Articles | Volume 19, issue 13
15 Jul 2022
Research article | 15 Jul 2022
Physiological control on carbon isotope fractionation in marine phytoplankton
Karen M. Brandenburg et al.
No articles found.
William Davis Rush, Jean Self-Trail, Yang Zhang, Appy Sluijs, Henk Brinkhuis, James Zachos, James Ogg, and Marci Robinson
This preprint is open for discussion and under review for Climate of the Past (CP).Short summary
The Eocene contains several brief warming periods referred to as “hyperthermals”. Studying these events and how they varied between locations can help provide insight into our future, warmer world. This study provides the first identification of 2 of these events in the Mid-Atlantic region of the United States. The records of climate we measured demonstrate significant changes during this time period, but the type and timing of these changes highlight the complexity of climatic changes.
Yord Willow Yedema, Francesca Sangiorgi, Appy Sluijs, Jaap Smede Sinninghe Damsté, and Francien Peterse
Revised manuscript accepted for BGShort summary
Terrestrial organic matter (TerrOM) is transported to the ocean by rivers, where its burial can potentially form a long-term carbon sink. This burial is dependent on the type and characteristics of the TerrOM. We used bulk sediment properties, biomarkers and palynology to identify the dispersal patterns of plant-, soil-, and aquatic-derived TerrOM in the northern Gulf of Mexico and show that plant TerrOM is transported further into the coastal zone than soil- and aquatic produced TerrOM.
Carolien M. H. van der Weijst, Koen J. van der Laan, Francien Peterse, Gert-Jan Reichart, Francesca Sangiorgi, Stefan Schouten, Tjerk J. T. Veenstra, and Appy Sluijs
Clim. Past, 18, 1947–1962,Short summary
The TEX86 proxy is often used by paleoceanographers to reconstruct past sea-surface temperatures. However, the origin of the TEX86 signal in marine sediments has been debated since the proxy was first proposed. In our paper, we show that TEX86 carries a mixed sea-surface and subsurface temperature signal and should be calibrated accordingly. Using our 15-million-year record, we subsequently show how a TEX86 subsurface temperature record can be used to inform us on past sea-surface temperatures.
Joost Frieling, Linda van Roij, Iris Kleij, Gert-Jan Reichart, and Appy Sluijs
Preprint under review for BGShort summary
We present a first species specific evaluation of marine core-top dinoflagellate cyst carbon isotope fractionation (εp) in order to establish natural pCO2 dependency and explore its geological deep-time paleo-pCO2 proxy potential. We build a first version of the paleo-CO2 proxy based on Operculodinium centrocarpum. εp differs between species and is controlled by pCO2 and nutrients. Our results illustrate the value of δ13C analyses on single micrometer-scale sedimentary organic carbon particles.
Carolien M. H. van der Weijst, Josse Winkelhorst, Wesley de Nooijer, Anna von der Heydt, Gert-Jan Reichart, Francesca Sangiorgi, and Appy Sluijs
Clim. Past, 18, 961–973,Short summary
A hypothesized link between Pliocene (5.3–2.5 million years ago) global climate and tropical thermocline depth is currently only backed up by data from the Pacific Ocean. In our paper, we present temperature, salinity, and thermocline records from the tropical Atlantic Ocean. Surprisingly, the Pliocene thermocline evolution was remarkably different in the Atlantic and Pacific. We need to reevaluate the mechanisms that drive thermocline depth, and how these are tied to global climate change.
Peter K. Bijl, Joost Frieling, Margot J. Cramwinckel, Christine Boschman, Appy Sluijs, and Francien Peterse
Clim. Past, 17, 2393–2425,Short summary
Here, we use the latest insights for GDGT and dinocyst-based paleotemperature and paleoenvironmental reconstructions in late Cretaceous–early Oligocene sediments from ODP Site 1172 (East Tasman Plateau, Australia). We reconstruct strong river runoff during the Paleocene–early Eocene, a progressive decline thereafter with increased wet/dry seasonality in the northward-drifting hinterland. Our critical review leaves the anomalous warmth of the Eocene SW Pacific Ocean unexplained.
Gerrit Müller, Jack J. Middelburg, and Appy Sluijs
Earth Syst. Sci. Data, 13, 3565–3575,Short summary
Rivers are major freshwater resources, connectors and transporters on Earth. As the composition of river waters and particles results from processes in their catchment, such as erosion, weathering, environmental pollution, nutrient and carbon cycling, Earth-spanning databases of river composition are needed for studies of these processes on a global scale. While extensive resources on water and nutrient composition exist, we provide a database of river particle composition.
Annique van der Boon, Klaudia F. Kuiper, Robin van der Ploeg, Margot J. Cramwinckel, Maryam Honarmand, Appy Sluijs, and Wout Krijgsman
Clim. Past, 17, 229–239,Short summary
40.5 million years ago, Earth's climate warmed, but it is unknown why. Enhanced volcanism has been suggested, but this has not yet been tied to a specific region. We explore an increase in volcanism in Iran. We dated igneous rocks and compiled ages from the literature. We estimated the volume of igneous rocks in Iran in order to calculate the amount of CO2 that could have been released due to enhanced volcanism. We conclude that an increase in volcanism in Iran is a plausible cause of warming.
Michiel Baatsen, Anna S. von der Heydt, Matthew Huber, Michael A. Kliphuis, Peter K. Bijl, Appy Sluijs, and Henk A. Dijkstra
Clim. Past, 16, 2573–2597,Short summary
Warm climates of the deep past have proven to be challenging to reconstruct with the same numerical models used for future predictions. We present results of CESM simulations for the middle to late Eocene (∼ 38 Ma), in which we managed to match the available indications of temperature well. With these results we can now look into regional features and the response to external changes to ultimately better understand the climate when it is in such a warm state.
Appy Sluijs, Joost Frieling, Gordon N. Inglis, Klaas G. J. Nierop, Francien Peterse, Francesca Sangiorgi, and Stefan Schouten
Clim. Past, 16, 2381–2400,Short summary
We revisit 15-year-old reconstructions of sea surface temperatures in the Arctic Ocean for the late Paleocene and early Eocene epochs (∼ 57–53 million years ago) based on the distribution of fossil membrane lipids of archaea preserved in Arctic Ocean sediments. We find that improvements in the methods over the past 15 years do not lead to different results. However, data quality is now higher and potential biases better characterized. Results confirm remarkable Arctic warmth during this time.
Margot J. Cramwinckel, Lineke Woelders, Emiel P. Huurdeman, Francien Peterse, Stephen J. Gallagher, Jörg Pross, Catherine E. Burgess, Gert-Jan Reichart, Appy Sluijs, and Peter K. Bijl
Clim. Past, 16, 1667–1689,Short summary
Phases of past transient warming can be used as a test bed to study the environmental response to climate change independent of tectonic change. Using fossil plankton and organic molecules, here we reconstruct surface ocean temperature and circulation in and around the Tasman Gateway during a warming phase 40 million years ago termed the Middle Eocene Climatic Optimum. We find that plankton assemblages track ocean circulation patterns, with superimposed variability being related to temperature.
Carolien Maria Hendrina van der Weijst, Josse Winkelhorst, Anna von der Heydt, Gert-Jan Reichart, Francesca Sangiorgi, and Appy Sluijs
Clim. Past Discuss.,
Manuscript not accepted for further review
Emily White, Clara J. M. Hoppe, and Björn Rost
Biogeosciences, 17, 635–647,Short summary
The Arctic picoeukaryote Micromonas pusilla was acclimated to two pCO2 levels under a constant and a dynamic light, simulating more realistic light fields. M. pusilla was able to benefit from ocean acidification with an increase in growth rate, irrespective of the light regime. In dynamic light M. pusilla optimised its photophysiology for effective light usage during both low- and high-light periods. This highlights M. pusilla is likely to cope well with future conditions in the Arctic Ocean.
Gabriel J. Bowen, Brenden Fischer-Femal, Gert-Jan Reichart, Appy Sluijs, and Caroline H. Lear
Clim. Past, 16, 65–78,Short summary
Past climate conditions are reconstructed using indirect and incomplete geological, biological, and geochemical proxy data. We propose that such reconstructions are best obtained by statistical inversion of hierarchical models that represent how multi–proxy observations and calibration data are produced by variation of environmental conditions in time and/or space. These methods extract new information from traditional proxies and provide robust, comprehensive estimates of uncertainty.
Johan Vellekoop, Lineke Woelders, Appy Sluijs, Kenneth G. Miller, and Robert P. Speijer
Biogeosciences, 16, 4201–4210,Short summary
Our micropaleontological analyses on three cores from New Jersey (USA) show that the late Maastrichtian warming event (66.4–66.1 Ma), characterized by a ~ 4.0 °C warming of sea waters on the New Jersey paleoshelf, resulted in a disruption of phytoplankton communities and a stressed benthic ecosystem. This increased ecosystem stress during the latest Maastrichtian potentially primed global ecosystems for the subsequent mass extinction following the Cretaceous–Paleogene boundary impact.
Christopher J. Hollis, Tom Dunkley Jones, Eleni Anagnostou, Peter K. Bijl, Margot J. Cramwinckel, Ying Cui, Gerald R. Dickens, Kirsty M. Edgar, Yvette Eley, David Evans, Gavin L. Foster, Joost Frieling, Gordon N. Inglis, Elizabeth M. Kennedy, Reinhard Kozdon, Vittoria Lauretano, Caroline H. Lear, Kate Littler, Lucas Lourens, A. Nele Meckler, B. David A. Naafs, Heiko Pälike, Richard D. Pancost, Paul N. Pearson, Ursula Röhl, Dana L. Royer, Ulrich Salzmann, Brian A. Schubert, Hannu Seebeck, Appy Sluijs, Robert P. Speijer, Peter Stassen, Jessica Tierney, Aradhna Tripati, Bridget Wade, Thomas Westerhold, Caitlyn Witkowski, James C. Zachos, Yi Ge Zhang, Matthew Huber, and Daniel J. Lunt
Geosci. Model Dev., 12, 3149–3206,Short summary
The Deep-Time Model Intercomparison Project (DeepMIP) is a model–data intercomparison of the early Eocene (around 55 million years ago), the last time that Earth's atmospheric CO2 concentrations exceeded 1000 ppm. Previously, we outlined the experimental design for climate model simulations. Here, we outline the methods used for compilation and analysis of climate proxy data. The resulting climate
atlaswill provide insights into the mechanisms that control past warm climate states.
Ilja J. Kocken, Margot J. Cramwinckel, Richard E. Zeebe, Jack J. Middelburg, and Appy Sluijs
Clim. Past, 15, 91–104,Short summary
Marine organic carbon burial could link the 405 thousand year eccentricity cycle in the long-term carbon cycle to that observed in climate records. Here, we simulate the response of the carbon cycle to astronomical forcing. We find a strong 2.4 million year cycle in the model output, which is present as an amplitude modulator of the 405 and 100 thousand year eccentricity cycles in a newly assembled composite record.
Clara Jule Marie Hoppe, Clara M. Flintrop, and Björn Rost
Biogeosciences, 15, 4353–4365,Short summary
Responses of the Arctic microalgae Micromonas pusilla to different pCO2 levels were investigated at two temperatures. We observed that warming and ocean acidification (OA) synergistically increased growth rates. Furthermore, elevated temperature shifted the pCO2 optimum of biomass production to higher levels. This seem to be caused by more efficient photosynthesis under warmer and more acidic conditions. Our findings explain the dominance of picoeukaryotes frequently observed in OA experiments.
Michiel Baatsen, Anna S. von der Heydt, Matthew Huber, Michael A. Kliphuis, Peter K. Bijl, Appy Sluijs, and Henk A. Dijkstra
Clim. Past Discuss.,
Revised manuscript not acceptedShort summary
The Eocene marks a period where the climate was in a hothouse state, without any continental-scale ice sheets. Such climates have proven difficult to reproduce in models, especially their low temperature difference between equator and poles. Here, we present high resolution CESM simulations using a new geographic reconstruction of the middle-to-late Eocene. The results provide new insights into a period for which knowledge is limited, leading up to a transition into the present icehouse state.
Helen M. Beddow, Diederik Liebrand, Douglas S. Wilson, Frits J. Hilgen, Appy Sluijs, Bridget S. Wade, and Lucas J. Lourens
Clim. Past, 14, 255–270,Short summary
We present two astronomy-based timescales for climate records from the Pacific Ocean. These records range from 24 to 22 million years ago, a time period when Earth was warmer than today and the only land ice was located on Antarctica. We use tectonic plate-pair spreading rates to test the two timescales, which shows that the carbonate record yields the best timescale. In turn, this implies that Earth’s climate system and carbon cycle responded slowly to changes in incoming solar radiation.
Joost Frieling, Gert-Jan Reichart, Jack J. Middelburg, Ursula Röhl, Thomas Westerhold, Steven M. Bohaty, and Appy Sluijs
Clim. Past, 14, 39–55,Short summary
Past periods of rapid global warming such as the Paleocene–Eocene Thermal Maximum are used to study biotic response to climate change. We show that very high peak PETM temperatures in the tropical Atlantic (~ 37 ºC) caused heat stress in several marine plankton groups. However, only slightly cooler temperatures afterwards allowed highly diverse plankton communities to bloom. This shows that tropical plankton communities may be susceptible to extreme warming, but may also recover rapidly.
Michiel Baatsen, Douwe J. J. van Hinsbergen, Anna S. von der Heydt, Henk A. Dijkstra, Appy Sluijs, Hemmo A. Abels, and Peter K. Bijl
Clim. Past, 12, 1635–1644,Short summary
One of the major difficulties in modelling palaeoclimate is constricting the boundary conditions, causing significant discrepancies between different studies. Here, a new method is presented to automate much of the process of generating the necessary geographical reconstructions. The latter can be made using various rotational frameworks and topography/bathymetry input, allowing for easy inter-comparisons and the incorporation of the latest insights from geoscientific research.
Niels A. G. M. van Helmond, Appy Sluijs, Nina M. Papadomanolaki, A. Guy Plint, Darren R. Gröcke, Martin A. Pearce, James S. Eldrett, João Trabucho-Alexandre, Ireneusz Walaszczyk, Bas van de Schootbrugge, and Henk Brinkhuis
Biogeosciences, 13, 2859–2872,Short summary
Over the past decades large changes have been observed in the biogeographical dispersion of marine life resulting from climate change. To better understand present and future trends it is important to document and fully understand the biogeographical response of marine life during episodes of environmental change in the geological past. Here we investigate the response of phytoplankton, the base of the marine food web, to a rapid cold spell, interrupting greenhouse conditions during the Cretaceous.
N. A. G. M. van Helmond, A. Sluijs, J. S. Sinninghe Damsté, G.-J. Reichart, S. Voigt, J. Erbacher, J. Pross, and H. Brinkhuis
Clim. Past, 11, 495–508,Short summary
Based on the chemistry and microfossils preserved in sediments deposited in a shallow sea, in the current Lower Saxony region (NW Germany), we conclude that changes in Earth’s orbit around the Sun led to enhanced rainfall and organic matter production. The additional supply of organic matter, depleting oxygen upon degradation, and freshwater, inhibiting the mixing of oxygen-rich surface waters with deeper waters, caused the development of oxygen-poor waters about 94 million years ago.
B. S. Slotnick, V. Lauretano, J. Backman, G. R. Dickens, A. Sluijs, and L. Lourens
Clim. Past, 11, 473–493,
A. Sluijs, L. van Roij, G. J. Harrington, S. Schouten, J. A. Sessa, L. J. LeVay, G.-J. Reichart, and C. P. Slomp
Clim. Past, 10, 1421–1439,
L. Contreras, J. Pross, P. K. Bijl, R. B. O'Hara, J. I. Raine, A. Sluijs, and H. Brinkhuis
Clim. Past, 10, 1401–1420,
J. S. Eldrett, D. R. Greenwood, M. Polling, H. Brinkhuis, and A. Sluijs
Clim. Past, 10, 759–769,
I. G. M. Wientjes, R. S. W. Van de Wal, G. J. Reichart, A. Sluijs, and J. Oerlemans
The Cryosphere, 5, 589–601,
Related subject area
Biogeochemistry: Environmental MicrobiologyInterdisciplinary strategy to assess the impact of meteorological variables on the biochemical composition of the rain and the dynamics of a small eutrophic lake under rain forcingDepth-related patterns in microbial community responses to complex organic matter in the western North Atlantic OceanAssessing the influence of ocean alkalinity enhancement on a coastal phytoplankton communityEddy-enhanced primary production sustains heterotrophic microbial activities in the Eastern Tropical North AtlanticNitrous oxide (N2O) synthesis by Microcystis aeruginosaComposition and niche-specific characteristics of microbial consortia colonizing Marsberg copper mine in the Rhenish MassifDiversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)Nitrophobic ectomycorrhizal fungi are associated with enhanced hydrophobicity of soil organic matter in a Norway spruce forestImplementation of mycorrhizal mechanisms into soil carbon model improves the prediction of long-term processes of plant litter decompositionImpact of dust addition on the microbial food web under present and future conditions of pH and temperatureFractionation of stable carbon isotopes during acetate consumption by methanogenic and sulfidogenic microbial communities in rice paddy soils and lake sedimentsHydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific OceanSedimentation rate and organic matter dynamics shape microbiomes across a continental marginDisturbance triggers non-linear microbe–environment feedbacksHydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the southern Indian Ocean and the Southern OceanMicrobial and geo-archaeological records reveal the growth rate, origin and composition of desert rock surface communitiesMetagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sedimentsSpatiotemporal patterns of N2 fixation in coastal waters derived from rate measurements and remote sensingBiotic and abiotic transformation of amino acids in cloud water: experimental studies and atmospheric implicationsPotential bioavailability of organic matter from atmospheric particles to marine heterotrophic bacteriaMicrobial functional signature in the atmospheric boundary layerNew insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystemImpact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamicsReviews and syntheses: Bacterial bioluminescence – ecology and impact in the biological carbon pumpSalinity-dependent algae uptake and subsequent carbon and nitrogen metabolisms of two intertidal foraminifera (Ammonia tepida and Haynesina germanica)On giant shoulders: how a seamount affects the microbial community composition of seawater and spongesSpatial variations in sedimentary N-transformation rates in the North Sea (German Bight)Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic RidgeCo-occurrence of Fe and P stress in natural populations of the marine diazotroph TrichodesmiumSenescence as the main driver of iodide release from a diverse range of marine phytoplanktonReviews and syntheses: Biological weathering and its consequences at different spatial levels – from nanoscale to global scaleDeep-sea sponge grounds as nutrient sinks: denitrification is common in boreo-Arctic spongesInducing the attachment of cable bacteria on oxidizing electrodesBacterial degradation activity in the eastern tropical South Pacific oxygen minimum zoneMacromolecular fungal ice nuclei in Fusarium: effects of physical and chemical processingEffects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime AntarcticaComprehensive characterization of an aspen (Populus tremuloides) leaf litter sample that maintained ice nucleation activity for 48 yearsThe origin and role of biological rock crusts in rocky desert weatheringPyrite oxidization accelerates bacterial carbon sequestration in copper mine tailingsBiogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort SeaFiltration artefacts in bacterial community composition can affect the outcome of dissolved organic matter biolability assaysPredominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissionsTrichodesmium physiological ecology and phosphate reduction in the western tropical South PacificPotential for phenol biodegradation in cloud watersColony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron biogeochemistryIn-depth characterization of diazotroph activity across the western tropical South Pacific hotspot of N2 fixation (OUTPACE cruise)Programmed cell death in diazotrophs and the fate of organic matter in the western tropical South Pacific Ocean during the OUTPACE cruiseRapid mineralization of biogenic volatile organic compounds in temperate and Arctic soilsA three-dimensional niche comparison of Emiliania huxleyi and Gephyrocapsa oceanica: reconciling observations with projectionsDistribution and drivers of symbiotic and free-living diazotrophic cyanobacteria in the western tropical South Pacific
Fanny Noirmain, Jean-Luc Baray, Frédéric Tridon, Philippe Cacault, Hermine Billard, Guillaume Voyard, Joël Van Baelen, and Delphine Latour
Biogeosciences, 19, 5729–5749,Short summary
We present a study linking rain, meteorology, and mountain lake phytoplankton dynamics on the basis of a case study at Aydat (France) in September 2020. The air mass origin mainly influences the rain chemical composition, which depends on the type of rain, convective or stratiform. Our results also highlighted a non-negligible presence of photosynthetic cells in rainwater. The impact of the atmospheric forcing on the lake could play a key role in phytoplankton dynamics in the temperate zone.
Sarah A. Brown, John Paul Balmonte, Adrienne Hoarfrost, Sherif Ghobrial, and Carol Arnosti
Biogeosciences, 19, 5617–5631,Short summary
Bacteria use extracellular enzymes to cut large organic matter to sizes small enough for uptake. We compared the enzymatic response of surface, mid-water, and deep-ocean bacteria to complex natural substrates. Bacteria in surface and mid-depth waters produced a much wider range of enzymes than those in the deep ocean and may therefore consume a broader range of organic matter. The extent to which organic matter is recycled by bacteria depends in part on its residence time at different depths.
Aaron Ferderer, Zanna Chase, Fraser Kennedy, Kai G. Schulz, and Lennart T. Bach
Biogeosciences, 19, 5375–5399,Short summary
Ocean alkalinity enhancement has the capacity to remove vast quantities of carbon from the atmosphere, but its effect on marine ecosystems is largely unknown. We assessed the effect of increased alkalinity on a coastal phytoplankton community when seawater was equilibrated and not equilibrated with atmospheric CO2. We found that the phytoplankton community was moderately affected by increased alkalinity and equilibration with atmospheric CO2 had little influence on this effect.
Quentin Devresse, Kevin W. Becker, Arne Bendinger, Johannes Hahn, and Anja Engel
Biogeosciences, 19, 5199–5219,Short summary
Eddies are ubiquitous in the ocean and alter physical, chemical, and biological processes. However, how they affect organic carbon production and consumption is largely unknown. Here we show how an eddy triggers a cascade effect on biomass production and metabolic activities of phyto- and bacterioplankton. Our results may contribute to the improvement of biogeochemical models used to estimate carbon fluxes in the ocean.
Federico Fabisik, Benoit Guieysse, Jonathan Procter, and Maxence Plouviez
We show, for the first time, that pure cultures of the cyanobacterium Microcystis aeruginosa can synthesize the potent greenhouse gas N2O using nitrite as substrate. Our findings have broad environmental implications because M. aeruginosa is globally found in freshwater ecosystems and is often the dominant species found in algae blooms. Further research is now needed to determine the occurrence and significance of N2O emissions from ecosystems rich with M. aeruginosa.
Sania Arif, Heiko Nacke, Elias Schliekmann, Andreas Reimer, Gernot Arp, and Michael Hoppert
Biogeosciences, 19, 4883–4902,Short summary
The natural enrichment of Chloroflexi (Ktedonobacteria) at the Kilianstollen Marsberg copper mine rocks being exposed to the acidic sulfate-rich leachate led to an investigation of eight metagenomically assembled genomes (MAGs) involved in copper and other transition heavy metal resistance in addition to low pH resistance and aromatic compounds degradation. The present study offers functional insights about a novel cold-adapted Ktedonobacteria MAG extremophily along with other phyla MAGs.
Chunmei Zhang, Huirong Li, Yinxin Zeng, Haitao Ding, Bin Wang, Yangjie Li, Zhongqiang Ji, Yonghong Bi, and Wei Luo
Biogeosciences, 19, 4639–4654,Short summary
The unique microbial eukaryotic community structure and lower diversity have been demonstrated in five freshwater lakes of the Fildes Peninsula, Antarctica. Stochastic processes and biotic co-occurrence patterns were shown to be important in shaping microbial eukaryotic communities in the area. Our study provides a better understanding of the dynamic patterns and ecological assembly processes of microbial eukaryotic communities in Antarctic oligotrophic lakes (Fildes Peninsula).
Juan Pablo Almeida, Nicholas P. Rosenstock, Susanne K. Woche, Georg Guggenberger, and Håkan Wallander
Biogeosciences, 19, 3713–3726,Short summary
Fungi living in symbiosis with tree roots can accumulate belowground, forming special tissues than can repel water. We measured the water repellency of organic material incubated belowground and correlated it with fungal growth. We found a positive association between water repellency and root symbiotic fungi. These results are important because an increase in soil water repellency can reduce the release of CO2 from soils into the atmosphere and mitigate the effects of greenhouse gasses.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490,Short summary
This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319,Short summary
Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Ralf Conrad, Pengfei Liu, and Peter Claus
Biogeosciences, 18, 6533–6546,Short summary
Acetate is an important intermediate during the anaerobic degradation of organic matter. It is consumed by methanogenic and sulfidogenic microorganisms accompanied by stable carbon isotope fractionation. We determined isotope fractionation under different conditions in two paddy soils and two lake sediments and also determined the composition of the microbial communities. Despite a relatively wide range of experimental conditions, the range of fractionation factors was quite moderate.
Natalie R. Cohen, Abigail E. Noble, Dawn M. Moran, Matthew R. McIlvin, Tyler J. Goepfert, Nicholas J. Hawco, Christopher R. German, Tristan J. Horner, Carl H. Lamborg, John P. McCrow, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 18, 5397–5422,Short summary
A previous study documented an intense hydrothermal plume in the South Pacific Ocean; however, the iron release associated with this plume and the impact on microbiology were unclear. We describe metal concentrations associated with multiple hydrothermal plumes in this region and protein signatures of plume-influenced microbes. Our findings demonstrate that resources released from these systems can be transported away from their source and may alter the physiology of surrounding microbes.
Sabyasachi Bhattacharya, Tarunendu Mapder, Svetlana Fernandes, Chayan Roy, Jagannath Sarkar, Moidu Jameela Rameez, Subhrangshu Mandal, Abhijit Sar, Amit Kumar Chakraborty, Nibendu Mondal, Sumit Chatterjee, Bomba Dam, Aditya Peketi, Ranadhir Chakraborty, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 18, 5203–5222,Short summary
Physicochemical determinants of microbiome architecture across continental shelves–slopes are unknown, so we explored the geomicrobiology along 3 m sediment horizons of seasonal (shallow coastal) and perennial (deep sea) hypoxic zones of the Arabian Sea. Nature, concentration, and fate of the organic matter delivered to the sea floor were found to shape the microbiome across the western Indian margin, under direct–indirect influence of sedimentation rate and water column O2 level.
Aditi Sengupta, Sarah J. Fansler, Rosalie K. Chu, Robert E. Danczak, Vanessa A. Garayburu-Caruso, Lupita Renteria, Hyun-Seob Song, Jason Toyoda, Jacqueline Wells, and James C. Stegen
Biogeosciences, 18, 4773–4789,Short summary
Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Cora Hörstmann, Eric J. Raes, Pier Luigi Buttigieg, Claire Lo Monaco, Uwe John, and Anya M. Waite
Biogeosciences, 18, 3733–3749,Short summary
Microbes are the main drivers of productivity and nutrient cycling in the ocean. We present a combined approach assessing C and N uptake and microbial community diversity across ecological provinces in the Southern Ocean and southern Indian Ocean. Provinces showed distinct genetic fingerprints, but microbial activity varied gradually across regions, correlating with nutrient concentrations. Our study advances the biogeographic understanding of microbial diversity across C and N uptake regimes.
Nimrod Wieler, Tali Erickson Gini, Osnat Gillor, and Roey Angel
Biogeosciences, 18, 3331–3342,Short summary
Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, and Orit Sivan
Biogeosciences, 18, 2091–2106,
Mindaugas Zilius, Irma Vybernaite-Lubiene, Diana Vaiciute, Donata Overlingė, Evelina Grinienė, Anastasija Zaiko, Stefano Bonaglia, Iris Liskow, Maren Voss, Agneta Andersson, Sonia Brugel, Tobia Politi, and Paul A. Bukaveckas
Biogeosciences, 18, 1857–1871,Short summary
In fresh and brackish waters, algal blooms are often dominated by cyanobacteria, which have the ability to utilize atmospheric nitrogen. Cyanobacteria are also unusual in that they float to the surface and are dispersed by wind-driven currents. Their patchy and dynamic distribution makes it difficult to track their abundance and quantify their effects on nutrient cycling. We used remote sensing to map the distribution of cyanobacteria in a large Baltic lagoon and quantify their contributions.
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Biogeosciences, 18, 1067–1080,Short summary
Our study is of interest to atmospheric scientists and environmental microbiologists, as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition with chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285,
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095,Short summary
The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032,Short summary
Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374,Short summary
This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778,Short summary
Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732,Short summary
Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486,Short summary
Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851,Short summary
The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519,Short summary
Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551,Short summary
Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471,Short summary
Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
Roger D. Finlay, Shahid Mahmood, Nicholas Rosenstock, Emile B. Bolou-Bi, Stephan J. Köhler, Zaenab Fahad, Anna Rosling, Håkan Wallander, Salim Belyazid, Kevin Bishop, and Bin Lian
Biogeosciences, 17, 1507–1533,Short summary
Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Christine Rooks, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann
Biogeosciences, 17, 1231–1245,Short summary
Sponge grounds are known as nutrient sources, providing nitrate and ammonium to the ocean. We found that they also can do the opposite: in six species from Arctic and North Atlantic sponge grounds, we measured high rates of denitrification, which remove these nutrients from the sea. Rates were highest when the sponge tissue got low in oxygen, which happens when sponges stop pumping because of stress. Sponge grounds may become nutrient sinks when exposed to stress.
Cheng Li, Clare E. Reimers, and Yvan Alleau
Biogeosciences, 17, 597–607,Short summary
Novel filamentous cable bacteria that grow in the top layer of intertidal mudflat sediment were attracted to electrodes poised at a positive electrical potential. Several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the electrode surface. These observations provide information to suggest conditions that will induce cable bacteria to perform electron donation to an electrode, informing future experiments that culture cable bacteria outside of sediment.
Marie Maßmig, Jan Lüdke, Gerd Krahmann, and Anja Engel
Biogeosciences, 17, 215–230,Short summary
Little is known about the rates of bacterial element cycling in oxygen minimum zones (OMZs). We measured bacterial production and rates of extracellular hydrolytic enzymes at various in situ oxygen concentrations in the OMZ off Peru. Our field data show unhampered bacterial activity at low oxygen concentrations. Meanwhile bacterial degradation of organic matter substantially contributed to the formation of the OMZ.
Anna T. Kunert, Mira L. Pöhlker, Kai Tang, Carola S. Krevert, Carsten Wieder, Kai R. Speth, Linda E. Hanson, Cindy E. Morris, David G. Schmale III, Ulrich Pöschl, and Janine Fröhlich-Nowoisky
Biogeosciences, 16, 4647–4659,Short summary
A screening of more than 100 strains from 65 different species revealed that the ice nucleation activity within the fungal genus Fusarium is more widespread than previously assumed. Filtration experiments suggest that the single cell-free Fusarium IN is smaller than 100 kDa (~ 6 nm) and that aggregates can be formed in solution. Exposure experiments, freeze–thaw cycles, and long-term storage tests demonstrate a high stability of Fusarium IN under atmospherically relevant conditions.
Qing Wang, Renbin Zhu, Yanling Zheng, Tao Bao, and Lijun Hou
Biogeosciences, 16, 4113–4128,Short summary
We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) in five Antarctic tundra patches, including penguin colony, seal colony, and tundra marsh. We have found (1) sea animal colonization increased AOB population size.; (2) AOB contributed to ammonia oxidation rates more than AOA in sea animal colonies; (3) community structures of AOB and AOA were closely related to soil biogeochemical processes associated with animal activities.
Yalda Vasebi, Marco E. Mechan Llontop, Regina Hanlon, David G. Schmale III, Russell Schnell, and Boris A. Vinatzer
Biogeosciences, 16, 1675–1683,Short summary
Ice nucleation particles (INPs) help ice form at temperatures as high as −4 °C and contribute to the formation of precipitation. Leaf litter contains a high concentration of INPs, but the organisms that produce them are unknown. Here, we cultured two bacteria and one fungus from leaf litter that produce INPs similar to those found in leaf litter. This suggests that leaf litter may be an important habitat of these organisms and supports a role of these organisms as producers of atmospheric INPs.
Nimrod Wieler, Hanan Ginat, Osnat Gillor, and Roey Angel
Biogeosciences, 16, 1133–1145,Short summary
In stony deserts, when rocks are exposed to atmospheric conditions, they undergo weathering. The cavernous (honeycomb) weathering pattern is one of the most common, but it is still unclear exactly how it is formed. We show that microorganisms, which differ from the surrounding soil and dust, form biological crusts on exposed rock surfaces. These microbes secrete polymeric substances that mitigate weathering by reducing evaporation rates and, consequently, salt transport rates through the rock.
Yang Li, Zhaojun Wu, Xingchen Dong, Zifu Xu, Qixin Zhang, Haiyan Su, Zhongjun Jia, and Qingye Sun
Biogeosciences, 16, 573–583,Short summary
This paper contributes to the study of bacterial carbon sequestration in mine tailings. Previous studies focused on carbonate mineral precipitation, while the role of autotrophs in carbon sequestration has been neglected. Carbon sequestration in two mine tailings treated with FeS2 was analyzed using 13C isotope labeling, pyrosequencing, and DNA SIP to identify carbon fixers. This paper is the first to investigate carbon sequestration by autotrophic groups in mine tailings.
Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Young Keun Jin, Helge Niemann, Young-Gyun Kim, and Kyung-Hoon Shin
Biogeosciences, 15, 7419–7433,Short summary
In this study, we provide first evidence of lipid biomarker patterns and phylogenetic identities of key microbes mediating anaerobic oxidation of methane (AOM) communities in active mud volcanoes (MVs) on the continental slope of the Canadian Beaufort Sea. Our lipid and 16S rRNA results indicate that archaea of the ANME-2c and ANME-3 clades are involved in AOM in the MVs investigated.
Joshua F. Dean, Jurgen R. van Hal, A. Johannes Dolman, Rien Aerts, and James T. Weedon
Biogeosciences, 15, 7141–7154,Short summary
Lakes, rivers, ponds and streams are significant contributors of the greenhouse gas carbon dioxide to the atmosphere. This is partly due to the decomposition of plant and soil organic matter transported through these aquatic systems by microbial communities. In determining how vulnerable this organic material is to decomposition during aquatic transport, we show that standardized treatments in experiments can affect the way microbial communities behave and potentially the experimental outcome.
Xi Wen, Viktoria Unger, Gerald Jurasinski, Franziska Koebsch, Fabian Horn, Gregor Rehder, Torsten Sachs, Dominik Zak, Gunnar Lischeid, Klaus-Holger Knorr, Michael E. Böttcher, Matthias Winkel, Paul L. E. Bodelier, and Susanne Liebner
Biogeosciences, 15, 6519–6536,Short summary
Rewetting drained peatlands may lead to prolonged emission of the greenhouse gas methane, but the underlying factors are not well described. In this study, we found two rewetted fens with known high methane fluxes had a high ratio of microbial methane producers to methane consumers and a low abundance of methane consumers compared to pristine wetlands. We therefore suggest abundances of methane-cycling microbes as potential indicators for prolonged high methane emissions in rewetted peatlands.
Kyle R. Frischkorn, Andreas Krupke, Cécile Guieu, Justine Louis, Mónica Rouco, Andrés E. Salazar Estrada, Benjamin A. S. Van Mooy, and Sonya T. Dyhrman
Biogeosciences, 15, 5761–5778,Short summary
Trichodesmium is a keystone genus of marine cyanobacteria that is estimated to supply nearly half of the ocean’s fixed nitrogen, fuelling primary productivity and the cycling of carbon and nitrogen in the ocean. In our study we characterize Trichodesmium ecology across the western tropical South Pacific using gene and genome sequencing and geochemistry. We detected genes for phosphorus reduction, providing a mechanism for the noted importance of this organism in the ocean's phosphorus cycle.
Audrey Lallement, Ludovic Besaury, Elise Tixier, Martine Sancelme, Pierre Amato, Virginie Vinatier, Isabelle Canet, Olga V. Polyakova, Viatcheslay B. Artaev, Albert T. Lebedev, Laurent Deguillaume, Gilles Mailhot, and Anne-Marie Delort
Biogeosciences, 15, 5733–5744,Short summary
The main objective of this work was to evaluate the potential degradation of phenol, a highly toxic pollutant, by cloud microorganisms. Phenol concentrations measured on five cloud samples collected at the PUY station in France were from 0.15 to 0.74 µg L−1. Metatranscriptomic analysis suggested that phenol could be biodegraded directly in clouds, likely by Gammaproteobacteria. A large screening showed that 93 % of 145 bacterial strains isolated from clouds were able to degrade phenol.
Sara J. Bender, Dawn M. Moran, Matthew R. McIlvin, Hong Zheng, John P. McCrow, Jonathan Badger, Giacomo R. DiTullio, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 15, 4923–4942,Short summary
Phaeocystis antarctica is an important phytoplankter of the Antarctic coastal environment where it dominates the early season bloom after sea ice retreat. Iron nutrition was found to be an important factor that results in Phaeocystis colony formation and a large restructuring of the proteome, including changes associated with the flagellate to colonial transition and adaptive responses to iron scarcity. Analysis of Phaeocystis proteins from the Ross Sea revealed the presence of both cell types.
Sophie Bonnet, Mathieu Caffin, Hugo Berthelot, Olivier Grosso, Mar Benavides, Sandra Helias-Nunige, Cécile Guieu, Marcus Stenegren, and Rachel Ann Foster
Biogeosciences, 15, 4215–4232,
Dina Spungin, Natalia Belkin, Rachel A. Foster, Marcus Stenegren, Andrea Caputo, Mireille Pujo-Pay, Nathalie Leblond, Cécile Dupouy, Sophie Bonnet, and Ilana Berman-Frank
Biogeosciences, 15, 3893–3908,Short summary
The way marine organisms die can determine the fate of organic matter (OM) in the ocean. We investigated whether a form of auto-induced programmed cell death (PCD) influenced phytoplankton mortality and fate of OM. Our results from high biomass blooms of the cyanobacterium Trichodesmium show evidence for PCD and high production of sticky carbon material termed transparent exopolymeric particles (TEP) that facilitates cellular aggregation and enhances the vertical flux of OM to depth.
Christian Nyrop Albers, Magnus Kramshøj, and Riikka Rinnan
Biogeosciences, 15, 3591–3601,
Natasha A. Gafar and Kai G. Schulz
Biogeosciences, 15, 3541–3560,Short summary
Emiliania huxleyi and Gephyrocapsa oceanica are the most prolific calcifying phytoplankton in today's oceans. We compare their sensitivity to combined anthropogenic stressors of temperature, light and CO2. For the future, we project a niche contraction for G. oceanica. Furthermore, there was good correlation of our new metric, the CaCO3 production potential, with satellite-derived concentrations in the modern ocean, indicating means of assessing overall coccolithophorid success in the future.
Marcus Stenegren, Andrea Caputo, Carlo Berg, Sophie Bonnet, and Rachel A. Foster
Biogeosciences, 15, 1559–1578,Short summary
We successfully performed quantitative PCR at sea. The qPCR data were procured within 3 h and used in decisions on further sampling on site. We designed and applied a new primer and probe set for quantifying the UCYN-A1 host and observed discrepancies between host and symbiont, which contradict previous studies. Lastly, we observed a clear vertical separation between a subsurface group (UCYN-A with hosts) and a surface group (remaining diazotrophs), mainly separated by temperature.
Bach, L. T., MacKinder, L. C. M., Schulz, K. G., Wheeler, G., Schroeder, D. C., Brownlee, C., and Riebesell, U.: Dissecting the impact of CO2 and pH on the mechanisms of photosynthesis and calcification in the coccolithophore Emiliania huxleyi, New Phytol., 199, 121–134, 2013.
Badger, M. P. S.: Alkenone isotopes show evidence of active carbon concentrating mechanisms in coccolithophores as aqueous carbon dioxide concentrations fall below 7 µmol L−1, Biogeosciences, 18, 1149–1160, https://doi.org/10.5194/bg-18-1149-2021, 2021.
Badger, M. P. S., Chalk, T. B., Foster, G. L., Bown, P. R., Gibbs, S. J., Sexton, P. F., Schmidt, D. N., Pälike, H., Mackensen, A., and Pancost, R. D.: Insensitivity of alkenone carbon isotopes to atmospheric CO2 at low to moderate CO2 levels, Clim. Past, 15, 539–554, https://doi.org/10.5194/cp-15-539-2019, 2019.
Badger, M. R., Andrews, T. J., Whitney, S. M., Ludwig, M., Yellowlees, D. C., Leggat, W., and Price, G. D.: The diversity and coevolution of Rubisco, plastids, pyrenoids, and chloroplast-based CO2-concentrating mechanisms in algae, Can. J. Botany, 76, 1052–1071, 1998.
Bates, D., Machler, M., Bolker, B., and Walker, S.: Fitting linear mixed-effects models using lme4, J. Stat. Softw., 67, 1–48, 2015.
Bice, K. L., Birgel, D., Meyers, P. A., Dahl, K. A., Hinrichs, K. U., and Norris, R. D.: A multiple proxy and model study of Cretaceous upper ocean temperatures and atmospheric CO2 concentrations, Paleoceanography, 21, 1–17, 2006.
Bidigare, R., Freeman, H., Hanson, L., Hayes, M., Jasper, P., King, L., Millero, J., Popp, N., Steinberg, A., and Wakeham, G.: Consistent fractionation of 13C in nature and in the laboratory: growth-rate effects in some haptophyte algae, Global Biogeochem. Cy., 11, 279–292, 1997.
Brandenburg, K. M.: Physiological control on carbon isotope fractionation in marine phytoplankton, Dryad [data set], https://doi.org/10.5061/dryad.hmgqnk9k8, 2022.
Boller, A. J., Thomas, P. J., Cavanaugh, C. M., and Scott, K. M.: Low stable carbon isotope fractionation by coccolithophore RubisCO, Geochim. Cosmochim. Ac., 75, 7200–7207, 2011.
Boller, A. J., Thomas, P. J., Cavanaugh, C. M., and Scott, K. M.: Isotopic discrimination and kinetic parameters of RubisCO from the marine bloom-forming diatom, Skeletonema costatum, Geobiology, 13, 33–43, 2015.
Bolton, C. T. and Stoll, H. M.: Late Miocene threshold response of marine algae to carbon dioxide limitation, Nature, 500, 558–562, 2013.
Bolton, C. T., Hernández-Sánchez, M. T., Fuertes, M. Á., González-Lemos, S., Abrevaya, L., Mendez-Vicente, A., Flores, J. A., Probert, I., Giosan, L., Johnson, J., and Stoll, H. M.: Decrease in coccolithophore calcification and CO2 since the middle Miocene, Nat. Commun., 7, 10284, https://doi.org/10.1038/ncomms10284, 2016.
Burkhardt, S., Riebesell, U., and Zondervan, I.: Effects of growth rate, CO2 concentration, and cell size on the stable carbon isotope fractionation in marine phytoplankton, Geochim. Cosmochim. Ac., 63, 3729–3741, 1999a.
Burkhardt, S., Riebesell, U., and Zondervan, I.: Stable carbon isotope fractionation by marine phytoplankton in response to daylength, growth rate, and CO2 availability, Mar. Ecol.-Prog. Ser., 184, 31–41, 1999b.
Cassar, N., Laws, E. A., and Popp, B. N.: Carbon isotopic fractionation by the marine diatom Phaeodactylum tricornutum under nutrient- and light-limited growth conditions, Geochim. Cosmochim. Ac., 70, 5323–5335, 2006.
Clark, I. D. and Lauriol, B.: Kinetic enrichment of stable isotopes in cryogenic calcites, Chem. Geol., 102, 217–228, 1992.
Dou, Z., Heinhorst, S., Williams, E. B., Murin, C. D., Shively, J. M., and Cannon, G. C.: CO2 fixation kinetics of Halothiobacillus neapolitanus mutant carboxysomes lacking carbonic anhydrase suggest the shell acts as a diffusional barrier for CO2, J. Biol. Chem., 283, 10377–10384, 2008.
Eichner, M., Thoms, S., Kranz, S. A., and Rost, B.: Cellular inorganic carbon fluxes in Trichodesmium: Aa combined approach using measurements and modelling, J. Exp. Bot., 66, 749–759, 2015.
Espie, G. S. and Kimber, M. S.: Carboxysomes: cyanobacterial RubisCO comes in small packages, Photosynth. Res., 109, 7–20, 2011.
Farquhar, G. D., Ehleringer, J. R., and Hubick, K. T.: Carbon isotope discrimination and photosynthesis, Annu. Rev. Plant Phys., 40, 503–537, 1989.
Finkel, Z. V., Sebbo, J., Feist-Burkhardt, S., Irwin, A. J., Katz, M. E., Schofield, O. M. E., Young, J. R., and Falkowski, P. G.: A universal driver of macroevolutionary change in the size of marine phytoplankton over the Cenozoic, P. Natl. Acad. Sci. USA, 104, 20416–20420, 2007.
Foster, G. L., Royer, D. L., and Lunt, D. J.: Future climate forcing potentially without precedent in the last 420 million years, Nat. Commun., 8, 1–8, 2017.
Freeman, H. and Hayes, J. M.: Fractionation of carbon isotopes by phytoplankton and estimates of ancient CO2 levels, Global Biogeochem. Cy., 6, 185–198, 1992.
Giordano, M., Beardall, J., and Raven, J. A.: CO2 concentrating mechanisms in algae: mechanisms, environmental modulation, and evolution, Annu. Rev. Plant Biol., 56, 99–131, 2005.
Hayes, J. M., Strauss, H., and Kaufman, A. J.: The abundance of 13C in marine organic matter and isotopic fractionation in the global biogeochemical cycle of carbon during the past 800 Ma, Chem. Geol., 161, 103–125, 1999.
Hermoso, M., Chan, I. Z. X., McClelland, H. L. O., Heureux, A. M. C., and Rickaby, R. E. M.: Vanishing coccolith vital effects with alleviated carbon limitation, Biogeosciences, 13, 301–312, https://doi.org/10.5194/bg-13-301-2016, 2016.
Hoins, M., Van de Waal, D. B., Eberlein, T., Reichart, G. J., Rost, B., and Sluijs, A.: Stable carbon isotope fractionation of organic cyst-forming dinoflagellates: evaluating the potential for a CO2 proxy, Geochim. Cosmochim. Ac., 160, 267–276, 2015.
Hoins, M., Eberlein, T., Van de Waal, D. B., Sluijs, A., Reichart, G. J., and Rost, B.: CO2-dependent carbon isotope fractionation in dinoflagellates relates to their inorganic carbon fluxes, J. Exp. Mar. Biol. Ecol., 481, 9–14, 2016a.
Hoins, M., Eberlein, T., Großmann, C. H., Brandenburg, K., Reichart, G.-J., Rost, B., Sluijs, A., and Van De Waal, D. B.: Combined effects of ocean acidification and light or nitrogen availabilities on 13C fractionation in marine dinoflagellates, PLoS One, 11, e0154370, https://doi.org/10.1371/journal.pone.0154370, 2016b.
Jasper, J. P. and Hayes, J. M.: A carbon isotope record of CO2 levels during the late Quaternary, Nature, 347, 462–464, 1990.
Keeling, P. J.: The number, speed, and impact of plastid endosymbioses in eukaryotic evolution, Annu. Rev. Plant Biol., 64, 583–607, 2013.
Kikutani, S., Nakajima, K., Nagasato, C., Tsuji, Y., Miyatake, A., and Matsuda, Y.: Thylakoid luminal Θ-carbonic anhydrase critical for growth and photosynthesis in the marine diatom Phaeodactylum tricornutum, P. Natl. Acad. Sci. USA, 113, 9828–9833, 2016.
Krumhardt, K. M., Lovenduski, N. S., Iglesias-Rodriguez, M. D., and Kleypas, J. A.: Coccolithophore growth and calcification in a changing ocean, Prog. Oceanogr., 159, 276–295, 2017.
Laws, E. A., Popp, B. N., Bidigare, R. R., Riebesell, U., Burkhardt, S., and Wakeham, S. G.: Controls on the molecular distribution and carbon isotopic composition of alkenones in certain haptophyte algae, Geochem. Geophy. Geosy., 2, 2000GC000057, https://doi.org/10.1029/2000GC000057, 2001.
Liu, Y. W., Eagle, R. A., Aciego, S. M., Gilmore, R. E., and Ries, J. B.: A coastal coccolithophore maintains pH homeostasis and switches carbon sources in response to ocean acidification, Nat. Commun., 9, 1–12, 2018.
Maberly, S. C., Raven, J. A., and Johnston, A. M.: Discrimination between 12C and 13C by marine plants, Oecologia, 91, 481–492, 1992.
Macdonald, F. A.: Deep-time paleoclimate proxies, AGU Adv., 1, 1–3, 2020.
Maeda, S. I., Badger, M. R., and Price, G. D.: Novel gene products associated with NdhD3/D4-containing NDH-1 complexes are involved in photosynthetic CO2 hydration in the cyanobacterium, Synechococcus sp. PCC7942, Mol. Microbiol., 43, 425–435, 2002.
Matsuda, Y., Hopkinson, B. M., Nakajima, K., Dupont, C. L., and Tsuji, Y.: Mechanisms of carbon dioxide acquisition and CO2 sensing in marine diatoms: a gateway to carbon metabolism, Philos. T. R. Soc. B, 372, 20160403, https://doi.org/10.1098/rstb.2016.0403, 2017.
McClelland, H. L. O., Bruggeman, J., Hermoso, M., and Rickaby, R. E. M.: The origin of carbon isotope vital effects in coccolith calcite, Nat. Commun., 8, 14511, https://doi.org/10.1038/ncomms14511, 2017.
McNevin, D. B., Badger, M. R., Whitney, S. M., Von Caemmerer, S., Tcherkez, G. G. B., and Farquhar, G. D.: Differences in carbon isotope discrimination of three variants of D-ribulose-1,5-bisphosphate carboxylase/oxygenase reflect differences in their catalytic mechanisms, J. Biol. Chem., 282, 36068–36076, 2007.
Mitchell, M., Muftakhidinov, B., and Winchen, T.: Engauge Digitizer 4.1, Zenodo, https://doi.org/10.5281/zenodo.3941227, 2020.
Nakajima, K., Tanaka, A., and Matsuda, Y.: SLC4 family transporters in a marine diatom directly pump bicarbonate from seawater, P. Natl. Acad. Sci. USA, 110, 1767–1772, 2013.
O'Leary, M. H.: Measurement of the isotope fractionation associated with diffusion of carbon dioxide in aqueous solution, J. Phys. Chem., 88, 823–825, 1984.
O'Leary, M. H., Madhavan, S., and Paneth, P.: Physical and chemical basis of carbon isotope fractionation in plants, Plant. Cell Environ., 15, 1099–1104, 1992.
Pagani, M., Zachos, J. C., Freeman, K. H., Tipple, B., and Bohaty, S.: Atmospheric science: marked decline in atmospheric carbon dioxide concentrations during the Paleogene, Science, 309, 600–603, 2005.
Phelps, S. R., Hennon, G. M. M., Dyhrman, S. T., Hernández Limón, M. D., Williamson, O. M., and Polissar, P. J.: Carbon isotope fractionation in Noelaerhabdaceae algae in culture and a critical evaluation of the alkenone paleobarometer, Geochem. Geophy. Geosy., 22, 1–20, 2021.
Popp, B. N., Laws, E. A., Bidigare, R. R., Dore, J. E., Hanson, K. L., and Wakeham, S. G.: Effect of phytoplankton cell geometry on carbon isotopic fractionation, Geochim. Cosmochim. Ac., 62, 69–77, 1998.
Price, G. D., Maeda, S. I., Omata, T., and Badger, M. R.: Modes of active inorganic carbon uptake in the cyanobacterium, Synechococcus sp. PCC7942, Funct. Plant Biol., 29, 131–149, 2002.
Price, G. D., Badger, M. R., Woodger, F. J., and Long, B. M.: Advances in understanding the cyanobacterial CO2-concentrating- mechanism (CCM): Functional components, Ci transporters, diversity, genetic regulation and prospects for engineering into plants, J. Exp. Bot., 59, 1441–1461, 2008.
Ratti, S., Giordano, M., and Morse, D.: CO2-concentrating mechanisms of the potentially toxic dinoflagellate Protoceratium reticulatum (Dinophyceae, Gonyaulacales), J. Phycol., 43, 693–701, 2007.
Rau, G. H., Riebesell, U., and Wolf-Gladrow, D.: A model of photosynthetic 13C fractionation by marine phytoplankton based on diffusive molecular CO2 uptake, Mar. Ecol.-Prog. Ser., 133, 275–285, 1996.
Raven, J. A. and Johnston, A.: Mechanisms of inorganic-carbon acquisition in marine phytoplankton and their implications for the use of other resources, Limnol. Oceanogr., 36, 1701–1714, 1991.
R Core Team: R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/ (last access: January 2022), 2020.
Reinfelder, J. R.: Carbon concentrating mechanisms in eukaryotic marine phytoplankton, Ann. Rev. Mar. Sci., 3, 291–315, 2011.
Riebesell, U., Burkhardt, S., Dauelsberg, A., and Kroon, B.: Carbon isotope fractionation by a marine diatom: dependence on the growth-rate-limiting resource, Mar. Ecol.-Prog. Ser., 193, 295–303, 2000a.
Riebesell, U., Revill, A. T., Holdsworth, D. G., and Volkman, J. K.: The effects of varying CO2 concentration on lipid composition and carbon isotope fractionation in Emiliania huxleyi, Geochim. Cosmochim. Ac., 64, 4179–4192, 2000b.
Roeske, C. A. and O'Leary, M. H.: Carbon isotope effects on the enzyme-catalyzed carboxylation of ribulose bisphosphate, Biochemistry, 23, 6275–6284, 1984.
Rohling, E. J., Sluijs, A., Dijkstra, H. A., Köhler, P., Van De Wal, R. S. W., Von Der Heydt, A. S., Beerling, D. J., Berger, A., Bijl, P. K., Crucifix, M., Deconto, R., Drijfhout, S. S., Fedorov, A., Foster, G. L., Ganopolski, A., Hansen, J., Hönisch, B., Hooghiemstra, H., Huber, M., Huybers, P., Knutti, R., Lea, D. W., Lourens, L. J., Lunt, D., Masson-Demotte, V., Medina-Elizalde, M., Otto-Bliesner, B., Pagani, M., Pälike, H., Renssen, H., Royer, D. L., Siddall, M., Valdes, P., Zachos, J. C., and Zeebe, R. E.: Making sense of palaeoclimate sensitivity, Nature, 491, 683–691, 2012.
Rokitta, S. D. and Rost, B.: Effects of CO2 and their modulation by light in the life-cycle stages of the coccolithophore Emiliania huxleyi, Limnol. Oceanogr., 57, 607–618, 2012.
Rokitta, S. D., Kranz, S. A., and Rost, B.: Inorganic carbon acquisition by aquatic primary producers, in: Blue planet, red and green photosynthesis, edited by: Maberly, S. and Gontero, B., ISTE Ltd, London, ISBN 9-781-78945-082-8, 2022.
Rost, B., Zondervan, I., and Riebesell, U.: Light-dependent carbon isotope fractionation in the coccolithophorid Emiliania huxleyi, Limnol. Oceanogr., 47, 120–128, 2002.
Rost, B., Riebesell, U., and Sültemeyer, D.: Carbon acquisition of marine phytoplankton: effect of photoperiod length, Limnol. Oceanogr., 51, 12–20, 2006.
Rost, B., Zondervan, I., and Wolf-Gladrow, D.: Sensitivity of phytoplankton to future changes in ocean carbonate chemistry: current knowledge, contradictions and research directions, Mar. Ecol.-Prog. Ser., 373, 227–237, 2008.
Samukawa, M., Shen, C., Hopkinson, B. M., and Matsuda, Y.: Localization of putative carbonic anhydrases in the marine diatom, Thalassiosira pseudonana, Photosynth. Res., 121, 235–249, 2014.
Schulz, K. G., Rost, B., Burkhardt, S., Riebesell, U., Thoms, S., and Wolf-Gladrow, D. A.: The effect of iron availability on the regulation of inorganic carbon acquisition in the coccolithophore Emiliania huxleyi and the significance of cellular compartmentation for stable carbon isotope fractionation, Geochim. Cosmochim. Ac., 71, 5301–5312, 2007.
Sharkey, T. D. and Berry, J. A.: Carbon isotope fractionation of algae as influenced by an inducible CO2 concentrating mechanism, in: Inorganic Carbon Uptake by Aquatic Photosynthetic Organisms, edited by: Lucas, W. J. and Berry, J. A., American Society of Plant Physiologists, 389–401, ISBN 10 0943088054, ISBN 13 9780943088051, 1985.
Siegenthaler, U. and Münnich, K. O.: 12C 13C fractionation during CO2 transfer from air to sea, Carbon Cycle Model., 249–251, 1981.
Sluijs, A., van Roij, L., Frieling, J., Laks, J., and Reichart, G. J.: Single-species dinoflagellate cyst carbon isotope ecology across the Paleocene-Eocene Thermal Maximum, Geology, 46, 79–82, 2018.
Stoll, H. M., Guitian, J., Hernandez-Almeida, I., Mejia, L. M., Phelps, S., Polissar, P., Rosenthal, Y., Zhang, H., and Ziveri, P.: Upregulation of phytoplankton carbon concentrating mechanisms during low CO2 glacial periods and implications for the phytoplankton pCO2 proxy, Quaternary Sci. Rev., 208, 1–20, 2019.
Tabita, F. R., Satagopan, S., Hanson, T. E., Kreel, N. E., and Scott, S. S.: Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships, J. Exp. Bot., 59, 1515–1524, 2008.
Tachibana, M., Allen, A. E., Kikutani, S., Endo, Y., Bowler, C., and Matsuda, Y.: Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana, Photosynth. Res., 109, 205–221, 2011.
Tierney, J. E., Poulsen, C. J., Montañez, I. P., Bhattacharya, T., Feng, R., Ford, H. L., Hönisch, B., Inglis, G. N., Petersen, S. V., Sagoo, N., Tabor, C. R., Thirumalai, K., Zhu, J., Burls, N. J., Foster, G. L., Goddéris, Y., Huber, B. T., Ivany, L. C., Turner, S. K., Lunt, D. J., McElwain, J. C., Mills, B. J. W., Otto-Bliesner, B. L., Ridgwell, A., and Zhang, Y. G.: Past climates inform our future, Science, 370, eaay3701, https://doi.org/10.1126/science.aay3701, 2020.
Tortell, P. D.: Evolutionary and ecological perspectives on carbon acquisition in phytoplankton, Limnol. Oceanogr., 45, 744–750, 2000.
Van De Waal, D. B., Eberlein, T., Bublitz, Y., John, U., and Rost, B.: Shake it easy: a gently mixed continuous culture system for dinoflagellates, J. Plankton Res., 36, 889–894, 2014.
Van de Waal, D. B., Brandenburg, K. M., Keuskamp, J., Trimborn, S., Rokitta, S., Kranz, S., and Rost, B.: Highest plasticity of carbon concentrating mechanisms in earliest evolved phytoplankton, Limnol. Oceanogr. Lett., 4, 37–43, 2019.
van Roij, L., Sluijs, A., Laks, J. J., and Reichart, G. J.: Stable carbon isotope analyses of nanogram quantities of particulate organic carbon (pollen) with laser ablation nano combustion gas chromatography/isotope ratio mass spectrometry, Rapid Commun. Mass Sp., 31, 47–58, 2017.
Whitney, S. M., Houtz, R. L., and Alonso, H.: Advancing our understanding and capacity to engineer nature's CO2-sequestering enzyme, Rubisco, Plant Physiol., 155, 27–35, 2011.
Wilkes, E. B. and Pearson, A.: A general model for carbon isotopes in red-lineage phytoplankton: interplay between unidirectional processes and fractionation by RubisCO, Geochim. Cosmochim. Ac., 265, 163–181, 2019.
Wilkes, E. B., Carter, S. J., and Pearson, A.: CO2-dependent carbon isotope fractionation in the dinoflagellate Alexandrium tamarense, Geochim. Cosmochim. Ac., 212, 48–61, 2017.
Witkowski, C. R., Weijers, J. W. H., Blais, B., Schouten, S., and Sinninghe Damsté, J. S.: Molecular fossils from phytoplankton reveal secular P trend over the phanerozoic, Sci. Adv., 4, 1–8, 2018.
Zeebe, R. E.: Kinetic fractionation of carbon and oxygen isotopes during hydration of carbon dioxide, Geochim. Cosmochim. Ac., 139, 540–552, 2014.
Zeebe, R. E. and Wolf-Gladrow, D. A.: CO2 in Seawater: Equilibrium, Kinetics, Isotopes, Elsevier Science Publishing Co., Amsterdam, the Netherlands, ISBN 9780444509468, 2001.
Zeebe, R. E., Wolf-Gladrow, D. A., and Jansen, H.: On the time required to establish chemical and isotopic equilibrium in the carbon dioxide system in seawater, Mar. Chem., 65, 135–153, 1999.
Zhang, H., Torres-Romero, I., Anjewierden, P., Jaggi, M., and Stoll, H. M.: The DIC carbon isotope evolutions during CO2 bubbling: implications for ocean acidification laboratory culture, Chem. Geol., 2022.
Zhang, Y. G., Pearson, A., Benthien, A., Dong, L., Huybers, P., Liu, X., and Pagani, M.: Refining the alkenone-pCO2 method I: Lessons from the Quaternary glacial cycles, Geochim. Cosmochim. Ac., 260, 177–191, 2019.
Zhu, J., Poulsen, C. J., and Otto-Bliesner, B. L.: High climate sensitivity in CMIP6 model not supported by paleoclimate, Nat. Clim. Chang., 10, 378–379, 2020.
Reconstructions of past CO2 concentrations rely on proxy estimates, with one line of proxies relying on the CO2-dependence of stable carbon isotope fractionation in marine phytoplankton. Culturing experiments provide insights into which processes may impact this. We found, however, that the methods with which these culturing experiments are performed also influence 13C fractionation. Caution should therefore be taken when extrapolating results from these experiments to proxy applications.
Reconstructions of past CO2 concentrations rely on proxy estimates, with one line of proxies...