrations of chlorophyll and POC were restricted to the inner shelf and were highly variable in time. The magnitude of the observed short-term temporal variability was of the same order as that of the seasonal variability reported in previous studies. Elevated concentrations of nondegraded chlorophyll and POM were observed near the bottom. Downwelling and rapid sinking are two mechanisms by which phytoplankton cells can be delivered to the bottom before being degraded. POM may be then transported across the shelf via the benthic nepheloid layer. Along the CP transect, concentrations of POM were generally higher than they were along the CH transect and extended farther across the shelf. Characteristics of surface POM, namely, C:N ratios and carbon:chlorophyll ratios, differed between the two sites. These differences can be attributed to differences in shelf circulation. INDEX TERMS: 4279 Oceanography: General: Upwelling and convergences; 4219 Oceanography: General: Continental shelf processes; 4805 Oceanography: Biological and Chemical: Biogeochemical cycles (1615); KEYWORDS: POM, upwelling, beam attenuation

Hydrodynamic effects of spines: A different spin

Many small planktonic organisms bear spines, some of whose potential functions have been explored, for example, in increasing drag during gravitational settling or in defense against predators. Using an immersed boundary framework, we performed computational fluid dynamic simulations that examine the rotational dynamics of model diatoms in shear flows with varying spine number, length, and angle. We found that the motion of spined cells could be accurately predicted from simple theory for motion of spheroids by applying that theory to the smallest spheroid that could inscribe the cell inclusive of its spines. The poorest fits were for small numbers or extreme angles of spines that left large volumes of the inscribing spheroid unoccupied by any spines. Although the present work provides a simple means of predicting motions of rigid, spined cells in shear flows, the effects of spines on nutrient exchange remain to be explored.

Allelopathic effects of Alexandrium fundyense (Dinophyceae) on Thalassiosira cf. gravida (Bacillariophyceae): a matter of size

Allelopathic interactions among phytoplankton are well documented. The potency of allelopathic species and responses of target species to allelochemicals are quite variable, however, limiting full understanding of the role these interactions may play in nature. One trait that may influence the sensitivity of an individual to allelochemicals is cell size. The few studies that have examined relationships between cell size and susceptibility to allelochemicals have compared different species and thus could not distinguish between the role of size and species‐specific physiological differences. Culturing an actively sexually reproducing diatom allowed us to focus on the influence of target cell size within a single species. We studied growth and nutrient acquisition by the chain‐forming Thalassiosira cf. gravida Clever in the presence and absence of allelochemicals released by Alexandrium fundyense Balech as a function of T. cf. gravida cell size. Upon exposure to filtrate of A. fundyense, T. cf. gravida cultures “bleached” and both growth and nutrient utilization ceased for up to 4 d. The magnitude of the effect was dependent on filtrate concentration and T. cf. gravida cell surface area:volume ratio. The greatest inhibition was observed on the smallest cells, while T. cf. gravida cultures that had undergone cell enlargement via sexual reproduction were least sensitive to A. fundyense filtrate. These results demonstrate that competitor cell size, independent from taxonomy, may influence the outcome of allelopathic interactions. The findings presented here suggest a potential ecological impact of diatom cell size reduction and sexual reproduction that has not yet been described and that may be important in determining diatom survival and success.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems.

The Elongated, the Squat and the Spherical: Selective Pressures for Phytoplankton Shape

While it is commonly accepted that the shape of a phytoplankter is not a fortuitous experiment of nature, the selective value of cell shape remains poorly understood. Here, we focus on diffusion as a primary selective force and ask how it might have influenced cell shapes? We describe phytoplankton cells as a series of spheroids and cylinders with varying aspect ratios and use published analytical solutions to examine the flux of solutes to spheroids and cylinders relative to the flux to a sphere with an equal volume. We then compare diffusional fluxes to prolate and oblate spheroids, as well as elongated cylinders and disks, of equal surface area and volume. Results from this analysis show that for the same volume and surface area, prolate spheroids or elongated cylinders experience a higher flux compared to oblate spheroids and disks. A sphere will always experience the lowest flux compared to other spheroids or cylindrical shapes of the same volume, because a sphere has the lowest surface area per unit volume. Based on this analysis, we propose that diffusion has set a selective pressure for rod-shaped cells rather than giving rise to any shape that equally maximizes the surface area to volume ratio. This theoretical prediction is consistent with observations that rod-shaped cells are more prevalent among microphytoplankton compared to disk-like or spherical cells. Other selective forces have likely contributed to shape selection in phytoplankton though their role remains speculative.

Judging Diatoms by Their Cover: Variability in Local Elasticity of Lithodesmium undulatum Undergoing Cell Division

Unique features of diatoms are their intricate cell covers (frustules) made out of hydrated, amorphous silica. The frustule defines and maintains cell shape and protects cells against grazers and pathogens, yet it must allow for cell expansion during growth and division. Other siliceous structures have also evolved in some chain-forming species as means for holding neighboring cells together. Characterization and quantification of mechanical properties of these structures are crucial for the understanding of the relationship between form and function in diatoms, but thus far only a handful of studies have addressed this issue. We conducted micro-indentation experiments, using atomic force microscopy (AFM), to examine local variations in elastic (Youngs) moduli of cells and linking structures in the marine, chain-forming diatom Lithodesmium undulatum. Using a fluorescent tracer that is incorporated into new cell wall components we tested the hypothesis that new siliceous structures differ in elastic modulus from their older counterparts. Results show that the local elastic modulus is a highly dynamic property. Elastic modulus of stained regions was significantly lower than that of unstained regions, suggesting that newly formed cell wall components are generally softer than the ones inherited from the parent cells. This study provides the first evidence of differentiation in local elastic properties in the course of the cell cycle. Hardening of newly formed regions may involve incorporation of additional, possibly organic, material but further studies are needed to elucidate the processes that regulate mechanical properties of the frustule during the cell cycle.