Diatoms are responsible for a large fraction of CO 2 export to deep seawater, a process responsible for low modern-day CO 2 concentrations in surface seawater and the atmosphere. Like other photosynthetic organisms, diatoms have adapted to these low ambient concentrations by operating a CO 2 concentrating mechanism (CCM) to elevate the concentration of CO 2 at the site of fixation. We used mass spectrometric measurements of passive and active cellular carbon fluxes and model simulations of these fluxes to better understand the stoichiometric and energetic efficiency and the physiological architecture of the diatom CCM. The membranes of diatoms are highly permeable to CO 2 , resulting in a large diffusive exchange of CO 2 between the cell and external milieu. An active transport of carbon from the cytoplasm into the chloroplast is the main driver of the diatom CCM. Only one-third of this carbon flux is fixed photosynthetically, and the rest is lost by CO 2 diffusion back to the cytoplasm. Both the passive influx of CO 2 from the external medium and the recycling of the CO 2 leaking out of the chloroplast are achieved by the activity of a carbonic anhydrase enzyme combined with the maintenance of a low concentration of HCO 3 − in the cytoplasm. To achieve the CO 2 concentration necessary to saturate carbon fixation, the CO 2 is most likely concentrated within the pyrenoid, an organelle within the chloroplast where the CO 2 -fixating enzyme is located.climate change | ocean acidification | phytoplankton D iatoms evolved during the Mesozoic era and have gradually become major actors in the oceanic cycles of elements (1). Their precipitation of siliceous frustules now dominates the reverse weathering of silica, and their photosynthetic activity contributes some 40% of modern-day oceanic primary production. Because of their large size and silica ballast, they contribute a major fraction of the downward flux of particulate organic carbon and thus, a major fraction of the export of CO 2 to deep seawater. The low modern-day CO 2 concentration in surface seawater and the atmosphere that results from this biological carbon pump poses a challenge to photosynthetic organisms, including diatoms themselves. Like most photosynthetic organisms, they fix carbon using RubisCO as the carboxylating enzyme. Diatom RubisCOs suffer from the same slow turnover rate and wasteful tendency to fix O 2 as other RubisCOs, and their affinity for CO 2 is only marginally better (2, 3). As in other photosynthetic organisms, the main adaptation of diatoms to the gradual decrease in ambient CO 2 and increase in O 2 over geological times has been the evolution of a CO 2 concentrating mechanism (CCM) to elevate the concentration of CO 2 at the site of fixation by RubisCO (4-7). It is perhaps not an exaggeration to posit that today's atmospheric CO 2 concentration is, in large part, determined by the efficiency of the CCM of diatoms.Despite its importance, the physiology/biochemistry of diatoms has been little studied compared with that of model photo...

The acidification caused by the dissolution of anthropogenic carbon dioxide (CO2) in the ocean changes the chemistry and hence the bioavailability of iron (Fe), a limiting nutrient in large oceanic regions. Here, we show that the bioavailability of dissolved Fe may decline because of ocean acidification. Acidification of media containing various Fe compounds decreases the Fe uptake rate of diatoms and coccolithophores to an extent predicted by the changes in Fe chemistry. A slower Fe uptake by a model diatom with decreasing pH is also seen in experiments with Atlantic surface water. The Fe requirement of model phytoplankton remains unchanged with increasing CO2. The ongoing acidification of seawater is likely to increase the Fe stress of phytoplankton populations in some areas of the ocean.

A typical marine bacterial cell in coastal seawater contains only B200 molecules of mRNA, each of which lasts only a few minutes before being degraded. Such a surprisingly small and dynamic cellular mRNA reservoir has important implications for understanding the bacterium's responses to environmental signals, as well as for our ability to measure those responses. In this perspective, we review the available data on transcript dynamics in environmental bacteria, and then consider the consequences of a small and transient mRNA inventory for functional metagenomic studies of microbial communities.

The photosynthetic picocyanobacteria and eukaryotic microorganisms that inhabit the open ocean must be able to supply iron for their photosynthetic and respiratory needs from the subnanomolar concentrations available in seawater. Neither group appears to produce siderophores, although some coastal cyanobacteria do. This is interpreted as an adaptation to the dilute oceanic environment rather than a phylogenetic constraint, since there are cases in which related taxa from different environments have the capacity to produce siderophores. Most photosynthetic marine microorganisms are presumably, however, capable of accessing iron from strong chelates since the majority of dissolved iron in seawater is complexed by organic ligands, including siderophores. Rather than direct internalization of siderophores and other iron chelates, marine organisms primarily appear to use uptake pathways that involve a reduction step to free bound iron, closely coupled with transport into the cell.

Reliably predicting how coral calcification may respond to ocean acidification and warming depends on our understanding of coral calcification mechanisms. However, the concentration and speciation of dissolved inorganic carbon (DIC) inside corals remain unclear, as only pH has been measured while a necessary second parameter to constrain carbonate chemistry has been missing. Here we report the first carbonate ion concentration ([CO32−]) measurements together with pH inside corals during the light period. We observe sharp increases in [CO32−] and pH from the gastric cavity to the calcifying fluid, confirming the existence of a proton (H+) pumping mechanism. We also show that corals can achieve a high aragonite saturation state (Ωarag) in the calcifying fluid by elevating pH while at the same time keeping [DIC] low. Such a mechanism may require less H+-pumping and energy for upregulating pH compared with the high [DIC] scenario and thus may allow corals to be more resistant to climate change related stressors.

Many microalgae induce an extracellular carbonic anhydrase (eCA), associated with the cell surface, at low carbon dioxide (CO 2 ) concentrations. This enzyme is thought to aid inorganic carbon uptake by generating CO 2 at the cell surface, but alternative roles have been proposed. We developed a new approach to quantify eCA activity in which a reaction-diffusion model is fit to data on 18 O removal from inorganic carbon. In contrast to previous methods, eCA activity is treated as a surface process, allowing the effects of eCA on cell boundary-layer chemistry to be assessed. Using this approach, we measured eCA activity in two marine diatoms (Thalassiosira pseudonana and Thalassiosira weissflogii), characterized the kinetics of this enzyme, and studied its regulation as a function of culture pH and CO 2 concentration. In support of a role for eCA in CO 2 supply, eCA activity specifically responded to low CO 2 rather than to changes in pH or HCO 3 2 , and the rates of eCA activity are nearly optimal for maintaining cell surface CO 2 concentrations near those in the bulk solution. Although the CO 2 gradients abolished by eCA are small (less than 0.5 mM concentration difference between bulk and cell surface), CO 2 uptake in these diatoms is a passive process driven by small concentration gradients. Analysis of the effects of short-term and long-term eCA inhibition on photosynthesis and growth indicates that eCA provides a small energetic benefit by reducing the surface-to-bulk CO 2 gradient. Alternative roles for eCA in CO 2 recovery as HCO 3 2 and surface pH regulation were investigated, but eCA was found to have minimal effects on these processes.To overcome the inefficiencies of Rubisco, many phytoplankton operate a CO 2 -concentrating mechanism (CCM) that increases Rubisco's rate of carbon fixation and reduces oxygen fixation by increasing the concentration of CO 2 around the enzyme. CCMs typically consist of inorganic carbon (C i ) pumps, carbonic anhydrases (CAs) to equilibrate HCO 3 2 and CO 2 , and a compartment to confine Rubisco, such as the pyrenoid or carboxysome, minimizing the volume in which CO 2 is elevated (Badger et al., 1998;Kaplan and Reinhold, 1999;Giordano et al., 2005). Intracellular carbonic anhydrases (iCAs) play multiple roles in CCMs, including the conversion of accumulated HCO 3 2 to CO 2 around Rubisco and the prevention of CO 2 leakage (Badger, 2003). Some organisms also have an extracellular carbonic anhydrase (eCA) associated with the cell wall, plasma membrane, or periplasmic space. The role of eCA has been enigmatic, although it is clearly related to the CCM. In Chlamydomonas reinhardtii, where eCA has been most thoroughly studied, the major eCA (Cah1) is up-regulated at low CO 2 , and its regulatory network includes a transcription factor that induces the expression of other CCM genes as well (Yoshioka et al., 2004;Ohnishi et al., 2010). In other organisms, eCA activity generally increases, in some cases dramatically, at low CO 2 , supporting its association with the CCM, but the...

In the pelagic environment, iron is a scarce but essential micronutrient. The iron acquisition capabilities of selected marine bacteria have been investigated, but the recent proliferation of marine prokaryotic genomes and metagenomes offers a more comprehensive picture of microbial iron uptake pathways in the ocean. Searching these data sets, we were able to identify uptake mechanisms for Fe(3+), Fe(2+) and iron chelates (e.g. siderophore and haem iron complexes). Transport of iron chelates is accomplished by TonB-dependent transporters (TBDTs). After clustering the TBDTs from marine prokaryotic genomes, we identified TBDT clusters for the transport of hydroxamate and catecholate siderophore iron complexes and haem using gene neighbourhood analysis and co-clustering of TBDTs of known function. The genomes also contained two classes of siderophore biosynthesis genes: NRPS (non-ribosomal peptide synthase) genes and NIS (NRPS Independent Siderophore) genes. The most common iron transporters, in both the genomes and metagenomes, were Fe(3+) ABC transporters. Iron uptake-related TBDTs and siderophore biosynthesis genes were less common in pelagic marine metagenomes relative to the genomic data set, in part because Pelagibacter ubique and Prochlorococcus species, which almost entirely lacked these Fe uptake systems, dominate the metagenomes. Our results are largely consistent with current knowledge of iron speciation in the ocean, but suggest that in certain niches the ability to acquire siderophores and/or haem iron chelates is beneficial.

Processes influencing phytoplankton bloom development in the southern Drake Passage were studied using shipboard iron-enrichment incubations conducted across a surface chlorophyll gradient near the Antarctic Peninsula, in a region of water mass mixing. Iron incubation assays showed that Antarctic Circumpolar Current (ACC) waters were severely iron limited, while shelf waters with high ambient iron concentrations (1-2 nmol L 21 ) were iron replete, demonstrating that mixing of the two water masses is a plausible mechanism for generation of the high phytoplankton biomass observed downstream of the Antarctic Peninsula. In downstream highchlorophyll mixed waters, phytoplankton growth rates were also iron limited, although responses to iron addition were generally more moderate as compared to ACC waters. Synthesizing results from all experiments, significant correlations were found between the initial measurements of Photosystem II (PSII) parameters (F v : F m , s PSII , and p) and the subsequent responses of these waters to iron addition. These correlations indicate that PSII parameters can be used to assess the degree of iron stress experienced in these waters and likely in other regions where photoinhibition and nitrogen stress are not confounding factors.