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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.

Biological nitrogen fixation constitutes the main input of fixed nitrogen to Earth’s ecosystems, and its isotope effect is a key parameter in isotope-based interpretations of the N cycle. The nitrogen isotopic composition (δ ¹⁵N) of newly fixed N is currently believed to be ∼–1‰, based on measurements of organic matter from diazotrophs using molybdenum (Mo)-nitrogenases. We show that the vanadium (V)- and iron (Fe)-only “alternative” nitrogenases produce fixed N with significantly lower δ ¹⁵N (–6 to –7‰). An important contribution of alternative nitrogenases to N ₂ fixation provides a simple explanation for the anomalously low δ ¹⁵N (<–2‰) in sediments from the Cretaceous Oceanic Anoxic Events and the Archean Eon. A significant role for the alternative nitrogenases over Mo-nitrogenase is also consistent with evidence of Mo scarcity during these geologic periods, suggesting an additional dimension to the coupling between the global cycles of trace elements and nitrogen.

Diatoms are responsible for a large fraction of CO₂ export to deep seawater, a process responsible for low modern-day CO₂ concentrations in surface seawater and the atmosphere. Like other photosynthetic organisms, diatoms have adapted to these low ambient concentrations by operating a CO₂ concentrating mechanism (CCM) to elevate the concentration of CO₂ 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 CO₂, resulting in a large diffusive exchange of CO₂ 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 CO₂ diffusion back to the cytoplasm. Both the passive influx of CO₂ from the external medium and the recycling of the CO₂ leaking out of the chloroplast are achieved by the activity of a carbonic anhydrase enzyme combined with the maintenance of a low concentration of HCO₃⁻ in the cytoplasm. To achieve the CO₂ concentration necessary to saturate carbon fixation, the CO₂ is most likely concentrated within the pyrenoid, an organelle within the chloroplast where the CO₂-fixating enzyme is located.

We derive explicit expressions of the Revelle factor and several other buffer factors of interest to climate change scientists and those studying ocean acidification. These buffer factors quantify the sensitivity of CO2 and H+ concentrations ([CO2] and [H+]) and CaCO3 saturation (Ω) to changes in dissolved inorganic carbon concentration (DIC) and alkalinity (Alk). The explicit expressions of these buffer factors provide a convenient means to compare the degree of buffering of [CO2], [H+], and Ω in different regions of the oceans and at different times in the future and to gain insight into the buffering mechanisms. All six buffer factors have roughly similar values, and all reach an absolute minimum when DIC = Alk (pH ∼ 7.5). Surface maps of the buffer factors generally show stronger buffering capacity in the subtropical gyres relative to the polar regions. As the dissolution of anthropogenic CO2 increases the DIC of surface seawater over the next century, all the buffer factors will decrease, resulting in a much greater sensitivity to local variations in DIC and Alk. For example, diurnal and seasonal variations in pH and Ω caused by photosynthesis and respiration will be greatly amplified. Buffer factors provide convenient means to quantify the effect that changes in DIC and Alk have on seawater chemistry. They should also help illuminate the role that various physical and biological processes have in determining the oceanic response to an increase in atmospheric CO2.

The formation of methylmercury (MeHg), which is biomagnified in aquatic food chains and poses a risk to human health, is effected by some iron- and sulfate-reducing bacteria (FeRB and SRB) in anaerobic environments. However, very little is known regarding the mechanism of uptake of inorganic Hg by these organisms, in part because of the inherent difficulty in measuring the intracellular Hg concentration. By using the FeRB Geobacter sulfurreducens and the SRB Desulfovibrio desulfuricans ND132 as model organisms, we demonstrate that Hg(II) uptake occurs by active transport. We also establish that Hg(II) uptake by G. sulfurreducens is highly dependent on the characteristics of the thiols that bind Hg(II) in the external medium, with some thiols promoting uptake and methylation and others inhibiting both. The Hg(II) uptake system of D. desulfuricans has a higher affinity than that of G. sulfurreducens and promotes Hg methylation in the presence of stronger complexing thiols. We observed a tight coupling between Hg methylation and MeHg export from the cell, suggesting that these two processes may serve to avoid the build up and toxicity of cellular Hg. Our results bring up the question of whether cellular Hg uptake is specific for Hg(II) or accidental, occurring via some essential metal importer. Our data also point at Hg(II) complexation by thiols as an important factor controlling Hg methylation in anaerobic environments.

Carbonic anhydrase, a zinc enzyme found in organisms from all kingdoms, catalyses the reversible hydration of carbon dioxide and is used for inorganic carbon acquisition by phytoplankton. In the oceans, where zinc is nearly depleted, diatoms use cadmium as a catalytic metal atom in cadmium carbonic anhydrase (CDCA). Here we report the crystal structures of CDCA in four distinct forms: cadmium-bound, zinc-bound, metal-free and acetate-bound. Despite lack of sequence homology, CDCA is a structural mimic of a functional β-carbonic anhydrase dimer, with striking similarity in the spatial organization of the active site residues. CDCA readily exchanges cadmium and zinc at its active site—an apparently unique adaptation to oceanic life that is explained by a stable opening of the metal coordinating site in the absence of metal. Given the central role of diatoms in exporting carbon to the deep sea, their use of cadmium in an enzyme critical for carbon acquisition establishes a remarkable link between the global cycles of cadmium and carbon. Cadmium fills a niche A major part of the carbon export from the atmosphere to the deep ocean is carried out by marine phytoplankton, using carbonic anhydrase to catalyse the reversible hydration of carbon dioxide. The active site of this enzyme usually contains zinc, but some diatoms substitute cadmium — usually regarded as a toxic element — as the catalytic metal atom. The X-ray crystal structures of four forms of this enzyme from the diatom Thalassiosira weissflogii — cadmium-bound, zinc-bound, metal-free and acetate-bound — have now been determined. The enzyme can easily exchange metals at its catalytic centre, suggesting that marine diatoms use of cadmium when zinc is rare, a considerable competitive advantage in the metal-poor environment of the oceans. The X-ray crystal structures of the cadmium-bound, zinc-bound, metal-free and acetate-bound forms of cadmium carbonic anhydrase are solved; the enzyme can incorporate either zinc or cadmium as its metal centre and can easily exchange one metal for the other.

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.

Dissolution of anthropogenic CO ₂ increases the partial pressure of CO ₂ (p CO ₂) and decreases the pH of seawater. The rate of Fe uptake by the dominant N ₂-fixing cyanobacterium Trichodesmium declines as pH decreases in metal-buffered medium. The slower Fe-uptake rate at low pH results from changes in Fe chemistry and not from a physiological response of the organism. Contrary to previous observations in nutrient-replete media, increasing p CO ₂/decreasing pH causes a decrease in the rates of N ₂ fixation and growth in Trichodesmium under low-Fe conditions. This result was obtained even though the bioavailability of Fe was maintained at a constant level by increasing the total Fe concentration at low pH. Short-term experiments in which p CO ₂ and pH were varied independently showed that the decrease in N ₂ fixation is caused by decreasing pH rather than by increasing p CO ₂ and corresponds to a lower efficiency of the nitrogenase enzyme. To compensate partially for the loss of N ₂ fixation efficiency at low pH, Trichodesmium synthesizes additional nitrogenase. This increase comes partly at the cost of down-regulation of Fe-containing photosynthetic proteins. Our results show that although increasing p CO ₂ often is beneficial to photosynthetic marine organisms, the concurrent decreasing pH can affect primary producers negatively. Such negative effects can occur both through chemical mechanisms, such as the bioavailability of key nutrients like Fe, and through biological mechanisms, as shown by the decrease in N ₂ fixation in Fe-limited Trichodesmium .

Biological nitrogen fixation, the main natural input of fixed nitrogen into the biosphere, is catalyzed by Mo-, V-, or Fe-only nitrogenase metalloenzymes. Although “alternative” V- and Fe-only nitrogenase genes are found in many environments, the contribution of these isoenzymes to N₂ fixation is unknown. Here we present a new method (ISARA, isotopic acetylene reduction assay) that distinguishes canonical Mo and alternative nitrogenase activities based on in vivo ¹³C fractionation of acetylene reduction to ethylene (¹³εMₒ = 13.1–14.7 ‰, ¹³εV = 7.5–8.8 ‰, ¹³εFₑ = 5.8–6.5 ‰). ISARA analyses indicate significant contributions of alternative nitrogen fixation in boreal cyanolichens and salt marshes (~10–40 % acetylene reduction, ~20–55 % N₂ fixed). These results affect the quantitative interpretation of natural abundance ¹⁵N data or traditional acetylene reduction assays. They also invite a reexamination of the conditions under which the different nitrogenase isozymes are active and suggest significant interactions between the cycles of nitrogen and trace metals.

It is common for bacteria to produce chemically diverse sets of small Fe-binding molecules called siderophores. Studies of siderophore bioinorganic chemistry have firmly established the role of these molecules in Fe uptake and provided great insight into Fe complexation. However, we still do not fully understand why microbes make so many siderophores. In many cases, the release of small structural variants or siderophore fragments has been ignored, or considered as an inefficiency of siderophore biosynthesis. Yet, in natural settings, microbes live in complex consortia and it has become increasingly clear that the secondary metabolite repertoires of microbes reflect this dynamic environment. Multiple siderophore production may, therefore, provide a window into microbial life in the wild. This minireview focuses on three biochemical routes by which multiple siderophores can be released by the same organism—multiple biosynthetic gene clusters, fragment release, and precursor-directed biosynthesis—and highlights emergent themes related to each. We also emphasize the plurality of reasons for multiple siderophore production, which include enhanced iron uptake via synergistic siderophore use, microbial warfare and cooperation, and non-classical functions such as the use of siderophores to take up metals other than Fe.