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Application of Stable Isotopes in Biogeosciences

This session is open to all contributions in biogeochemistry and ecology where stable isotope techniques are used as analytical tools, with a focus on stable isotopes of light elements (C, H, O, N, S, ...). We welcome studies from both terrestrial and aquatic (including marine) environments as well as methodological and experimental, theoretical and modeling studies that introduce new approaches or techniques (including natural abundance work, labeling studies, multi-isotope approaches, clumped and metal isotopes).

Convener: Michael E. Böttcher | Co-conveners: Kirstin Dähnke, Gerd Gleixner, Nikolaus Gussone
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Tue, 27 Apr, 13:30–15:00

Chairpersons: Michael E. Böttcher, Gerd Gleixner

5-minute convener introduction

Jochem Baan et al.

Hydrogen stable isotope analyses of plant derived n‑alkanes have been developed as potential tools for ecological, environmental and palaeoclimatological studies. The hydrogen stable isotope composition (δ2H) of source and leaf water influence n‑alkane δ2H values (δ2Halkane), but hydrogen isotope fractionation occurs during plant carbon metabolism. Large variation in δ2Halkane values among species at a single geographic location have been observed, suggesting that metabolic isotope effects are large, but the origin of this biochemical variation remains poorly understood. To explore the variation in δ2Halkane, and test if phylogenetic relatedness structures variation in δ2Halkane values across species, we measured δ2H values of n‑alkanes in a total of 218 samples and 183 eudicot plant species grown in a single common garden during the 2019 growing season. Our results show that most variation in δ2Halkane values could be explained by family and genus identity, and δ2Halkane values significantly evolved along the phylogeny. To identify the intracellular location where the variation in δ2Halkane is induced, we measured δ2Halkane values as well as δ2H values of plastid‑produced precursors, as the acetogenic pathway in higher plants is spatially separated within cells, where fatty acids up to 18 carbon units are produced in the plastid, and additional chain elongation (e.g., for n‑alkane synthesis) occurs in the endoplasmic reticulum. Specifically, during the 2020 growing season, we measured δ2H values of n-alkanes and n‑C16:0 fatty acids (palmitic acid; δ2Hn‑C16:0) in a total of 61 samples and 58 eudicot plant species grown in a single common garden and determined how the two spatially separated parts of the acetogenic pathway influenced δ2Halkane values by comparing to δ2Hn‑C16:0 values. δ2Hn‑C16:0 and δ2Halkane values showed a significant positive correlation, suggesting that δ2Halkane biosynthetic isotopic variability is largely shaped by processes in the plastid leading up to the synthesis of palmitic acid. Strikingly, δ2Hn‑C16:0 values were almost always higher than δ2Halkane values, and the offset between these values (as an enrichment factor; ƐC16:0‑alkane in ‰) was also related to phylogeny. This illustrates that the extent to which the two spatially separated parts of the acetogenic pathway influence δ2H values of n‑alkanes depends on species identity due to phylogenetic effects. Our results demonstrate that variation in δ2Halkane values among species is strongly related to phylogenetic effects, and that most of these effects are generated early in lipid biosynthesis. Future studies should address if the observed variability can be explained by metabolic traits.

How to cite: Baan, J., Holloway-Phillips, M., Nelson, D. B., de Vos, J. M., and Kahmen, A.: Biosynthetic sources of hydrogen isotope variability in acetogenic lipids are driven by phylogeny in eudicot plants, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-4389, https://doi.org/10.5194/egusphere-egu21-4389, 2021.

Getachew A. Adnew et al.

Stable isotope (δ13C and δ18O) and mole fraction measurements of CO2 are used to constrain the carbon cycle. However, the gross fluxes of the carbon cycle, especially photosynthesis and respiration, remain uncertain due to the challenging task of distinguishing individual flux terms from each other. The clumped isotope composition (Δ47) of CO2 has been suggested as an additional tracer for gross CO2 fluxes since it depends mainly on temperature but not on the bulk isotopic composition of leaf, soil and surface water, unlike δ18O of CO2.

In this study, we quantify the effect of photosynthetic gas exchange on Δ47 of CO2 using leaf cuvette experiments with two C3 and one C4 plants and discuss challenges and possible applications of clumped isotope measurements. The experimental results are supported by calculations with a leaf cuvette model. Our results demonstrate how the effect of gas exchange on Δ47 is controlled by CO2-H2O isotope exchange (using plants with different carbonic anhydrase activity), and kinetic fractionation as CO2 diffuses into and out of the leaf (using plants with different stomatal and mesophyll conductance). We experimentally confirm the previously suggested dependence of Δ47­­ on the stomatal conductance and back-diffusion flux.

How to cite: Adnew, G. A., Hofmann, M. E. G., Pons, T. L., Koren, G., Ziegler, M., Lourens, L. J., Peters, W., and Röckmann, T.: Fractionation of clumped isotopes of CO2 during photosynthesis, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-9164, https://doi.org/10.5194/egusphere-egu21-9164, 2021.

Yajun Li et al.

Studies on particulate inorganic carbon (PIC) in inland waters are relatively scarce due to the low concentration of PIC which makes it difficult to be measured accurately. In other studies, a characteristic ratio of PIC in total suspended solids in the water column has been proposed to estimate the river PIC flux to the sea, and a titration method to measure the PIC fluxes in karst rivers has been reported. Therefore, we used the Gas Bench Ⅱ-IRMS coupled technique method to analyze the δ13CPIC and PIC concentration in inland waters. The method has the advantage of being suitable for the accurate determination of the isotopic composition of trace PIC samples.

The purging time and carbon content of samples are the important factors affecting experimental accuracy. This study proposed the optimal purge time and the lowest carbon content of the inland water sample. The samples in the experiment included laboratory calcium carbonate standard (99.95 % purity) and PIC samples from the Wujiang River. The PIC samples from Wujiang River were collected on glass fiber filters. Datasets from the experiment demonstrated that the ideal purge time is 500-700 s, and at least 25 μg C should be included in the sample. The instrument signal value is low and the isotopic value fluctuates widely when the purge time is less than 500 s. The phosphoric acid cannot be injected into the sample bottle due to the high pressure in it when the purge time is more than 700 s. Therefore, a purging time of 600 s was used for the field sample analyses. The peak area displayed by the device is correlated with the carbon content in the sample, and the datasets show a good linear relationship between the peak area and carbon content in the sample when the sample be analyzed contained more than 25 μg of inorganic carbon. The carbon content of the sample can be calculated from the peak area of the same batch of calcium carbonate standard. While the peak signal is too low to detect the sample accurately when the C content is less than 25 μg. Therefore, the sample should contain more than 25 μg for the field sample analyses. This study will help to provide a reference for the method of determining the PIC content and isotopic composition in inland water.

How to cite: Li, Y., Meng, F., and Wang, B.: A method for the analyses of carbon stable isotope and content of particulate inorganic carbon in inland waters , EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-5484, https://doi.org/10.5194/egusphere-egu21-5484, 2021.

Yuntao Wu and Zhaoliang Song

Carbon (C) and nitrogen (N) isotopes are important traits to characterize terrestrial ecosystems. Studying the relationships between carbon and nitrogen isotopes of soils and plants in different grassland types and under different environmental conditions is of great importance to the reconstruction of past climate. In this study, we selected three different grassland ecosystems (temperate meadow steppe, temperate typical steppe and temperate desert steppe) in northern China, collected meteorological data and plant and soil samples, determined the basic physical and chemical properties, C and N isotopes to explore the patterns and controlling factors of C and N isotopes in plants and soils of grasslands in northern China. The results showed that there were significant differences in soil δ13C and δ15N between different grassland types in the northern temperate zone. The soil δ13C and δ15N of different depths of the northern temperate grassland soil increased with the increase of soil depth. The surface soil δ13C of temperate meadow steppe and temperate desert steppe had a good correlation with plant sample δ13C. The surface soil δ15N temperate typical steppe and temperate desert steppe had a good correlation with plant sample δ15N. Mean annual temperature (MAT) and mean annual precipitation (MAP) had a complicated relationship with carbon and nitrogen isotopes of surface soil and plant sample in northern temperate grassland. The surface soil δ13C and δ15N and the plant sample δ15N can be used as indicators of the change of MAT.

Keywords: carbon isotopes, nitrogen isotopes, grasslands, climate, soil depth

How to cite: Wu, Y. and Song, Z.: Carbon and nitrogen isotopes in grasslands of northern China, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2041, https://doi.org/10.5194/egusphere-egu21-2041, 2021.

Vao Fenotiana Razanamahandry et al.

Madagascar is an island characterized by a sharp vegetation gradients in landscape and the extent to which the central highlands were once covered by forest is still under debate. Stable carbon isotope ratios have been an important tracer to understand vegetation shifts in a landscape over time because forest plants (following the C3 photosynthetic pathway) and grasses (following the C4 pathway for the majority of tropical and subtropical species) show a different degree of isotope fractionation. The main aim of this study is to provide insight into the past vegetation history of the grasslands in the Lake Alaotra region (central Madagascar). This region is under high anthropogenic pressure as it is the most important rice-producing region in Madagascar. While much of the Lake Aloatra catchment consists of grassland-covered hills, with a high density of lavaka (large erosional features), pristine forests are located just east of the lake and these form the most western part of a larger rainforest-covered region extending up to the east coast of the island. Soil profiles were sampled along the hillslope gradient at both forested and grassland sites, whereby carbon stocks were quantified and δ13C values of soil organic carbon (OC) were measured to find evidence for past forest vegetation in the grassland sites. The soil organic carbon content of grassland soil profile was extremely low, from 0.4 to 1.8% in the top layer and rapidly decreasing to 0.2 % below 100 cm depth. The current vegetation predominantly consists of C4 grasses (δ13C ~-13 ‰), yet soil δ13C-OC ranges between -25.9 and -16.6‰, and most profiles show a decrease in δ13C-OC with depth, in contrast to observations in the (C3-dominated) forest profiles, which show a typical enrichment in 13C with depth. δ13C values in grassland and forest profiles converge to similar values (within 2.1 ±1.8 ‰) at depths below ~80cm, suggesting that the grasslands in the Lake Alaotra region have developed on formerly forested soils. Moreover, the soil OC stock of grasslands was ~55.6% lower than along the forested hillslopes for the upper 30 cm layer. Our results are consistent with the hypothesis that a vegetation change has occurred in the lake Alaotra region, and offer a promising avenue to expand this approach on a wider scale to help understand the vegetation cover change in the central highland of Madagascar.

How to cite: Razanamahandry, V. F., Dewaele, M., Govers, G., Brosens, L., Campforts, B., Jacobs, L., Razafimbelo, T., Rafolisy, T., and Bouillon, S.: Stable isotope profiles of soil organic carbon in forested and grassland landscapes in the Lake Alaotra catchment (Madagascar): insights in past vegetation changes., EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8382, https://doi.org/10.5194/egusphere-egu21-8382, 2021.

Magdalena E. G. Hofmann et al.

Oxygen (18O/16O) and deuterium (D/H) isotopes are a widespread tool to trace physical and chemical processes in hydrology and biogeosciences. Precision and throughput are key parameters for water isotope analysis. Here, we will present two new methodologies for the Picarro L2130-i Cavity Ring-Down Spectroscopy (CRDS) water isotope analyzer that allow to increase the throughput with no compromise of data quality.

The Picarro Express Method now distinguishes between a memory reduction stage and a sample analysis stage and allows to measure up to 50 samples per day while maintaining the excellent precision of CRDS (i.e. 0.01‰ for δ18O and 0.05‰ for δD). This corresponds to doubling the throughput compared to the standard Picarro methodology. The Picarro Survey Method makes use of ultrafast injections and sorts the samples by their measured isotopic values, enabling a powerful new strategy to reduce memory effects.

We will discuss different measurement strategies to increase the throughput for routine water isotope analysis. The improved methodologies do not require any hardware changes and are solely based on modifications of the injection procedure. If you are interested in Picarro’s off-the-shelve solution for increasing productivity of your existing and future installations, please visit the Picarro vEGU 2021 booth for a free voucher.

How to cite: Hofmann, M. E. G., Lin, Z., Woźniak, J., and Drori, K.: Improved throughput for δ18O and δD measurements of water with Cavity Ring-Down Spectroscopy, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14254, https://doi.org/10.5194/egusphere-egu21-14254, 2021.

Marlene Dordoni et al.
The appearance of a Metalimnetic Oxygen Minimum (MOM) has been recorded in many natural lakes and reservoirs. However, its isotopic characterization with oxygen and carbon stable isotopes have not yet been fully constrained. The purpose of this work is to apply stable isotopes of carbon and oxygen to characterize photosynthetic and respiratory activities in the Rappbode Reservoir, Germany. Here we present the results of a 48 hours intensive sampling in July 2020. We provide preliminary data of dissolved oxygen (DO) concentration and saturation profiles, together with dissolved inorganic carbon (DIC). This includes data of oxygen (δ18ODO) and carbon (δ13CDIC) stable isotopes with particular focus on the metalimnion. Our profiles identified minor differences from day to day, such as an additional respiration-like peak above the MOM. Samples from within the MOM were characterized by the lowest oxygen content and saturation (7.05 mg L-1 and 75 %, respectively) and the highest δ18ODO (up to +30.1‰). These samples also showed the lowest δ13CDIC values (down to -12.8‰). Surface layers (between 0 and 9 meters) and the deepest water sample (65 meters) did not follow the expected depth profiles for δ18ODO and δ13CDIC. Surface layers were likely influenced by equilibration with the atmosphere that was enhanced by windy conditions. On the other hand, samples from 65 meters depth could have been perturbed by the presence of organic material from sediments. Moreover, oxygen and carbon stable isotopes patterns were able to show that the MOM can migrate within the water column up to 5 meters within 12 hours. These findings offer an interesting basis to establish mass balances of oxygen and carbon turnover in water bodies.

How to cite: Dordoni, M., Rinke, K., Seewald, M., Schmidmeier, J., and Barth, J. A. C.: Stable isotopes of oxygen to characterize a Metalimnetic Oxygen Minimum: insights from a 48 hours field campaign at Rappbode Reservoir, Germany, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-10279, https://doi.org/10.5194/egusphere-egu21-10279, 2021.

Christian Alexander Schöpke et al.

Stable isotope measurements have been used as a tool for understanding landfill processes for over two decades. The stable isotope natural abundance signatures of CH4 and CO2 give insight into the extent and duration of processes forming and consuming landfill gas, based on known kinetic fractionation factors for carbon turnover, carbon decomposition, methanogenesis and methane oxidation. Variations in isotopic ratios of carbon in CH4 isotopocules have been documented for many landfills and can be interpreted in terms of methanogenesis, gaseous transport (both diffusive and by mass-flow) and oxidation. The aim of this contribution is to test that δ13C signatures of inorganic carbon in leachate and in CO2/CH4 as well as the DH signature of CH4 and leachate can also be used to estimate the biodegradability of remaining organic matter in a closed landfill based on principles of Rayleigh fractionation. Our strategy is to perform laboratory experiments with excavated landfill waste from three different landfills in Norway with contrasting waste quality. Apparent fractionation coefficients will be compared with independently measured biodegradation potentials and physicochemical properties of the waste. Laboratory results will be integrated with field measurements of the isotopic composition of seeped and collected landfill gas and integrated into a landfill isotopic model. The landfill isotopic model will be used to estimate the remaining CH4 emission potential of decommissioned and covered municipal landfills. The results from this study are relevant for landfill owners and operators as a tool to estimate the duration and volume of gas emissions at a particular site and to define the landfill management strategy appropriately.

How to cite: Schöpke, C. A., Johansen, I., Polteau, S., Mørkved, P. T., Yarushina, V., and Dörsch, P.: Using stable isotopes as an indicator for the remaining gas generation potential in decommissioned municipal waste landfills – a concept study, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14955, https://doi.org/10.5194/egusphere-egu21-14955, 2021.

Christoph Malik et al.

The biogeochemistry of sulfur and carbon in groundwater of a Quaternary porous aquifer system and associated surface (lake) waters was investigated to identify processes of water mixing and the sources of dissolved sulfate and dissolved inorganic carbon (DIC). The study area is situated in North-Eastern Germany (Mecklenburg-Western Pomerania) close to the Baltic Sea coastline. The area is under impact by agricultural activity on a regional scale. A major goal was to identify the natural and anthropogenic key hydrobiogeochemical processes controlling the coupled element cycles upon groundwater development. Besides major and minor elements, redox-sensitive trace elements, nutrients, and stable mulit-isotope signatures (H, C, O, S) were considered.

While water isotopes of most groundwaters are positioned on the meteoric water line, surface waters are affected by an evaporation-induced enrichment of heavy isotopes. These shifts allow for a quantification of mixing proportions in influenced groundwater wells between direct precipitation-derived groundwater and  infiltrating lake water born fractions.

Major element hydrochemical and the carbon isotope composition of DIC indicate soil CO2 and the subterrestrial dissolution of carbonate minerals within the aquifer matrix as primary sources for DIC. Furthermore, contributions from oxidized dissolved organic carbon (DOC) under water-saturated conditions are found.

The coupled sulfur and oxygen isotope composition of dissolved sulfate indicates an origin dominatly  from the subterrestrial oxidation of iron sulfides, mainly pyrite. These iron sulfides are found in the sediments making the modern porous aquifer, in the study area with a deduced sulfur isotope composition of about -12 per mil vs. VCDT. These findings coupled to enhanced loads in dissolved iron and manganese, but low nutrient concentrations indicate nitrate as an important driver for lithoautothrophic pyrite oxidation. At several sites, the enhanced sulfate loads led to dissimilatory sulfate reduction and, thereby, to in-situ transformation of DOC (and/or Methane) to DIC. The enhancements of sulfate and DIC seems to be a typical feature in North German younger groundwaters and strongly (in)directly impacted by anthropogenic forces.

How to cite: Malik, C., Jenner, A.-K., Schmiedinger, I., and Böttcher, M. E.: Excess of sulfate and dissolved inorganic carbon in groundwaters fueled by pyrite oxidation and organic matter loads – A multi-isotope approach, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-6580, https://doi.org/10.5194/egusphere-egu21-6580, 2021.

Lucas Winski et al.

Land-ocean interactions in the coastal zone (LOICZ) are of particular interest regarding the exchange of water and elements, like nutrients, carbon, sulfur, and metals. Processes impacting groundwater fluxes at these boundaries belong to the still unsolved problems in hydrology (Blöschl et al., 2019). Stable isotope signatures (H, C, O, S), major and trace element contents in surface waters of a rewetted coastal peatland were investigated to understand the impact of storm-induced flooding by brackish seawater on hydrology and biogeochemical element cycling.

The study area is the Hütelmoor, a wetland located at the coastline of the southern Baltic Sea. The area is characterized by a continuous release of fresh water to the Baltic Sea via submarine groundwater discharge (Jurasinski et al., 2018). Surface water is partly drained to a nearby river, but the introduction of brackish waters into the peatland is typically precluded by a small dune and limited to storm-induced flooding events. In the present study, the spatially distributed composition of surface waters was investigated briefly after a flooding event. The results are compared with previous campaigns without actual salt water impact.

Conservative elements and water isotopes demonstrate the importance of seasonal variations due to varying evapotranspiration during pre-flood times and allow for a quantification of mixing processes in the post-flood waters. The impact of soil respired CO2, and/or the mineralization of organic matter or methane on the surface waters is indicated by a shift of the C isotope composition of DIC towards lighter data. The S and O isotopic composition of dissolved sulfate indicates an impact by solutions modified by net microbial sulfate reduction on pre-flood surface waters and a potential oxidation of reduced sulfur species in post-flooding solutions.

Previous flooding events already impacted element cycling in the peatland’s past and are also reflected by a sulfidization of peat layers (Fernández-Fernández et al., 2017) and the observation of local areas with enhanced dissolved concentrations in the central part of the peatland.

The study is supported by DFG during GK Baltic TRANSCOAST, DAAD, and Leibniz IOW.



  • Blöschl G. et al. (2019) Twenty-three unsolved problems in hydrology (UPH) – a community perspective. Hydrol. Sci. J. 64, 1141-1158.
  • Jurasinski G. et al. (2018) Understanding the coastal ecocline: Assessing sea-land-interactions at non-tidal, low-lying coasts through interdisciplinary research. Front. Mar. Sci. 5, 1-22.
  • Fernández-Fernández L.E. et al. (2017) Sulfur isotope biogeochemistry of soils from an episodically flooded coastal wetland, southern Baltic Sea. Geophys. Res. Abs. 19, EGU2017-14335.

How to cite: Winski, L., Rach, B., Jenner, A.-K., Westphal, J., Schmiedinger, I., von Ahn, C. M. E., Zeller, M., Malik, C., and Böttcher, M. E.: After the flood: Impact of salt water intrusions on the isotope biogeochemistry of a rewetted coastal peatland, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-3507, https://doi.org/10.5194/egusphere-egu21-3507, 2021.

Anna-Kathrina Jenner et al.

Peatlands serve as important ecosystems since they store a substantial fraction of global soil carbon. Through draining the internal biogeochemical processes may be changed impacting the transformation of stored carbon and plant material. Pristine peatlands are primarily associated with methanogenic and iron-cycling conditions, however, minor sulfur cycling may contribute to carbon mineralization in these ecosystems depending on the amount of atmospheric sulfur deposition and accumulation. In near coastal peatlands the element budget may be altered through natural or artificial flooding by brackish/marine waters. When introducing sulfate-bearing solutions, the concentrations of electron acceptors for anaerobic mineralization or organic matter increase when compared to fresh water conditions. The investigated area is planned to be flooded by Baltic Sea coastal waters in the near future.

Here we present results from a study from a drained peatland located in the southern part of the Baltic Sea. In the past the area was agriculturally used as grassland. Soil cores were retrieved along a transect perpendicular to the coast line for (isotope) biogeochemical analyses of pore water and solid phases. Analyses included the CNS composition of soils, and dissolved major elements, nutrients, sulphide, trace metals and stable isotopes of water, DIC, and sulfate (H, O, C, S). Furthermore, acid-extractions of metals were carried out to identify zones of dissolution and formation of authigenic phases. For quantification of microbial sulphate reduction rates (SRR) additional cores were retrieved and SRR were measured in whole-core incubations. 

The pore water isotopic composition is close to the local meteoric water line at the German Baltic Seas coast line. Concentration and stable isotope composition of DIC indicate mineralization of C3 type organic matter. Pore water trace metals content indicates the importance of anaerobic mineralization for release of metals into the pore and surface waters.


Acknowledgement: This study is supported by the DFG research training group BALTIC TRANSCOAST and Leibniz IOW.

How to cite: Jenner, A.-K., Schmiedinger, I., Kallmeyer, J., Gutekunst, C., Jurasinski, G., and Böttcher, M. E.: Biogeochemical carbon transformations in a drained coastal peatland of the southern Baltic Sea: An isotope and trace element perspective, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8022, https://doi.org/10.5194/egusphere-egu21-8022, 2021.

Mary Lipton et al.

Hydration levels influence carbon and nutrient cycles in soils. The rapid carbon release and nutrient utilization upon hydration in desiccated soils has been observed for decades, but little is known about the controls and timing of the underlying molecular events. This research is aimed at developing and using novel isotope based techniques to map the interdependence of carbon and nutrient cycling in soils using 13C labeled substrates as a tracer of nutrient fluxes in desiccated soil microbiomes after rewetting in combination with our novel Real Time Mass Spectrometry (RTMS) system 1, isotope ratio mass spectrometry (IRMS) and omics measurements.

Our experiments involve mapping the initial microbial response to wetting, by using a combination of an atmospheric monitoring RTMS instrument that measures the levels of CO2, O2, N2, H2O and their isotopologues, simultaneously in real time and IRMS which will be used to determine the biological fate of the carbon from each substrate. In each experiment desiccated soil that has been kept at drought conditions for 2 weeks was placed in the incubation chamber. Deionized water (control), 13C glucose and 13C alanine dissolved in water was added to the soil through a syringe to mimic a rewetting event. An identical initial hydration response measured by tracing the production of 12CO2 every 5 sec for the first 10 minutes after the addition of water was seen for all the samples potentially indicating that the carbon respired in this initial burst had formed an association with the cell (either intracellular or EPS bound) during dry down. The metabolism and respiration of glucose and alanine, measured by the production of 13CO2 occurred at a much slower time frame (60 to 90 minutes) where the rate of 13CO2 production of the glucose was about 10x that of alanine.

IRMS measurements were used to determine the preferential metabolic pathway of each substrate. The soil was removed from the chamber, treated with a mixture of methanol/chloroform/water, beadbeat, sonicated and centrifuged in a modified Folch extraction.  The resulting supernatant was allowed to separate into 3 fractions of polar metabolites (methanol layer), proteins (middle layer) and lipids (chloroform layer).  Each fraction was analyzed by IRMS to quantify the extent of 13C label incorporation into the soil phase to help guide interpretation of the 13CO2 production rates (measured via RTMS), the preferential metabolic pathway of each substrate will be determined. While it was seen that glucose was taken up into all of the biomass partitions as well as respired into CO2, alanine was metabolized to a lesser extent and was predominantly used in protein synthesis.

These studies represent approaches that showcase advanced stable isotope analyses to determine molecular provenance in ecosystems by developing an understanding of the molecular mechanisms involved in carbon and nutrient cycles in terrestrial ecosystems.

How to cite: Lipton, M., Smith, M., Moran, J., Thompson, A., Weitz, K., and Hofmockel, K.: Using 13C to Unravel the Molecular Mechanisms of Microbiome Response to Rewetting in Soil, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13880, https://doi.org/10.5194/egusphere-egu21-13880, 2021.

Catia Milene Ehlert von Ahn et al.

Submarine groundwater discharge (SGD) acts as a source of fresh water and dissolved substances for coastal ecosystems. Evaluation of the actual controls on SGD and corresponding chemical fluxes require a closer understanding of the processes that take place in the mixing zone between SGD and the coastal waters. It is hypothesized that artificial infrastructures, like sediment channeling, may ease the hydrological connection between coastal aquifer and coastal bottom water. The resultant, increase of SGD, changes the residence time in the mixing zone, and thereby, reduces the impact of early diagenesis. The present study focuses on the distribution of SGD, including the characterization of different mixing zones in the urbanized Wismar Bay (WB), southern Baltic Sea. Short sediment cores were retrieved for geochemical porewaters and sediment analyses. Surface sea water samples were collected along across-shore transects in the WB.  Besides major ions, Ba, Fe, and Mn, the water samples were analyzed for nutrients, dissolved inorganic carbon (DIC), stable isotopes (H, O, C, S), and Ra isotopes. Sediments were analyzed for C, N, S, Hg contents as well as reactive components (e.g. Fe, Mn, P) by HCl extractions. Organic matter mineralization rates, DIC, and SO4 fluxes for the sediment-water interface were modeled from porewater profiles. Shallow seismic techniques were applied to identify potential litho-morphological controls on SGD. Geochemical porewater data allow identification of active SGD sites in the WB. In the central part, the freshening of porewaters in the top surface sediments indicates the upward flow of SGD originating from a coastal aquifer. The acoustic profiles show that the bottom sediments in the central bay are under local impact of excavation, reducing the sediment thickness above the coastal aquifer. Overall, the impact of SGD on the coastal water body of the WB is diffuse and promoted by local anthropogenic activity. The water isotope composition of porewaters at this site are close to the local meteoric water line at Warnemünde (located 50 km east of the WB), suggesting a discharge of relatively modern fresh waters. The (isotope) hydrochemical composition of the fresh water discharging is controlled by water-rock interactions in the aquifer and modulated by intense diagenesis in the brackish surface sediments. Furthermore, the SGD facilitates the upward migration of elements and enhances their fluxes across the sediment-water interface, e.g. DIC concentrations in the fresh groundwater are further enhanced in the mixing zone, indicating that SGD is a potential source of excess CO2 in the investigated coastal waters.

The investigations are supported by the DAAD, DFG RTS Baltic TRANSCOAST, KiSnet project, BONUS SEAMOUNT, FP7 EU Marie Curie career integration grant, DAM-MFG, and IOW.

How to cite: Ehlert von Ahn, C. M., Scholten, J., Malik, C., Feldens, P., Liu, B., Dellwig, O., Jenner, A.-K., Papenmeier, S., Schmiedinger, I., Zeller, M., and Böttcher, M.: Controls on submarine groundwater discharge in an urbanized bay of the southern Baltic Sea: An isotope and trace metal perspective., EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-2470, https://doi.org/10.5194/egusphere-egu21-2470, 2021.

Gesa Schulz et al.

Estuaries are nutrient filters for coastal waters and can act as nitrate sink or source depending on predominant microbial processes, environmental conditions and geomorphological characteristics. Such environmental factors can change along the estuary itself. This study aims to identify different zones of nitrogen turnover in the Ems estuary and to determine the main processes.

Water column properties, dissolved inorganic nitrogen and dual stable isotopes of nitrate were measured along the Ems estuary during two research cruises in August 2014 and June 2020. Based on mixing calculations and stable isotope changes, we found that the estuary in both years is clearly divided into three zones that vary in the predominant nitrate turnover pathways. This was confirmed by principle component analysis.

The zonation mainly corresponded to changes in the geomorphology of the estuary, but a spatial shift of the zones occurred between 2014 and 2020. In both years, the most upstream zone acted as a clear nitrate sink. A strong fractionation (~30 ‰) of nitrate stable isotopes points towards removal by water column denitrification in this hyperturbid estuarine section.  In the middle reach of the estuary, nitrification gained in importance, turning this section into a net nitrate source during both sampling campaigns. In contrast to the biogeochemical active inner zones, mixing dominates nitrate distribution in the outermost section of the estuary.

Overall, the Ems estuary acted as a nitrate sink in both years. However, the zonation showed that relative stable zones of nitrification and denitrification existed along the estuary, which can change – and possibly move – when biogeochemical properties vary. 

How to cite: Schulz, G., Sanders, T., and Dähnke, K.: Biogeochemical zonation reveals three zones of nitrogen turnover in the Ems estuary, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7808, https://doi.org/10.5194/egusphere-egu21-7808, 2021.

Mary Zeller et al.

Seagrasses are often considered important players in the global carbon cycle, due to their role in sequestering and protecting sedimentary organic matter as “Blue Carbon”.  However, in shallow calcifying systems the ultimate role of seagrass meadows as a sink or source of atmospheric CO2 is complicated by carbonate precipitation and dissolution processes, which produce and consume CO2, respectively.  In general, microbial sulfate, iron, and nitrate reduction produce total alkalinity (TA), and the reverse reaction, the re-oxidation of the reduced species, consumes TA. Therefore, net production of TA only occurs when these reduced species are protected from re-oxidation, for example through the burial of FeSx or the escape of N2.  Seagrasses also affect benthic biogeochemistry by pumping O2 into the rhizosphere, which for example may allow for direct H2S oxidation.

Our study investigated the role of these factors and processes (seagrass density, sediment biogeochemistry, carbonate precipitation/dissolution, and ultimately air-sea CO2 exchange), on CO2 source-sink behavior in a shallow calcifying (carbonate content ~90%) seagrass meadow (Florida Bay, USA), dominated by Thalassia testudinum. We collected sediment cores from high and low seagrass density areas for flow through core incubations (N2, O2, DI13C, sulfide, DO13C flux), solid phase chemistry (metals, PO13C, Ca13C18O3, AVS: FeS + H2S, CRS: FeS2 + S0), and porewater chemistry (major cations, DI13C, sulfide, 34S18O4). An exciting aspect of this study is that it was conducted inside the footprint of an Eddy Covariance tower (air-sea CO2 exchange), allowing us to directly link benthic processes with CO2 sink-source dynamics.

During the course of our week long study, the seagrass meadow was a consistent source of CO2 to the atmosphere (610 ± 990 µmol·m-2·hr-1).  Elevated porewater DIC near 15 cmbsf suggests rhizosphere O2 induced carbonate dissolution, while consumption of DIC in the top 5-10 cm suggests reprecipitation.  With high seagrass density, enriched δ13CDIC in the DIC maximum zone (10-25 cm) suggests continual reworking of the carbonates through dissolution/precipitation processes towards more stable PIC, indicating that seagrasses can promote long-term stability of PIC.  We constructed a simple elemental budget, which suggests that net alkalinity consumption by ecosystem calcification explains >95% of the observed CO2 emissions.  Net alkalinity production through net denitrification (and loss of N2) and net sulfate reduction (and subsequent burial of FeS2 + S0), as well as observed organic carbon burial, could only minimally offset ecosystem calcification.   

How to cite: Zeller, M., Van Dam, B., Lopes, C., Smyth, A., Böttcher, M., Osburn, C., Zimmerman, T., Pröfrock, D., Fourqurean, J., and Thomas, H.: When “Blue Carbon” turns white: Isotopic evidence of calcification-driven CO2 emissions in a carbonate seagrass meadow, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-4539, https://doi.org/10.5194/egusphere-egu21-4539, 2021.

Dmitriy Malinovskiy et al.

For many years, it has been recommended that analysts performing stable isotope analysis of H, C, N, O and/or S prepare their own in-house reference materials (RMS) for daily use. These RMs can be used for calibration/normalization of instrumental data as well as for quality control and/or assurance purposes. In this way, commercially available RMs that are the source of traceability for all isotope delta analyses are preserved, ensuring that the isotope delta scales can be maintained for a longer period of time. Furthermore, in-house RMs can be prepared to supplement those that are commercially available, either by extending the available calibration range in terms of isotope delta values, or by consisting of a matrix which is not yet available from RM producers.

Some guidance is available regarding the required nature or properties of an in-house RM including stability, homogeneity, hygroscopicity and other chemical properties [e.g. Dunn & Carter 2018]. There are also a small number of publications providing some guidance on how to prepare in-house RMs for particular applications [e.g. Carter & Fry 2013, Heile & Hillarie-Marcel 2020]. There is, however, far less guidance available regarding the process of assigning an isotope delta value and associated uncertainty to an in-house RM. The guidance available to certified RM producers such as ISO/IEC 17034:2016 tend to have somewhat stricter requirements than those to be met by an in-house RM for QC purposes.

Building upon the National Measurement Laboratory’s experience as a CRM producer accredited to ISO/IEC 17034:2016, this presentation will distil the requirements for RM production into simple and clear guidelines for fit-for-purpose production and value-assignment of in-house RMs. This guidance covers five areas: (i) planning and prerequisites; (ii) material selection, preparation and storage; (iii) measurements and assessments; (iv) value assignment and uncertainty estimation; and (v) monitoring and use.


Dunn PJH, Carter JF. Good Practice Guide for Isotope Ratio Mass Spectrometry. 2nd ed. FIRMS; 2018. ISBN 978-0-948926-33-4. https://www.forensic-isotopes.org/gpg.html

Carter JF, Fry B. “Do it yourself” reference materials for δ13C determinations by isotope ratio mass spectrometry. Anal Bioanal Chem. 2013;405(14):4959-4962.

Heile J-F, Hillaire-Marcel C. Designing internal reference materials for stable H, C & O isotope measurements in CO2 and H2O. Rapid Commun Mass Spectrom. 2021;35(5)e9008.

ISO/IEC 17034:2016. General requirements for the competence of reference material producers. Published online 2016.

How to cite: Malinovskiy, D., Dunn, P., Cowen, S., Holcombe, G., and Goenaga-Infante, H.: Guidance for preparation of in-house reference materials for stable isotope analysis of HCNOS, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-10421, https://doi.org/10.5194/egusphere-egu21-10421, 2021.

Nikita Kaushal et al.

Rivers deliver ~0.25 Pg C year-1 of terrigenous dissolved organic carbon (tDOC) from land to shelf seas. As tDOC moves along the river, coastal ocean and deep ocean continuum, it undergoes complex biogeochemical processing that results in both chemical alteration and remineralisation. Remineralisation of tDOC to CO2 can contribute significantly to coastal ocean acidification and CO2 emissions to the atmosphere. Our understanding of tDOC processing in coastal seas is still limited, in part because it is challenging to distinguish between marine and terrigenous DOC. The stable carbon isotope ratios (d13C) of the dissolved inorganic and organic carbon pools are commonly used to quantify tDOC, because terrestrial vegetation is typically more isotopically depleted (-32 to -25 ‰) compared to marine organic carbon (-24 to -20 ‰). However, this relatively small difference between the marine and terrigenous end-members can introduce large uncertainties in d13C-based estimates, particularly if tDOC originates from both C3 and C4 vegetation. End-member isotope ratio values with larger separation could potentially help to better quantify tDOC. Recent studies in freshwater ecosystems have shown that the stable isotope ratios (d2H) of the carbon bound non-exchangeable hydrogen fraction of dissolved organic matter (DOM) typically differs by more than 50 ‰ between terrestrially derived and aquatically derived dissolved organic matter. However, d2H has not yet been used as a tracer for tDOC in marine environments.

Here, we present results from a one year-long monthly time series of δ13C and δ2H at a coastal location in Southeast Asia’s Sunda Shelf Sea, where the southwest monsoon delivers a seasonal input of tDOC from tropical peatlands on Sumatra. We found that δ2H of solid-phase extracted DOM, as measured after dual water steam equilibration, ranged between -130 to ­­-150 ‰ during the southwest monsoon, but between -160 to -167 ‰ during other months. Fresh tDOC from peatland-draining rivers had values close to -100‰, and decreased somewhat upon partial photodegradation, while DOM produced in plankton enrichment cultures had values around -174‰. Values of d13C of DOC ranged from -25.5 to -23.0 ‰ during the southwest monsoon, and between -23.0 to -21.0 ‰ at other times. We will present preliminary mass balance calculations to estimate tDOC concentrations based on δ13C and δ2H. Our results suggest that δ2H can be a sensitive tracer of tDOC in the marine environment.

How to cite: Kaushal, N., Gudasz, C., Zhou, Y., Lopes dos Santos, A., Kaur, A., and Martin, P.: Novel insights into the origin of dissolved organic carbon in the Sunda Shelf Sea using stable isotope ratios of hydrogen (d2H) and carbon (d13C). , EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-3642, https://doi.org/10.5194/egusphere-egu21-3642, 2021.

Rachel Schwartz-Narbonne et al.

Bacteria play key roles in the carbon cycle. In many sediments and peatlands, methanotrophic bacteria consume a portion of released methane, reducing the emissions of this potent greenhouse gas. In marine oxygen minimum zones (OMZ) and other anoxic settings, anaerobic ammonium oxidizing (anammox) bacteria remove bioavailable nitrogen while performing chemoautotrophic carbon fixation. Methanotrophic and anammox bacteria synthesize a wide number of complex bacteriohopanepolyols (BHPs), comprising notably several stereoisomers of bacteriohopanetetrols (BHT), which are used as biomarker lipids.  While BHT-17β(H), 21β(H), 22R, 32R, 33R, 34S (BHT-34S) is ubiquitous in the environment, its 34R stereoisomer (BHT-17β(H), 21β(H), 22R, 32R, 33R, 34R; BHT-34R) has only five known producers: the freshwater anammox genera ‘Candidatus Brocadia’, the aerobic acidic peatland methanotroph Methylocella palustris, the nitrogen-fixing aerobic bacteria Frankia spp., and the aerobic acetic acid-producing bacteria Acetobacter pasteurianus and Komagataeibacter xylinus. BHT-x—another BHT isomer of unknown stereochemistry—has only one known producer, the marine anammox bacteria ‘Candidatus Scalindua’ (Schwartz-Narbonne et al., 2020). The occurrence and extent of these different carbon cycle processes can be assessed by measuring the concentrations of these BHT stereoisomers and changes in their δ13C values (Hemingway et al., 2018; Lengger et al., 2019).However, the 13C fractionation associated with the different carbon assimilation pathways of these bacteria has been minimally assessed, resulting in poorly constrained ranges in δ13C values and difficulty in interpreting isotope results.

We used a gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) method to measure the δ13C of BHT-34S, BHT34R, and BHT-x of cultured bacteria (‘Ca. Scalindua’, ‘Ca. Brocadia’, Methylocella tundrae, Frankia spp., and Komagataeibacter xylinus). These δ13C values were combined with bulk isotopic measurements of the bacterial biomass and δ13C analyses of the bacterial growth substrates to establish carbon isotopic fractionation from substrate to biomass to BHT lipid. We demonstrated that bacteria using different metabolic pathways produced distinct fractionation factors between substrate and BHTs, which potentially allows for distinguishing BHT-34R produced by ‘Ca. Brocadia’ and methanotrophs from other freshwater producers (e.g. in peatlands). Measurement of BHT-specific fractionation factors allowed us to better constrain the contribution of anammox bacteria to fixed carbon in OMZ. This work expands the application of BHT isomers to isotopically identify carbon cycle processes.



Hemingway, Jordon D., et al. "A novel method to measure the 13C composition of intact bacteriohopanepolyols." Organic Geochemistry 123 (2018): 144-147.

Lengger, Sabine K., et al. "Dark carbon fixation in the Arabian Sea oxygen minimum zone contributes to sedimentary organic carbon (SOM)." Global Biogeochemical Cycles 33.12 (2019): 1715-1732.

Schwartz-Narbonne, Rachel, et al. "A unique bacteriohopanetetrol stereoisomer of marine anammox." Organic Geochemistry (2020): 103994.

How to cite: Schwartz-Narbonne, R., Schaeffer, P., Lengger, S., Blewett, J., Jones, D. M., Motsch, E., Charlton, A., Crombie, A., Hardy, S., Haquee, M. F. U., Jetten, M. S. M., Mikkelsen, D., Normand, P., Nuijten, G. H. L., and Rush, D.: δ13C compositions of bacteriohopanetrol isomers reveal bacterial processes involved in the carbon cycle, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8486, https://doi.org/10.5194/egusphere-egu21-8486, 2021.

Karin Hain et al.

By analysing the two long-lived anthropogenic Uranium (U) isotopes U-233 and U-236 in different compartments of the environment affected by releases of nuclear power production or by global fallout from nuclear weapons tests, we showed that the corresponding isotopic ratios U-233/U-236 differ by one order of magnitude. Based on these experimental results which were obtained with the ultra-sensitive detection method Accelerator Mass Spectrometry, we suggested a representative ratio for nuclear weapons fallout of U-233/U-236 = (1.40 ± 0.15) ·10-2 and (0.12 ± 0.01) ·10-2 for releases from nuclear power production. Consequently, the U-233/U-236 ratio not only has the potential to become a novel sensitive fingerprint for releases from nuclear industry, but could also serve as a powerful oceanographic tracer due to the conservative behaviour of U in ocean water which does not suffer from chemical fractionation.

As a first application of this paired tracer, we studied the distribution of U-233 and U-236 concentrations in addition to I-129 in the Baltic Sea which is known to have received inputs of radionuclides from various contamination sources including the two European reprocessing plants, global fallout from weapons testings and fallout from the Chernobyl accident. Our data indicate an additional unidentified source of reactor U-236 in the Baltic Sea demonstrating the high sensitivity of the U-233/U-236 ratio to distinguish different emission sources in water mixing processes.

How to cite: Hain, K., Aldahan, A., Eriksson, M., Golser, R., Henderson, G. M., Hou, X., Qiao, J., Possnert, G., Steier, P., Vartti, V.-P., and Zhang, H.: Detection of an unknown emission source in the Baltic Sea using the new oceanographic tracer U-233/U-236, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14111, https://doi.org/10.5194/egusphere-egu21-14111, 2021.

Tiantian Sun et al.

In the Black Sea, sediment cores covering the last brackish-limnic transition were recovered and investigated for anaerobic biogeochemical processes controlling sulfur, carbon, and metal cycling. The development of a sulfate-methane transition zone (SMTZ) is nowadays found below the brackish zone in the limnic part of the sediments that limits the upward migration of biogenic methane into surface sediments and the water column. The position of the SMTZ may have changed in the past due to dynamic fluxes of dissolved species in the pore water. Besides dissolved sulfate, metal-bearing minerals have been shown to serve as potential reactants, also converting CH4 into dissolved inorganic carbon (DIC). The pore water and sediment stable isotope (C, S, O) and geochemical composition were investigated, as well as in-situ microbial rates of sulfate reduction and total anaerobic oxidation of CH4 (AOM) obtained from sediment incubations for the identification of a potential contribution of manganese-bearing minerals to AOM in the limnic part of the sediments (Mn-AOM). In the limnic Black Sea sediments Mn-AOM is causes an upward flux of dissolved Mn whereas intense SO4-AOM located in shalower sediments leads to an increase in pH and a maximum in DIC concentrations in the SMTZ. The resulting change in saturation states leads to the precipitation of mixed MnCa-carbonate solid-solutions (‘rhodochrozitization front’) and the development of a zone enriched in excess sedimentary Mn(II). We further argue that these authigenic fronts may survive changes in pore water composition and are stable in the anoxic sedimentary record, marking the position of paleo-SMTZs. The persisting formation of this geochemical marker has advantage in application over the transient development of a sulfidization front of metastable mackinawite, that is fromed by the reaction of downard migrating sulfide with upward diffusing Fe(II), originating from SO4-AOM and Fe-AOM, respectively.

How to cite: Sun, T., Böttcher, M. E., Kallmeyer, J., Treude, T., Lipka, M., Schmiedinger, I., Eckert, S., Wehausen, R., Jørgensen, B. B., and Martinez-Ruiz, F.: Mn(II) carbonate authigenesis marks the benthic SMTZ and is fueled by Mn-driven anaerobic oxidation of methane: A Black Sea evidence, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-1890, https://doi.org/10.5194/egusphere-egu21-1890, 2021.

Michael E. Böttcher et al.

Carbonated hydroxy-apatite (CHAP) was experimentally synthesized in batch-type set-ups by mixing of calcium (Ca)- and phosphate-bearing aqueous solutions and the transformation of calcite powder in aqueous solution between 11° and 65°C (Gussone et al., 2020). Compositional changes of the experimental solution and solid phase products were followed by elemental analysis, Raman spectroscopy, scanning-electron microscopy, and powder XRD. In the mixing experiments, crystallization of CHAP took place following the precipitation of metastable brushite as precursor that was then transformed into CHAP. In the transformation experiments using synthetic calcite as a precursor phase it was found that the reaction at pH values between 7.5 and 7.9 occurs via the direct replacement of calcium carbonate by CHAP.

Calcium isotope fractionation led to an enrichment of the light isotope in the solid CHAP compared to the aqueous solution by about -0.5 to -1.1 ‰, independent from the experimental approach, and the magnitude was essentially independent of temperature. The metastable brushite formed prior to transformation to CHAP showed a reduced fractionation compared to the CHAP. The observed Ca isotope fractionation into the CHAP lattice resembles that of natural phosphorites and lies within the range of the view existing theoretical and experimental studies.


Reference: Gussone N., Böttcher M.E., Conrad A.C., Fiebig J., Pelz M., Grathoff G., Schmidt B.C. (2020) Calcium isotope fractionation upon experimental apatite formation. Chem. Geol., 551, 119737

The study was supported by German Science Foundation (DFG) to M.E.B and J.F. within the EXCALIBOR project (BO1548/8 and FI 948/7), and to N.G. (GU1035/10), and by Leibniz IOW.

How to cite: Böttcher, M. E., Gussone, N., Conrad, A. C., Schmiedinger, I., Fiebig, J., Peltz, M., Grathoff, G., and Schmidt, B. C.: Ca isotope fractionation upon synthesis of carbonated apatite, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-3384, https://doi.org/10.5194/egusphere-egu21-3384, 2021.

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