The origin of carbon isotope vital effects in coccolith calcite

Calcite microfossils are widely used to study climate and oceanography in Earth’s geological past. Coccoliths, readily preserved calcite plates produced by a group of single-celled surface-ocean dwelling algae called coccolithophores, have formed a significant fraction of marine sediments since the Late Triassic. However, unlike the shells of foraminifera, their zooplankton counterparts, coccoliths remain underused in palaeo-reconstructions. Precipitated in an intracellular chemical and isotopic microenvironment, coccolith calcite exhibits large and enigmatic departures from the isotopic composition of abiogenic calcite, known as vital effects. Here we show that the calcification to carbon fixation ratio determines whether coccolith calcite is isotopically heavier or lighter than abiogenic calcite, and that the size of the deviation is determined by the degree of carbon utilization. We discuss the theoretical potential for, and current limitations of, coccolith-based CO2 paleobarometry, that may eventually facilitate use of the ubiquitous and geologically extensive sedimentary archive

Constraints on the vital effect in coccolithophore and dinoflagellate calcite by oxygen isotopic modification of seawater

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 141 (2014): 612-627, doi:10.1016/j.gca.2014.05.002.In this study, we show that there are independent controls of 18O/16O and 13C/12C fractionation in coccolithophore and dinoflagellate calcite due to the contrasting kinetics of each isotope system. We demonstrate that the direction and magnitude of the oxygen isotope fractionation with respect to equilibrium is related to the balance between calcification rate and the replenishment of the internal pool of dissolved inorganic carbon (DIC). As such, in fast growing cells, such as those of Emiliania huxleyi and Gephyrocapsa oceanica (forming the so-called “heavy group”), calcification of the internal carbon pool occurs faster than complete isotopic re-adjustment of the internal DIC pool with H2O molecules. Hence, coccoliths reflect the heavy oxygen isotope signature of the CO2 overprinting the whole DIC pool. Conversely, in large and slow growing cells, such as Coccolithus pelagicus ssp. braarudii, complete re-equilibration is achieved due to limited influx of CO2 leading to coccoliths that are precipitated in conditions close to isotopic equilibrium (“equilibrium group”). Species exhibiting the most negative oxygen isotope composition, such as Calcidiscus leptoporus (“light group”), precipitate coccolith under increased pH in the coccolith vesicle, as previously documented by the “carbonate ion effect”. We suggest that, for the carbon isotope system, any observed deviation from isotopic equilibrium is only “apparent”, as the carbon isotopic composition in coccolith calcite is controlled by a Rayleigh fractionation originating from preferential incorporation of 12C into organic matter. Therefore, species with low PIC/POC ratios as E. huxleyi and G. oceanica are shifted towards positive carbon isotope values as a result of predominant carbon fixation into the organic matter. By contrast, cells with higher PIC/POC as C. braarudii and C. leptoporus maintain, to some extent, the original negative isotopic composition of the CO2. The calcareous dinoflagellate Thoracosphaera heimii exhibits different behaviour for both isotopic systems, in particular with respect to its very negative carbon isotope composition, owing to coeval intra and extracellular biomineralisation in this group. In this study, we also investigate the sensitivity of 18O/16O fractionation to varying ambient oxygen isotope composition of the medium for inorganic, coccolithophore, and dinoflagellate calcite precipitated under controlled laboratory conditions. The varying responses of different taxa to increased oxygen isotope composition of the growth medium may point to a potential bias in sea surface temperature reconstructions that are based on the oxygen isotopic compositions of sedimentary calcite, especially during times of changing seawater oxygen isotopic composition. Overall, this study represent an important step towards establishing a mechanistic understanding of the “vital effect” in coccolith and dinoflagellate calcite, and provides valuable information for interpreting the geochemistry of the calcareous nannofossils in the sedimentary record, at both monospecific and interspecies levels.MH is grateful to the Natural Environment Research Council (NERC) for funding through Postdoctoral Fellowship (NE/H015523/1). TJH is supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Doherty Foundation. REMR was supported through European Research Council (ERC) grant SP2-GA-2008-200915

Silicon isotopes in Antarctic sponges : an interlaboratory comparison

Cycling of deepwater silicon (Si) within the Southern Ocean, and its transport into other ocean basins, may be an important player in the uptake of atmospheric carbon, and global climate. Recent work has shown that the Si isotope (denoted by δ29Si or δ30Si) composition of deep sea sponges reflects the availability of dissolved Si during growth, and is a potential proxy for past deep and intermediate water silicic acid concentrations. As with any geochemical tool, it is essential to ensure analytical precision and accuracy, and consistency between methodologies and laboratories. Analytical bias may exist between laboratories, and sponge material may have matrix effects leading to offsets between samples and standards. Here, we report an interlaboratory evaluation of Si isotopes in Antarctic and sub-Antarctic sponges. We review independent methods for measuring Si isotopes in sponge spicules. Our results show that separate subsamples of non-homogenized sponges measured by three methods yield isotopic values within analytical error for over 80% of specimens. The relationship between δ29Si and δ30Si in sponges is consistent with kinetic fractionation during biomineralization. Sponge Si isotope analyses show potential as palaeoceaongraphic archives, and we suggest Southern Ocean sponge material would form a useful additional reference standard for future spicule analyses

A Combination of EPR, Microscopy, Electrophoresis and Theory to Elucidate the Chemistry of W- and N-Doped TiO2 Nanoparticle/Water Interface

Funding: The authors thank the European Commission (FP7-ENV-2011-ECO-INNO-TwoStage 283062) for funding. C.J.K. gratefully acknowledges funding from the National Science Foundation Major Research Instrumentation program (GR# MRI/DMR-1040229).Peer reviewedPublisher PD

Reply to Morel : cadmium as a micronutrient and macrotoxin in the oceans

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 110 (2013): E1878, doi:10.1073/pnas.1305068110.We thank François Morel for his interest in our study. Morel states that our conclusions are based on the approximate match between the Cd-isotope composition of cultured bacteria and the fractionation of Cd isotopes seen in seawater (1). This match is only a minor component of our argument, and we welcome the opportunity to reiterate our case

Globally enhanced calcification across the coccolithophore Gephyrocapsa complex during the mid-Brunhes interval

Evolutionary or adaptative changes in Noelaerhabdaceae coccolithophores occurred in parallel with major changes in carbonate export and burial during scenarios of low orbital eccentricity, with a ∼400 kyr recurrence, during the Pleistocene. Coeval with these conditions of enhanced proliferation, here we report that the calcification of specimens was enhanced at a global scale and across multiple species or morphotypes within the Gephyrocapsa complex during the Mid-Brunhes (MB) interval. This acme of increased production of organic and inorganic carbon by Gephyrocapsa, suggests that such global changes may originate from a common driver. Increased seawater alkalinity, with an appropriately long residence time, is proposed as environmental trigger on the selection of a wide variety of highly calcified and prolific Gephyrocapsa taxa. This new perspective highlights the role of orbital forcing in phytoplankton evolution or adaptation, via a global environmental driver in the form of seawater carbon chemistry. Our results fit with earlier proposals appealing for an intensified biological pump and respiration dissolution during this interval. We hypothesize that the Gephyrocapsa acme may play a double-edged role, by increasing shallow respiration dissolution rates, limiting the removal of alkalinity by burial, which may help to recycle alkalinity and maintain constant levels at the ∼400 kyr scale. This idea suggests the potential capacity of the Noelaerhabdaceae coccolithophore acmes to modify the typical behaviour of carbonate compensation in the ocean and that the changes in coccolithophore calcification may be indicative of changes in ocean carbonate chemistry and the operation of the global carbon cycle in the past

Plant cysteine oxidase oxygen-sensing function is conserved in early land plants and algae

All aerobic organisms require O2 for survival. When their O2 is limited (hypoxia), a response is required to reduce demand and/or improve supply. A hypoxic response mechanism has been identified in flowering plants: stability of proteins with N-terminal cysteine residues is regulated in an O2-dependent manner by the Cys/Arg branch of the N-degron pathway. Oxidation of these cysteine residues is catalysed by plant cysteine oxidases (PCOs) which destabilises proteins in normoxia; PCO inactivity in hypoxia results in protein stabilisation. Biochemically, the PCOs are sensitive to O2 availability and can therefore act as plant O2 sensors and regulation of the stability of proteins such as Group VII ethylene response factors (ERF-VIIs) can initiate adaptive responses to hypoxia. It is not known whether oxygen-sensing mechanisms exist in other phyla from the plant kingdom. Known PCO targets are only conserved in flowering plants, however PCO-like sequences are conserved in all planta. We sought to determine whether PCO-like enzymes from the liverwort, Marchantia polymorpha (MpPCO) and the freshwater algae, Klebsormidium nitens (KnPCO) have a similar function to PCO enzymes from Arabidopsis thaliana . We report that MpPCO and KnPCO show O2-sensitive N-terminal cysteine dioxygenase activity towards known AtPCO ERF-VII substrates as well as a putative endogenous substrate, MpERF-like, which was identified by homology to the Arabidopsis ERF-VIIs transcription factors. This work confirms functional and O2-dependent PCOs from Bryophyta and Charophyta, indicating the potential for PCO-mediated O2-sensing pathways in these organisms and suggesting PCO O2-sensing function could be important throughout the plant kingdom

A Blind Test of Computational Technique for Predicting the Likelihood of Peptide Sequences to Cyclize

An in silico computational technique for predicting peptide sequences that can be cyclized by cyanobactin macrocyclases, e.g., PatGmac, is reported. We demonstrate that the propensity for PatGmac-mediated cyclization correlates strongly with the free energy of the so-called pre-cyclization conformation (PCC), which is a fold where the cyclizing sequence C and N termini are in close proximity. This conclusion is driven by comparison of the predictions of boxed molecular dynamics (BXD) with experimental data, which have achieved an accuracy of 84%. A true blind test rather than training of the model is reported here as the in silico tool was developed before any experimental data was given, and no parameters of computations were adjusted to fit the data. The success of the blind test provides fundamental understanding of the molecular mechanism of cyclization by cyanobactin macrocyclases, suggesting that formation of PCC is the rate-determining step. PCC formation might also play a part in other processes of cyclic peptides production and on the practical side the suggested tool might become useful for finding cyclizable peptide sequences in general

Calcification response of a key phytoplankton family to millennial-scale environmental change

Coccolithophores are single-celled photosynthesizing marine algae, responsible for half of the calcification in the surface ocean, and exert a strong influence on the distribution of carbon among global reservoirs, and thus Earth’s climate. Calcification in the surface ocean decreases the buffering capacity of seawater for CO2, whilst photosynthetic carbon fixation has the opposite effect. Experiments in culture have suggested that coccolithophore calcification decreases under high CO2 concentrations ([CO2(aq)]) constituting a negative feedback. However, the extent to which these results are representative of natural populations, and of the response over more than a few hundred generations is unclear. Here we describe and apply a novel rationale for size-normalizing the mass of the calcite plates produced by the most abundant family of coccolithophores, the Noëlaerhabdaceae. On average, ancient populations subjected to coupled gradual increases in [CO2(aq)] and temperature over a few million generations in a natural environment become relatively more highly calcified, implying a positive climatic feedback. We hypothesize that this is the result of selection manifest in natural populations over millennial timescales, so has necessarily eluded laboratory experiments

Transcriptomic analysis of cutaneous squamous cell carcinoma reveals a multi-gene prognostic signature associated with metastasis.

BackgroundMetastasis of cutaneous squamous cell carcinoma (cSCC) is uncommon. Current staging methods are reported to have sub-optimal performances in metastasis prediction. Accurate identification of patients with tumours at high risk of metastasis would have a significant impact on management.ObjectiveTo develop a robust and validated gene expression profile (GEP) signature for predicting primary cSCC metastatic risk using an unbiased whole transcriptome discovery-driven approach.MethodsArchival formalin-fixed paraffin-embedded primary cSCC with perilesional normal tissue from 237 immunocompetent patients (151 non-metastasising and 86 metastasising) were collected retrospectively from four centres. TempO-seq was used to probe the whole transcriptome and machine learning algorithms were applied to derive predictive signatures, with a 3:1 split for training and testing datasets.ResultsA 20-gene prognostic model was developed and validated, with an accuracy of 86.0%, sensitivity of 85.7%, specificity of 86.1%, and positive predictive value of 78.3% in the testing set, providing more stable, accurate prediction than pathological staging systems. A linear predictor was also developed, significantly correlating with metastatic risk.LimitationsThis was a retrospective 4-centre study and larger prospective multicentre studies are now required.ConclusionThe 20-gene signature prediction is accurate, with the potential to be incorporated into clinical workflows for cSCC