Microbial community transcriptional patterns vary in response to mesoscale forcing in the North Pacific Subtropical Gyre.

The physical and biological dynamics that influence phytoplankton communities in the oligotrophic ocean are complex, changing across broad temporal and spatial scales. Eukaryotic phytoplankton (e.g., diatoms), despite their relatively low abundance in oligotrophic waters, are responsible for a large component of the organic matter flux to the ocean interior. Mesoscale eddies can impact both microbial community structure and function, enhancing primary production and carbon export, but the mechanisms that underpin these dynamics are still poorly understood. Here, mesoscale eddy influences on the taxonomic diversity and expressed functional profiles of surface communities of microeukaryotes and particle-associated heterotrophic bacteria from the North Pacific Subtropical Gyre were assessed over 2 years (spring 2016 and summer 2017). The taxonomic diversity of the microeukaryotes significantly differed by eddy polarity (cyclonic versus anticyclonic) and between sampling seasons/years and was significantly correlated with the taxonomic diversity of particle-associated heterotrophic bacteria. The expressed functional profile of these taxonomically distinct microeukaryotes varied consistently as a function of eddy polarity, with cyclones having a different expression pattern than anticyclones, and between sampling seasons/years. These data suggest that mesoscale forcing, and associated changes in biogeochemistry, could drive specific physiological responses in the resident microeukaryote community, independent of species composition.

Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms.

Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.

Transcriptional patterns of Emiliania huxleyi in the North Pacific Subtropical Gyre reveal the daily rhythms of its metabolic potential.

Emiliania huxleyi is a calcifying haptophyte, contributing to both the organic and inorganic marine carbon cycles. In marine ecosystems, light is a major driver of phytoplankton physiology and ultimately carbon flow through the ecosystem. Here, we analysed a Lagrangian time-series of metatranscriptomes collected in the North Pacific Subtropical Gyre (NPSG) to examine how in situ populations of E. huxleyi modulate gene expression over day-night transitions. Many E. huxleyi contigs had a diel expression pattern, with 61% of contigs clustering into modules with statistically significant diel periodicity. Contigs involved in processes that build up energy stores, like carbon fixation and lipid synthesis, peaked around dawn. In contrast, contigs involved in processes that released energy stores, like respiration and lipid degradation, peaked mid-day and towards dusk. These patterns suggest an orchestrated cycle of building, then consuming energy stores in E. huxleyi populations in the NPSG. Selected contigs related to the cell cycle also exhibited significant diel periodicity consistent with phased modulations of division observed in culture. Overall, these patterns of gene expression suggest a daily metabolic cascade that could contribute to both organic and inorganic carbon flow in this nutrient depleted ecosystem.

SeaFlow data v1, high-resolution abundance, size and biomass of small phytoplankton in the North Pacific.

SeaFlow is an underway flow cytometer that provides continuous shipboard observations of the abundance and optical properties of small phytoplankton (<5 µm in equivalent spherical diameter, ESD). Here we present data sets consisting of SeaFlow-based cell abundance, forward light scatter, and pigment fluorescence of individual cells, as well as derived estimates of ESD and cellular carbon content of picophytoplankton, which includes the cyanobacteria Prochlorococcus, Synechococcus and small-sized Crocosphaera (<5 µm ESD), and picophytoplankton and nanophytoplankton (2-5 µm ESD). Data were collected in surface waters (≈5 m depth) from 27 oceanographic cruises carried out in the Northeast Pacific Ocean between 2010 and 2018. Thirteen cruises provide high spatial resolution (≈1 km) measurements across 32,500 km of the Northeast Pacific Ocean and 14 near-monthly cruises beginning in 2015 provide seasonal distributions at the long-term sampling site (Station ALOHA) of the Hawaii Ocean Time-Series. These data sets expand our knowledge of the current spatial and temporal distributions of picophytoplankton in the surface ocean.

Non-linear Physiology and Gene Expression Responses of Harmful Alga Heterosigma akashiwo to Rising CO2.

Heterosigma akashiwo is a raphidophyte known for forming ichthyotoxic blooms. In order to predict the potential impacts of rising CO2 on H. akashiwo it is necessary to understand the factors influencing growth rates over a range of CO2 concentrations. Here we examined the physiology and gene expression response of H. akashiwo to concentrations from 200 to 1000ppm CO2. Growth rate data were combined from this and previous studies and fit with a CO2 limitation-inhibition model that revealed an apparent growth optimum around 600-800ppm CO2. Physiological changes included a significant increase in C:N ratio at ∼800ppm CO2 and a significant decrease in hydrogen peroxide concentration at ∼1000ppm. Whole transcriptome sequencing of H. akashiwo revealed sharp distinctions in metabolic pathway gene expression between ∼600 and ∼800ppm CO2. Hierarchical clustering by co-expression identified groups of genes with significant correlations to CO2 and growth rate. Genes with significant differential expression with CO2 included carbon concentrating mechanism genes such as beta-carbonic anhydrases and a bicarbonate transporter, which may underpin shifts in physiology. Genes involved in cell motility were significantly changed by both elevated CO2 and growth rate, suggesting that future ocean conditions could modify swimming behavior in this species.

The impact of elevated CO2 on Prochlorococcus and microbial interactions with 'helper' bacterium Alteromonas.

Prochlorococcus is a globally important marine cyanobacterium that lacks the gene catalase and relies on 'helper' bacteria such as Alteromonas to remove reactive oxygen species. Increasing atmospheric CO2 decreases the need for carbon concentrating mechanisms and photorespiration in phytoplankton, potentially altering their metabolism and microbial interactions even when carbon is not limiting growth. Here, Prochlorococcus (VOL4, MIT9312) was co-cultured with Alteromonas (strain EZ55) under ambient (400 p.p.m.) and elevated CO2 (800 p.p.m.). Under elevated CO2, Prochlorococcus had a significantly longer lag phase and greater apparent die-offs after transfers suggesting an increase in oxidative stress. Whole-transcriptome analysis of Prochlorococcus revealed decreased expression of the carbon fixation operon, including carboxysome subunits, corresponding with significantly fewer carboxysome structures observed by electron microscopy. Prochlorococcus co-culture responsive gene 1 had significantly increased expression in elevated CO2, potentially indicating a shift in the microbial interaction. Transcriptome analysis of Alteromonas in co-culture with Prochlorococcus revealed decreased expression of the catalase gene, known to be critical in relieving oxidative stress in Prochlorococcus by removing hydrogen peroxide. The decrease in catalase gene expression was corroborated by a significant ~6-fold decrease in removal rates of hydrogen peroxide from co-cultures. These data suggest Prochlorococcus may be more vulnerable to oxidative stress under elevated CO2 in part from a decrease in ecosystem services provided by heterotrophs like Alteromonas. This work highlights the importance of considering microbial interactions in the context of a changing ocean.The ISME Journal advance online publication, 31 October 2017; doi:10.1038/ismej.2017.189.

Diverse CO2-Induced Responses in Physiology and Gene Expression among Eukaryotic Phytoplankton.

With rising atmospheric CO2, phytoplankton face shifts in ocean chemistry including increased dissolved CO2 and acidification that will likely influence the relative competitive fitness of different phytoplankton taxa. Here we compared the physiological and gene expression responses of six species of phytoplankton including a diatom, a raphidophyte, two haptophytes, and two dinoflagellates to ambient (~400 ppm) and elevated (~800 ppm) CO2. Dinoflagellates had significantly slower growth rates and higher, yet variable, chlorophyll a per cell under elevated CO2. The other phytoplankton tended to have increased growth rates and/or decreased chlorophyll a per cell. Carbon and nitrogen partitioning of cells shifted under elevated CO2 in some species, indicating potential changes in energy fluxes due to changes in carbon concentrating mechanisms (CCM) or photorespiration. Consistent with these phenotypic changes, gene set enrichment analyses revealed shifts in energy, carbon and nitrogen metabolic pathways, though with limited overlap between species in the genes and pathways involved. Similarly, gene expression responses across species revealed few conserved CO2-responsive genes within CCM and photorespiration categories, and a survey of available transcriptomes found high diversity in biophysical CCM and photorespiration expressed gene complements between and within the four phyla represented by these species. The few genes that displayed similar responses to CO2 across phyla were from understudied gene families, making them targets for further research to uncover the mechanisms of phytoplankton acclimation to elevated CO2. These results underscore that eukaryotic phytoplankton have diverse gene complements and gene expression responses to CO2 perturbations and highlight the value of cross-phyla comparisons for identifying gene families that respond to environmental change.

Acclimation conditions modify physiological response of the diatom Thalassiosira pseudonana to elevated CO2 concentrations in a nitrate-limited chemostat.

Diatoms are responsible for a large proportion of global carbon fixation, with the possibility that they may fix more carbon under future levels of high CO2 . To determine how increased CO2 concentrations impact the physiology of the diatom Thalassiosira pseudonana Hasle et Heimdal, nitrate-limited chemostats were used to acclimate cells to a recent past (333 ± 6 µatm) and two projected future concentrations (476 ± 18 µatm, 816 ± 35 µatm) of CO2 . Samples were harvested under steady-state growth conditions after either an abrupt (15-16 generations) or a longer acclimation process (33-57 generations) to increased CO2 concentrations. The use of un-bubbled chemostat cultures allowed us to calculate the uptake ratio of dissolved inorganic carbon relative to dissolved inorganic nitrogen (DIC:DIN), which was strongly correlated with fCO2 in the shorter acclimations but not in the longer acclimations. Both CO2 treatment and acclimation time significantly affected the DIC:DIN uptake ratio. Chlorophyll a per cell decreased under elevated CO2 and the rates of photosynthesis and respiration decreased significantly under higher levels of CO2 . These results suggest that T. pseudonana shifts carbon and energy fluxes in response to high CO2 and that acclimation time has a strong effect on the physiological response.