Fundamentally different global marine nitrogen cycling in response to severe ocean deoxygenation.

The present-day marine nitrogen (N) cycle is strongly regulated by biology. Deficiencies in the availability of fixed and readily bioavailable nitrogen relative to phosphate (P) in the surface ocean are largely corrected by the activity of diazotrophs. This feedback system, termed the "nitrostat," is thought to have provided close regulation of fixed-N speciation and inventory relative to P since the Proterozoic. In contrast, during intervals of intense deoxygenation such as Cretaceous ocean anoxic event (OAE) 2, a few regional sedimentary δ15N records hint at the existence of a different mode of marine N cycling in which ammonium plays a major role in regulating export production. However, the global-scale dynamics during this time remain unknown. Here, using an Earth System model and taking the example of OAE 2, we provide insights into the global marine nitrogen cycle under severe ocean deoxygenation. Specifically, we find that the ocean can exhibit fundamental transitions in the species of nitrogen dominating the fixed-N inventory--from nitrate (NO3-) to ammonium (NH4+)--and that as this transition occurs, the inventory can partially collapse relative to P due to progressive spatial decoupling between the loci of NH4+ oxidation, NO3- reduction, and nitrogen fixation. This finding is relatively independent of the specific state of ocean circulation and is consistent with nitrogen isotope and redox proxy data. The substantive reduction in the ocean fixed-N inventory at an intermediate state of deoxygenation may represent a biogeochemical vulnerability with potential implications for past and future (warmer) oceans.

Near-equilibrium glycolysis supports metabolic homeostasis and energy yield.

Glycolysis plays a central role in producing ATP and biomass. Its control principles, however, remain incompletely understood. Here, we develop a method that combines 2H and 13C tracers to determine glycolytic thermodynamics. Using this method, we show that, in conditions and organisms with relatively slow fluxes, multiple steps in glycolysis are near to equilibrium, reflecting spare enzyme capacity. In Escherichia coli, nitrogen or phosphorus upshift rapidly increases the thermodynamic driving force, deploying the spare enzyme capacity to increase flux. Similarly, respiration inhibition in mammalian cells rapidly increases both glycolytic flux and the thermodynamic driving force. The thermodynamic shift allows flux to increase with only small metabolite concentration changes. Finally, we find that the cellulose-degrading anaerobe Clostridium cellulolyticum exhibits slow, near-equilibrium glycolysis due to the use of pyrophosphate rather than ATP for fructose-bisphosphate production, resulting in enhanced per-glucose ATP yield. Thus, near-equilibrium steps of glycolysis promote both rapid flux adaptation and energy efficiency.

Dominant eukaryotic export production during ocean anoxic events reflects the importance of recycled NH4+.

The Mesozoic is marked by several widespread occurrences of intense organic matter burial. Sediments from the largest of these events, the Cenomanian-Turonian Oceanic Anoxic Event (OAE 2) are characterized by lower nitrogen isotope ratios than are seen in modern marine settings. It has remained a challenge to describe a nitrogen cycle that could achieve such isotopic depletion. Here we use nitrogen-isotope ratios of porphyrins to show that eukaryotes contributed the quantitative majority of export production throughout OAE 2, whereas cyanobacteria contributed on average approximately 20%. Such data require that any explanation for the OAE nitrogen cycle and its isotopic values be consistent with a eukaryote-dominated ecosystem. Our results agree with models that suggest the OAEs were high-productivity events, supported by vigorous upwelling. Upwelling of anoxic deep waters would have supplied reduced N species (i.e., NH(4)(+)) to primary producers. We propose that new production during OAE 2 primarily was driven by direct NH(4)(+)-assimilation supplemented by diazotrophy, whereas chemocline denitrification and anammox quantitatively consumed NO(3)(−) and NO(2)(−). A marine nitrogen reservoir dominated by NH(4)(+), in combination with known kinetic isotope effects, could lead to eukaryotic biomass depleted in (15)N.

A method for determining the nitrogen isotopic composition of porphyrins.

We describe a new method for analysis of the nitrogen isotopic composition of sedimentary porphyrins. This method involves separation and purification of geoporphyrins from sediment samples using liquid chromatography and HPLC, oxidation of the nitrogen within porphyrin-enriched fractions using a two-step process, and isotopic analysis of the resulting nitrate using the denitrifier method. By analysis of these degradation products of chlorophylls, we are able to measure an isotopic signature that reflects the nitrogen utilized by primary producers. The high sensitivity of the denitrifier method allows measurement of small samples that contain low concentrations of porphyrins. Extraction of only 50 nmol of nitrogen (nmol N) allows the following five analyses to be made (each on approximately 10 nmol N): nitrogen concentration, an assessment of potential contamination by nonporphyrin N, and three replicate isotopic measurements. The measured values of delta15N have an average analytical precision of +/-0.5 per thousand (1sigma) and an average contribution from Rayleigh fractionation of 0.7 per thousand from incomplete oxidation of porphyrin N to nitrate. The overall method will enable high-resolution records of delta15N values to be obtained for geological and ecological applications.

Antifolate-induced depletion of intracellular glycine and purines inhibits thymineless death in E. coli.

Despite the therapeutic importance of antifolates, the links between their direct antimetabolite activity and downstream consequences remain incompletely understood. Here we employ metabolomics to examine the complete metabolic effects of the antibiotic trimethoprim in E. coli. In rich media, trimethoprim treatment causes thymineless death. In minimal media, in contrast, trimethoprim addition results in rapid stoppage of cell growth and stable cell stasis. We show that initial impairment of cell growth is due to rapid depletion of glycine and associated activation of the stringent response. Long-term stasis is due to purine insufficiency. Thus, E. coli has dual systems for surviving folate depletion and avoiding thymineless death: a short-term response based on sensing of amino acids and a long-term response based on sensing of nucleotides.

Novel hopanoid cyclases from the environment.

Hopanoids are ubiquitous isoprenoid lipids found in modern biota, in recent sediments and in low-maturity sedimentary rocks. Because these lipids primarily are derived from bacteria, they are used as proxies to help decipher geobiological communities. To date, much of the information about sources of hopanoids has come from surveys of culture collections, an approach that does not address the vast fraction of prokaryotic communities that remains uncharacterized. Here we investigated the phylogeny of hopanoid producers using culture-independent methods. We obtained 79 new sequences of squalene-hopene cyclase genes (sqhC) from marine and lacustrine bacterioplankton and analysed them along with all 31 sqhC fragments available from existing metagenomics libraries. The environmental sqhCs average only 60% translated amino acid identity to their closest relatives in public databases. The data imply that the sources of these important geologic biomarkers remain largely unknown. In particular, genes affiliated with known cyanobacterial sequences were not detected in the contemporary environments analysed here, yet the geologic record contains abundant hopanoids apparently of cyanobacterial origin. The data also suggest that hopanoid biosynthesis is uncommon: < 10% of bacterial species may be capable of producing hopanoids. A better understanding of the contemporary distribution of hopanoid biosynthesis may reveal fundamental insight about the function of these compounds, the organisms in which they are found, and the environmental signals preserved in the sedimentary record.