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Despite the global significance of the subsurface biosphere, the degree to which it depends on surface organic carbon (OC) is still poorly understood. Here, we compare stable and radiogenic carbon isotope compositions of microbial phospholipid fatty acids (PLFAs) with those of in situ potential microbial C sources to assess the major C sources for subsurface microorganisms in biogeochemical distinct shallow aquifers (Critical Zone Exploratory, Thuringia Germany). Despite the presence of younger OC, the microbes assimilated 14C-free OC to varying degrees; ~31% in groundwater within the oxic zone, ~47% in an iron reduction zone, and ~70% in a sulfate reduction/anammox zone. The persistence of trace amounts of mature and partially biodegraded hydrocarbons suggested that autochthonous petroleum-derived hydrocarbons were a potential 14C-free C source for heterotrophs in the oxic zone. In this zone, Δ14C values of dissolved inorganic carbon (-366 ± 18‰) and 11MeC16:0 (-283 ± 32‰), an important component in autotrophic nitrite oxidizers, were similar enough to indicate that autotrophy is an important additional C fixation pathway. In anoxic zones, methane as an important C source was unlikely since the 13C-fractionations between the PLFAs and CH4 were inconsistent with kinetic isotope effects associated with methanotrophy. In the sulfate reduction/anammox zone, the strong 14C-depletion of 10MeC16:0 (-942 ± 22‰), a PLFA common in sulfate reducers, indicated that those bacteria were likely to play a critical part in 14C-free sedimentary OC cycling. Results indicated that the 14C-content of microbial biomass in shallow sedimentary aquifers results from complex interactions between abundance and bioavailability of naturally occurring OC, hydrogeology, and specific microbial metabolisms.

Ignoring the diurnal cycle in surface-to-atmosphere CO2 fluxes leads to a systematic bias in CO2 mole fraction simulations sampled at daytime, because the daily mean flux systematically misses the CO2 uptake during the daytime hours. In an atmospheric inversion using daytime-selected CO2 measurements at most continental sites and not resolving diurnal cycles in the flux, this leads to systematic biases in the estimates of the annual sources and sinks of atmospheric CO2. This study focuses on quantifying the impact of this diurnal cycle effect on the annual carbon fluxes estimated with the CarboScope (CS) atmospheric inversion at regional, continental, and global scales for the period of time 2010–2020. Biogenic fluxes of hourly Net Ecosystem Exchange (NEE) obtained from the data-driven FLUXCOM estimates are used in the inversion together with global and regional atmospheric transport models. Differences between CO2 mixing ratios simulated with daily averaged and hourly NEE range between around -2.5 and 7 ppm averaged annually throughout a site network across the world. As a consequence, these differences lead to systematic biases in CO2 flux estimates when ignoring the diurnal variations of the CO2 flux in the atmospheric inversions. Although the impact on the global average of estimated annual flux is negligible (around 2 % of the overall land flux of -1.79 Pg C yr-1), we find significant biases in the annual flux budgets at continental and regional scales. For Europe, the annual mean difference in the fluxes arising from the diurnal cycle of CO2 represents around 48 % of the annual posterior fluxes (0.31 Pg C yr-1) estimated with CarboScope-Regional (CSR). Furthermore, the differences in NEE estimates calculated with CS increase the magnitude of the flux budgets for some regions such as northern American temperate and northern Africa by a factor of about 1.5. To the extent that FLUXOM diurnal cycles are realistic at all latitudes and for the station set used in our inversions here, we conclude that ignoring the diurnal variations in the land CO2 flux leads to overestimation of both CO2 sources in the tropical lands and CO2 sinks in the temperate zones. [ABSTRACT FROM AUTHOR]

We present an analysis of atmospheric transport impact on estimating CO 2 fluxes using two atmospheric inversion systems (CarboScope-Regional (CSR) and Lund University Modular Inversion Algorithm (LUMIA)) over Europe in 2018. The main focus of this study is to quantify the dominant drivers of spread amid CO 2 estimates derived from atmospheric tracer inversions. The Lagrangian transport models STILT (Stochastic Time-Inverted Lagrangian Transport) and FLEXPART (FLEXible PARTicle) were used to assess the impact of mesoscale transport. The impact of lateral boundary conditions for CO 2 was assessed by using two different estimates from the global inversion systems CarboScope (TM3) and TM5-4DVAR. CO 2 estimates calculated with an ensemble of eight inversions differing in the regional and global transport models, as well as the inversion systems, show a relatively large spread for the annual fluxes, ranging between - 0.72 and 0.20 PgC yr -1 , which is larger than the a priori uncertainty of 0.47 PgC yr -1. The discrepancies in annual budget are primarily caused by differences in the mesoscale transport model (0.51 PgC yr -1), in comparison with 0.23 and 0.10 PgC yr -1 that resulted from the far-field contributions and the inversion systems, respectively. Additionally, varying the mesoscale transport caused large discrepancies in spatial and temporal patterns, while changing the lateral boundary conditions led to more homogeneous spatial and temporal impact. We further investigated the origin of the discrepancies between transport models. The meteorological forcing parameters (forecasts versus reanalysis obtained from ECMWF data products) used to drive the transport models are responsible for a small part of the differences in CO 2 estimates, but the largest impact seems to come from the transport model schemes. Although a good convergence in the differences between the inversion systems was achieved by applying a strict protocol of using identical prior fluxes and atmospheric datasets, there was a non-negligible impact arising from applying a different inversion system. Specifically, the choice of prior error structure accounted for a large part of system-to-system differences. [ABSTRACT FROM AUTHOR]

We present an analysis of atmospheric transport impact on estimating CO2 fluxes using two atmospheric inversion systems (CarboScope Regional (CSR) and LUMIA) over Europe for 2018. The main focus of this study is to quantify the dominant drivers of spread amid CO2 estimates derived from atmospheric tracer inversions. The Lagrangian transport models STILT and FLEXPART were used to assess the impact of mesoscale transport. The impact of lateral boundary conditions for CO2 was assessed by applying the global transport models TM3 and TM5. CO2 estimates calculated with an ensemble of eight inversions differing in the regional and global transport models, as well as the inversion systems show a relatively large spread for the annual domain wide flux ranging between -0.72 and 0.20 PgC yr-1 with a mean estimate of - 0.29 PgC. The largest discrepancies resulted from varying the mesoscale transport model, which amounted to a difference of 0.51 (PgC yr-1), in comparison with 0.23 and 0.10 (PgC yr-1) that resulted from the far-field contributions and the inversion systems, respectively. Additionally, varying the mesoscale transport caused large discrepancies in spatial and temporal patterns, while changing the lateral boundary conditions lead to more homogeneous spatial and temporal impact. We further investigated the origin of the discrepancies between transport models. The meteorological forcing parameters (forecasts versus reanalysis obtained from ECMWF data products) used to drive the transport models are responsible for a small part of the differences in CO2 estimates, but the largest impact seems to come from the models themselves. Although a good convergence in the differences between the inversion systems was achieved by applying a strict protocol of using identical priors, and atmospheric datasets, there was a non-negligible impact arising from applying a different inversion system. Specifically, the choice of prior error structure accounted for a large part of system-to-system differences. [ABSTRACT FROM AUTHOR]

Iron-cyanide complexes are present in soil and ground water because of anthropogenic inputs. We studied the sorption and the transport of the complexes ferrocyanide, [[Fe[(CN).sub.6]].sup.4-], and ferricyanide, [[Fe[(CN).sub.6]].sup.3-], in goethite-coated sand in column experiments under saturated conditions as influenced by flow velocity and flow interruption. Isotherm parameters obtained from batch experiments of Fecyanide complex sorption on goethite were used to simulate breakthrough curves in goethite-coated sand. The breakthrough curves of ferrocyanide were inversely modeled. The transport of both complexes was retarded and rate-limited. Only ferricyanide breakthrough curves revealed concentration drops after flow interruption. Simulations with batch parameters roughly reflected breakthrough curves of ferricyanide, but not of ferrocyanide. Ferricyanide sorption and desorption could not be described with the same isotherm indicating hysteresis. Since the sorption fronts of ferrocyanide breakthrough curves revealed the formation of a shoulder, it was concluded that ferrocyanide sorption in column experiments could not be described by a single isotherm, which is based on a singular sorption process. Therefore, sorption of ferrocyanide on goethite was assumed to be influenced by more than one sorption mechanism. Inverse modeling of ferrocyanide breakthrough data using the Langmuir isotherm resulted in erroneous sorption maxima.

3-hourly Net Ecosystem Exchange (NEE) is estimated at spatial scales of 0.25 degrees over the European continent, based on the pre-operational inverse modelling framework "CarboScope Regional" (CSR) for the years 2006 to 2019. To assess the uncertainty originating from the choice of a-priori flux models and observational data, ensembles of inversions were produced using three terrestrial ecosystem flux models, two ocean flux models, and three sets of atmospheric stations. We find that the station set ensemble accounts for 61% of the total spread of the annually aggregated fluxes over the full domain when varying all these elements, while the biosphere and ocean ensembles resulted in much smaller contributions to the spread of 28% and 11%, respectively. These percentages differ over the specific regions of Europe, based on the availability of atmospheric data. For example, the spread of the biosphere ensemble is prone to be larger in regions that are less constrained by CO2 measurements. We further investigate the unprecedented increase of temperature and simultaneous reduction of Soil Water Content (SWC) observed in 2018 and 2019. We find that NEE estimates during these two years suggest an impact of drought occurrences represented by the reduction of Net Primary Productivity (NPP), which in turn lead to less CO[sub 2] uptake across Europe in 2018 and 2019, resulting in anomalies up to 0.13 and 0.07 PgC yr-1 above the climatological mean, respectively. Annual temperature anomalies also exceeded the climatological mean by 0.46 °C in 2018 and by 0.56 °C in 2019, while standardized-precipitation-evaporation-index (SPEI) anomalies declined to -0.20 and -0.05 SPEI units below the climatological mean in both 2018 and 2019, respectively. Therefore, the biogenic fluxes showed a weaker sink of CO2 in both 2018 and 2019 (-0.22±0.05 and -0.28±0.06 PgC yr-1, respectively) in comparison with the mean -0.36±0.07 PgC yr[sup -1] calculated over the full analysed period (i.e., fourteen years). These translate into a continental-wide reduction of the annual sink by 39 % and 22 %, respectively, larger than the typical year-to-year standard deviation of 19 % observed over the full period. [ABSTRACT FROM AUTHOR]

Dissolved organic matter (DOM) plays a prominent role in the transport of contaminants in porous media. As DOM has to be considered as a reactive component, flow regime and sorbent reactivity should affect overall DOM transport in an important way. We focused on DOM transport in unsaturated column experiments using quartz sand (QS) and goethite-coated quartz sand (GS). Rate constrictions to DOM sorption were investigated by varying the volumetric flow rate, while extent and reversibility of sorption were studied in consecutive adsorption and desorption steps. In the QS, DOM retention was low and unaffected by changes in flow rate. Desorption-step breakthrough curves (BTCs) and mass balances show full reversibility of the sorption process. However, DOM retention in GS was significant and sensitive to flow variation, indicative of nonequilibrium sorption. At lower flow rates, DOM breakthrough exhibited a change in curvature (shoulder) due to the superimposition of two BTCs representing reactive and nonreactive DOM fractions. Transport was successfully modeled assuming these two fractions governed overall DOM mobility. At higher flow rates, the BTC shoulder vanished due to reduced contact time between the DOM and the solid phase (rate-limited sorption). Sorption of DOM on GS is accompanied by a marked rise in effluent pH, indicative of a ligand-exchange mechanism. Recovery of DOM during desorption was incomplete due to either partially irreversible sorption or strongly rate-limited desorption. Increased DOM mobility in the consecutive adsorption step resulted from partial blocking of sorption sites by the initial pulse of DOM.

Determining the biogeochemical pathways utilized by microbes living in groundwater is essential for understanding the subsurface C cycle and the fate of organic compounds, including pollutants. The radiocarbon signature (Δ14C) of fatty acid methyl esters derived from microbial phospholipids (PLFA) provides useful information for differentiating microbial C sources and infering microbial metabolism. However, in subsurface environments, those analyses remain challenging. Here we present a method combining large volume groundwater filtration (up to 10,000 L) and PLFA purification for subsequent compound‐specific radiocarbon analyses. The analytical method involves conventional chemical extraction of PLFA followed by purification of individual compounds by semipreparative high‐performance liquid chromatography. Different saturated PLFA in amounts of up to 10 μg each can be simultaneously separated on a C18 high‐load column using a mixture of MeOH/water and acetonitrile as the mobile phase. Our procedure introduced dead‐Cext contaminations of 0.57 ± 0.29 and 0.35 ± 0.18 μg for the high‐performance liquid chromatography and combustion/graphitization steps of the sample preparation, respectively. However, tests on different high‐performance liquid chromatography C18 columns revealed a large difference in dead Cext associated with column bleed. Modern Cext in the amount of 0.40 ± 0.20 μg was introduced by the combustion/graphitization step of the sample preparation, but other steps did not add modern Cext. The entire method recovered ∼50% of the purified compounds on average, but this did not affect their 14C content. This method will allow routine analysis of the Δ14C of PLFA isolated from groundwaters or other sample types, revealing the relationships between microbial and soil‐derived C, sedimentary or dissolved C sources. Key Points: Fatty acid methyl esters derived from microbial phospholipids were purified and concentrated for compound‐specific radiocarbon analysesThe method involves chemical extraction followed by semipreparative high‐performance liquid chromatography of diverse saturated FAMELarge differences in the degree of extraneous C contamination were observed depending on the HPLC columns used for separations [ABSTRACT FROM AUTHOR]

Despite the global significance of the subsurface biosphere, the degree to which it depends on surface organic carbon (OC) is still poorly understood. Here, we compare stable and radiogenic carbon isotope compositions of microbial phospholipid fatty acids (PLFAs) with those of in situ potential microbial C sources to assess the major C sources for subsurface microorganisms in biogeochemical distinct shallow aquifers (Critical Zone Exploratory, Thuringia Germany). Despite the presence of younger OC, the microbes assimilated 14C‐free OC to varying degrees; ~31% in groundwater within the oxic zone, ~47% in an iron reduction zone, and ~70% in a sulfate reduction/anammox zone. The persistence of trace amounts of mature and partially biodegraded hydrocarbons suggested that autochthonous petroleum‐derived hydrocarbons were a potential 14C‐free C source for heterotrophs in the oxic zone. In this zone, Δ14C values of dissolved inorganic carbon (−366 ± 18‰) and 11MeC16:0 (−283 ± 32‰), an important component in autotrophic nitrite oxidizers, were similar enough to indicate that autotrophy is an important additional C fixation pathway. In anoxic zones, methane as an important C source was unlikely since the 13C‐fractionations between the PLFAs and CH4 were inconsistent with kinetic isotope effects associated with methanotrophy. In the sulfate reduction/anammox zone, the strong 14C‐depletion of 10MeC16:0 (−942 ± 22‰), a PLFA common in sulfate reducers, indicated that those bacteria were likely to play a critical part in 14C‐free sedimentary OC cycling. Results indicated that the 14C‐content of microbial biomass in shallow sedimentary aquifers results from complex interactions between abundance and bioavailability of naturally occurring OC, hydrogeology, and specific microbial metabolisms. Key Points: Microbial lipids (PLFAs) and C sources in aquifers with different subsurface‐surface relationships were analyzed for their 14C‐contentSubsurface microbes incorporated 14C‐free C in proportions depending on the physiological strategies of the microorganism communityAutotrophic nitrite oxidation occurred in oxic zone, whereas heterotrophy on sedimentary C dominated in sulfate reduction/anammox zone [ABSTRACT FROM AUTHOR]