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Similarly, it is clear that, when viewed from the perspective of agricultural protection, plant physiology, or ecological restoration, microbial ecology plays a pivotal role in understanding ecological processes. In this case, we obtained an interesting collection of papers from different fields, such as animal ecology, focusing on the impact of agricultural activities on nocturnal mammals and small mammals [[1]]; plant-animal interactions [[3]]; wild felid diversity [[5]]; ecological microbiology from different perspectives [[6], [8], [10]]; aquatic ecology [[11]]; and plant ecology [[13]]. Plant-animal interactions can be considered a fundamental area within ecology, while the description of plant communities and biogeochemical processes significantly contribute to our understanding of ecological functioning. [Extracted from the article]

Atmospheric changes could strongly influence how terrestrial ecosystems function by altering nutrient cycling. We examined how the dynamics of nutrient release from leaf litter responded to two important atmospheric changes: rising atmospheric CO2 and tropospheric O3. We evaluated the independent and combined effects of these gases on foliar litter nutrient dynamics in aspen ( Populus tremuloides Michx) and birch ( Betula papyrifera Marsh)/aspen communities at the Aspen FACE Project in Rhinelander, WI. Naturally senesced leaf litter was incubated in litter bags in the field for 735 days. Decomposing litter was sampled six times during incubation and was analyzed for carbon, and both macro (N, P, K, S, Ca, and Mg) and micro (Mn, B, Zn and Cu) nutrient concentrations. Elevated CO2 significantly decreased the initial litter concentrations of N (−10.7%) and B (−14.4%), and increased the concentrations of K (+23.7%) and P (+19.7%), with no change in the other elements. Elevated O3 significantly decreased the initial litter concentrations of P (−11.2%), S (−8.1%), Ca (−12.1%), and Zn (−19.5%), with no change in the other elements. Pairing concentration data with litterfall data, we estimated that elevated CO2 significantly increased the fluxes to soil of all nutrients: N (+12.5%), P (+61.0%), K (+67.1%), S (+28.0%), and Mg (+40.7%), Ca (+44.0%), Cu (+38.9%), Mn (+62.8%), and Zn (+33.1%). Elevated O3 had the opposite effect: N (−22.4%), P (−25.4%), K (−27.2%), S (−23.6%), Ca (−27.6%), Mg (−21.7%), B (−16.2%), Cu (−20.8%), and Zn (−31.6%). The relative release rates of the nine elements during the incubation was: K ≥ P ≥ mass ≥ Mg ≥ B ≥ Ca ≥ S ≥ N ≥ Mn ≥ Cu ≥ Zn. Atmospheric changes had little effect on nutrient release rates, except for decreasing Ca and B release under elevated CO2 and decreasing N and Ca release under elevated O3. We conclude that elevated CO2 and elevated O3 will alter nutrient cycling more through effects on litter production, rather than litter nutrient concentrations or release rates. [ABSTRACT FROM AUTHOR]

In this paper we propose a probabilistic framework for an uncertainty quantification study of a carbon cycle model. A Global Sensitivity Analysis (GSA) study indicates the parameters and parameter couplings that are important at different times of the year for Quantities of Interest obtained with the Data Assimilation Linked Ecosystem Carbon (DALEC) model. We then employ a Bayesian approach to calibrate the parameters of DALEC using net ecosystem exchange observations at the Harvard Forest site. The calibration exercise is guided by GSA and by Fisher information matrix results that quantify the amount of information carried by the experimental data about specific model parameters. The calibration results are employed in the second part of the paper to assess the predictive skill of the model via posterior predictive checks. These checks show a better performance for the non-steady state model during the growing season compared to the one employing steady state assumptions. Overall, this study leads to a 40% improvement in the predictive skill of DALEC and highlights the importance of considering correlations in the model parameters as informed by the data. [ABSTRACT FROM AUTHOR]

Thanks to the abundant observation data, we are able to deploy the traditional point-topoint comparison and statistical measures in combination with a comprehensive model validation scheme to assess the skills of the biogeochemical model ERGOM in provid- ing an operational service for the Baltic Sea. The model assessment concludes that the operational products can resolve the main observed seasonal features for phytoplankton biomass, dissolved inorganic nitrogen, dissolved inorganic phosphorus and dissolved oxygen in euphotic layers, as well as their vertical profiles. This assessment reflects that the model errors of the operational system at the current stage are mainly caused by insufficient light penetration, excessive organic particle export downward, insufficient regional adaptation and some of improper initialization. This study highlights the importance of applying multiple schemes in order to assess model skills rigidly and identify main causes for major model errors. [ABSTRACT FROM AUTHOR]

Eucalypt plantations in India are an important source of fiber for paper making and fuel for local villagers. Large areas of land have supported eucalypt plantations for several rotations, and productivity has generally been declining through successive rotations. In 1997, we initiated a project to examine site management options as a way to improve the productivity of these sites. We established a large experimental infrastructure at each of four sites in Kerala, consisting of up to five separate fully randomized block experiments at each site, examining inter-rotation management options (organic matter manipulation, N and P fertilizer input, legume cover cropping, weed control). Two of the sites were typical lowland plantations with Eucalytus tereticornis, and the other two sites were typical upland plantations with Eucalytus grandis. Following treatments, we monitored plantation productivity and impacts on soil and nutrient cycling for one full rotation (6.5 years). We found it is possible to increase the volume growth of E. grandis by up to 48%, and E. tereticornis by up to 268% through a combination of optimum site practices (mostly weed control and nutrient addition), hut productivity responses are dependent on site-specific factors. Key outcomes of this research are presented, with special reference to application in the broader context of tropical eucalypt plantations. [ABSTRACT FROM AUTHOR]

The Mediterranean Sea is one of the most oligotrophic regions of the oceans, and nutrients have been shown to limit both phytoplankton and bacterial activities. This has direct implications on the stock of dissolved organic carbon (DOC), whose high variability has already been well-documented even if measurements are still sparse and are associated with important uncertainties. We here propose a Mediterranean Basin-scale view of the export of organic carbon, under its dissolved and particulate forms. For this purpose, we have used a coupled model combining a mechanistic biogeochemical model (Eco3M-MED) and a high-resolution (eddy-resolving) hydrodynamic simulation (NEMO-MED12). This is the first Basin-scale application of the biogeochemical model Eco3M-MED and is shown to reproduce the main spatial and seasonal biogeochemical characteristics of the Mediterranean Sea. Model estimations of carbon export are of the same order of magnitude as estimations from in situ observations, and their respective spatial patterns are consistent with each other. As for surface chlorophyll, nutrient concentrations, and productivity, strong differences between the Western and Eastern Basins are evidenced by the model for organic carbon export, with only 39% of organic carbon (particulate and dissolved) export taking place in the Western Basin. The major result is that except for the Alboran Sea, dissolved organic carbon (DOC) contribution to organic carbon export is higher than that of particulate (POC) in the whole Basin, especially in the Eastern Basin. This paper also investigates the seasonality of DOC and POC exports as well as the differences in the processes involved in DOC and POC exports. [ABSTRACT FROM AUTHOR]

We present a new coupled ocean circulation - ice model configuration of the Baltic Sea. The model features, contrary to most existing configurations, a high horizontal resolution of ≈ 1 nautical mile which is eddy resolving over much of the domain. The vertical discretisation comprises a total of 47 vertical levels. Results from a 1987 to 1999 hind cast simulation show that the model's fidelity is competitive. As suggested by a comparison with sea surface temperatures observed from space, this applies especially to near-surface processes. Hence, the configuration is well suited to serve as a nucleus of a full-fledged coupled ocean circulation biogeochemical model (which is yet to be developed). A caveat is that the model fails to reproduce major inflow events. We trace this back to spurious vertical circulation patterns at the sills which may well be endemic to high resolution models based on geopotential coordinates. Further, we present indications that - so far neglected - eddy/wind effects exert significant control on wind-induced up- and downwelling. [ABSTRACT FROM AUTHOR]

The annual average CO2 difference between baseline data from Mauna Loa and the southern Hemisphere increased by ~ 0.8 µmolmol-1 (0.8 ppm) between 2009 and 2010, a step unprecedented in over 50 years of reliable data. We find no evidence for coinciding, sufficiently large and rapid, source/sink changes. A statistical anomaly is unlikely due to the highly systematic nature of the variation in observations. An explanation for the step, and the subsequent 5 year stability in this north-south difference, involves inter-hemispheric atmospheric exchange variation. The selected data describing this episode provide a critical test for studies that employ atmospheric transport models that interpret global carbon budgets and inform management of anthropogenic emissions. [ABSTRACT FROM AUTHOR]

Mussel shells are potential bioarchives of proxies for changes of the physico-chemical conditions in the bivalve's habitat. One such proxy is the distribution of the Rare Earths and Yttrium (REY) in seawater, as REY speciation in seawater is sensitive to pH and temperature variations, due to the impact of these parameters on the activity of CO32 in seawater. We present a new protocol for sample preparation and determination of REY concentrations in bivalve shells, that includes sample treatment with NaOCl followed by REY separation and preconcentration. The data obtained was further used to calculate REY partition coefficients between shells of M. edulis and ambient seawater, and acquired results were then used in the investigation of the potential effects of pH and temperature on REY partitioning. Shells of M. edulis mussels from the North Sea show consistent shale-normalized ("SN") REY patterns that increase from the light REY to the middle REY and decrease from the middle REY to the heavy REY. Despite being different to the general seawater REYSN pattern, the shells still display distinct REY features of seawater such as a negative CeSN anomaly and small positive YSN and GdSN anomalies. Apparent partition coefficients for the REY between the shell and seawater (appDREYshell/seawater) are low and decrease strongly from the light REY (4.04 for La) to the heavy REY (0.34 for Lu). However, assuming that only the free REY3+ are incorporated into the shell, appDREY3+shell/seawater values are higher and rather similar for all REY (102.46 for La; 113.44 for Lu), but show a slight maximum at Tb (199.18). Although the impact of vital effects i.e. REY speciation in a mussel's extrapallial fluid from which the carbonate minerals precipitate, cannot be quantified yet, it appears that M. edulis shells are bioarchives of some REY features of seawater. We modelled the REYSN patterns of a hypothetical mussel shell at pH 8.2 and 7.6 and at temperatures of 25 and 5 °C assuming that only REY3+ are incorporated into the carbonate's crystal lattice. The results suggest that with lower pH, REY concentrations in a shells increase, but with little effect on the shape of the REYSN patterns, while a temperature change has an impact on the REYSN pattern, but only minor effects on REY concentrations. [ABSTRACT FROM AUTHOR]

In our recent publication on the biodiversity of Paleozoic phytoplankton (Kroeck et al., 2022) we cited several works of Martin (Martin, 1996; Martin and Quigg, 2012; Martin and Servais, 2020) to present the hypothesis that during the late Paleozoic nutrient availability in the oceans increased significantly from a rather (super-) oligotrophic early to middle Paleozoic. We put this view in contrast to the notion, based on data on terrestrial sediment input, that nutrient availability generally decreased over the course of the Paleozoic. In his discussion paper, Martin (2022) expands on this hypothesis and the role of nutrients for biodiversification, and clarifies the use of the term "superoligotrophy" (Martin, 1996) for the early to middle Paleozoic interval. Martin (2022) highlights factors we neglected in our review of marine phytoplankton diversity in the Paleozoic. We largely agree with the arguments presented, and therefore consider this discussion as an excellent addition to our review. [ABSTRACT FROM AUTHOR]

MEDUSA-1.0 (Model of Ecosystem Dynamics, nutrient Utilisation, Sequestration and Acidification) was developed as an "intermediate complexity" plankton ecosystem model to study the biogeochemical response, and especially that of the so-called "bi- ological pump", to anthropogenically-driven change in the World Ocean (Yool et al., 2011). The base currency in this model was nitrogen from which fluxes of organic carbon, including export to the deep ocean, were calculated by invoking fixed C : N ratios in phytoplankton, zooplankton and detritus. Since the beginning of the industrial era, the atmospheric concentration of carbon dioxide (CO2) has significantly increased above its natural, inter-glacial background concentration. Simulating and predicting the carbon cycle in the ocean in its entirety, including ventilation of CO2 with the atmosphere and the resulting impact of ocean acidification on marine ecosystems, therefore requires that both organic and inorganic carbon be afforded a full representation in the model specification. Here, we introduce MEDUSA-2.0, an expanded successor model which includes additional state variables for dissolved inorganic carbon, alkalinity, dissolved oxygen and detritus carbon (permitting variable C : N in exported organic matter), as well as a simple benthic formulation and extended parameterisations of phytoplankton growth, calcification and detritus remineralisation. A full description of MEDUSA-2.0, including its additional functionality, is provided and a multi-decadal hindcast simulation described (1860-2005), to evaluate the biogeochemical performance of the model. [ABSTRACT FROM AUTHOR]

Continued oceanic uptake of anthropogenic CO2 is projected to significantly alter the chemistry of the upper oceans, potentially having serious consequences for the marine ecosystems. Projections of ocean acidification are primarily determined from prescribed emission pathways within large scale earth system models. Rather than running the cumbersome earth system models, we can use a reduced-form model to quickly emulate the CMIP5 models for projection studies under arbitrary emission pathways and for uncertainty analyses of the marine carbonate system. In this study we highlight the capability of Hector v1.1, a reduced-form model, to project changes in the upper ocean carbonate system over the next three centuries. Hector is run under historical emissions and a high emissions scenario (Representative Concentration Pathway 8.5), comparing its output to observations and CMIP5 models that contain ocean biogeochemical cycles. Ocean acidification changes are already taking place, with significant changes projected to occur over the next 300 years. We project a low latitude (> 55°) surface ocean pH decrease from preindustrial conditions by 0.4 units to 7.77 at 2100, and an additional 0.27 units to 7.50 at 2300. Aragonite saturations decrease by 1.85 units to 2.21 at 2100 and an additional 0.80 units to 1.42 at 2300. Under a high emissions scenario, for every 1 °C of future warming we find a 0.107 unit pH decrease and a 0.438 unit decrease in aragonite saturations. Hector reproduces the global historical trends, and future projections with equivalent rates of change over time compared to observations and CMIP5 models. Hector is a robust tool that can be used for quick ocean acidification projections, accurately emulating large scale climate models under multiple emission pathways. [ABSTRACT FROM AUTHOR]

The article presents a study that determines the applications of the spin-up for marine ecosystem model based on the Transport Matrix method on the graphics processing units (GPUs). It details the method of the study that uses two matrix-vector multiplications and biogeochemical model. It notes the result of the study, which shows that consumer GPU can beat significant number of central processing unit (CPU) without further using code optimization.

Land models, which have been developed by the modeling community in the past two decades to predict future states of ecosystems and climate, have to be critically evaluated for their performance skills of simulating ecosystem responses and feedback to climate change. Benchmarking is an emerging procedure to measure and evaluate performance of models against a set of defined standards. This paper proposes a benchmarking framework for evaluation of land models. The framework includes (1) targeted aspects of model performance to be evaluated; (2) a set of benchmarks as defined references to test model performance; (3) metrics to measure and compare performance skills among models so as to identify model strengths and deficiencies; and (4) model improvement. Component 4 may or may not be involved in a benchmark analysis but is an ultimate goal of general modeling research. Land models are required to simulate exchange of water, energy, carbon and sometimes other trace gases between the atmosphere and the land-surface, and should be evaluated for their simulations of biophysical processes, biogeochemical cycles, and vegetation dynamics across timescales in response to both weather and climate change. Benchmarks that are used to evaluate models generally consist of direct observations, data-model products, and data-derived patterns and relationships. Metrics of measuring mismatches between models and benchmarks may include (1) a priori thresholds of acceptable model performance and (2) a scoring system to combine data-model mismatches for various processes at different temporal and spatial scales. The benchmark analyses should identify clues of weak model performance for future improvement. Iterations between model evaluation and improvement via benchmarking shall demonstrate progress of land modeling and help establish confidence in land models for their predictions of future states of ecosystems and climate. [ABSTRACT FROM AUTHOR]

Dissolved oxygen (DO) is one of the most important drivers of ocean biogeochemical cycles and marine life, and in many areas its concentration has declined due to climate change. In recent decades, a growing number of autonomous oceanographic platforms has been equipped with sensors for direct in situ measurements of oxygen levels. However, to ensure high quality and comparable data, these observations need to be validated or, if necessary, corrected. In this paper, we compiled all the available DO data collected by Argo floats and gliders in the South Adriatic Pit (Mediterranean Sea) between 2014 and 2020. This dataset includes data for which it was not possible to apply conventional quality-control methods. Therefore, we had to apply tailored procedures based on well-established best practices for correction. The aim is to showcase how these tailored procedures allowed us to achieve the best possible quality of data and generate consistent datasets. The drift of the glider DO sensors related to storage was also estimated. The described procedure could be useful in similar cases where the conventional methods are not viable, thus making available potentially useful data. [ABSTRACT FROM AUTHOR]

A number of nonlinear microbial models of soil carbon decomposition have been developed. Some of them have been applied globally but have yet to be shown to realistically represent soil carbon dynamics in the field. Therefore a thorough analysis of their key differences will be very useful for the future development of these models. Here we compare two nonlinear microbial models of soil carbon decomposition: one is based on reverse Michaelis-Menten kinetics (model A) and the other on regular Michaelis- Menten kinetics (model B). Using a combination of analytic solutions and numerical simulations, we find that the oscillatory responses of carbon pools model A to a small perturbation in the initial pool sizes have a higher frequency and damps faster than model B. In response to soil warming, soil carbon always decreases in model A; but likely decreases in cool regions and increases in warm regions in model B. Maximum CO2 efflux from soil carbon decomposition (Fmax) after an increased carbon addition decreases with an increase in soil temperature in both models, and the sensitivity of Fmax to the amount of carbon input increases with soil temperature in model A; but decreases monotonically with an increase in soil temperature in model B. These differences in the responses to soil warming and carbon input between the two nonlinear models can be used to differentiate which model is more realistic with field or laboratory experiments. This will lead to a better understanding of the significance of soil microbial processes in the responses of soil carbon to future climate change at regional or global scales. [ABSTRACT FROM AUTHOR]

The closed chamber technique is widely used to measure the exchange of methane (CH4) and carbon dioxide (CO2) from terrestrial ecosystems. There is, however, large uncertainty about which model should be used to calculate the gas flux from the measured gas concentrations. Due to experimental uncertainties the robust linear regression model (first order polynomial) is often applied, even though theoretical considerations of the technique suggest the application of other, curvilinear models. High-resolution automatic chamber systems which sample gas concentrations several hundred times per flux measurement make it possible to resolve the curvilinear behavior and study the information imposed by the natural variability of the temporal concentration changes. We used more than 50 000 such flux measurements of CH4 and CO2 from five field sites located in peat forming wetlands to calculate fluxes with different models. The flux differences from independent linear estimates are generally found to be smaller than the local flux variability on the plot scale. The curvilinear behavior of the gas concentrations within the chamber is strongly influenced by wind driven chamber leakage, and less so by changing gas concentration gradients in the soil during chamber closure. Such physical processes affect both gas species equally, which makes it possible to isolate biochemical processes affecting the gases differently, such as photosynthesis limitation by chamber headspace CO2 concentrations under high levels of incoming solar radiation. We assess the possibility to exploit this effect for a partitioning of the net CO2 flux into photosynthesis and ecosystem respiration and argue that high-resolution automatic chamber measurements could be used for purposes beyond the estimation of the net gas flux. [ABSTRACT FROM AUTHOR]

Soil microbial respiration is a central process in the terrestrial carbon (C) cycle. In this study I tested the effect of the carbon-to-nitrogen (C : N) ratio of soil litter layers on microbial respiration in absolute terms and per unit microbial biomass C. For this purpose, a global dataset on microbial respiration per unit microbial biomass C - termed the metabolic quotient (qCO2) - was compiled form literature data. It was found that the qCO2 in the soil litter layers was positively correlated with the litter C : N ratio and negatively related with the litter nitrogen (N) concentration. The positive relation between qCO2 and litter C : N ratio resulted from an increase in respiration with the C : N ratio in combination with no significant effect of the litter C : N ratio on the soil microbial biomass C concentration. The results suggest that soil microorganisms respire more C both in absolute terms and per unit microbial biomass C when decomposing N-poor substrate. Thus, the findings indicate that atmospheric N deposition, leading to decreased litter C : N ratios, might decrease microbial respiration in soils. [ABSTRACT FROM AUTHOR]

Fire has always been an important component of many ecosystems, but anthropogenic global climate change is now altering fire regimes over much of Earth's land surface, spurring a more urgent need to understand the physical, biological, and chemical processes associated with fire as well as its effects on human societies. In 2020, AGU launched a Special Collection that spanned 10 journals, soliciting papers under the theme "Fire in the Earth System" to encourage state‐of‐the‐art publications in fire‐related science. The completed Special Collection comprises more than 100 papers. Here, we summarize the articles published in this collection, considering them to be grouped into seven themes: paleofire and its ties to climate; evolution of fire patterns in the recent past and the future, including the effects of ongoing climate change; physical (atmospheric) and chemical processes associated with fire; ecosystem effects, including on biogeochemical cycles; physical landscape change after fire and its associated hazards; fire effects on water quality, air quality, and human health; and new methods and technologies applied to fire research. Plain Language Summary: In 2020, AGU launched a Special Collection that spanned 10 journals, soliciting papers under the theme "Fire in the Earth System" to encourage state‐of‐the‐art publications in fire‐related science. The completed Special Collection comprises more than 100 papers. This Introduction summarizes the articles published in the Special Collection. Key Points: This introduction summarizes papers published through the Fire in the Earth System Special Collection [ABSTRACT FROM AUTHOR]

Lichens and bryophytes are abundant globally and they may even form the dominant autotrophs in (sub)polar ecosystems, in deserts and at high altitudes. Moreover, they can be found in large amounts as epiphytes in old-growth forests. Here, we present the first process-based model which estimates the net carbon uptake by these organisms at the global scale, thus assessing their significance for biogeochemical cycles. The model uses gridded climate data and key properties of the habitat (e.g. disturbance intervals) to predict processes which control net carbon uptake, namely photosynthesis, respiration, water uptake and evaporation. It relies on equations used in many dynamical vegetation models, which are combined with concepts specific to lichens and bryophytes, such as poikilohydry or the effect of water content on CO2 diffusivity. To incorporate the great functional variation of lichens and bryophytes at the global scale, the model parameters are characterised by broad ranges of possible values instead of a single, globally uniform value. The predicted terrestrial net carbon uptake of 0.34 to 3.3 (GtC) yr-1 and global patterns of productivity are in accordance with empirically-derived estimates. Considering that the assimilated carbon can be invested in processes such as weathering or nitrogen fixation, lichens and bryophytes may play a significant role in biogeochemical cycles. [ABSTRACT FROM AUTHOR]

We compared the functional response of a biogeochemical data assimilation model versus an empirical satellite-derived algorithm in describing the variation of four phytoplankton (diatoms, cyanobacteria, coccolithophores and chlorophytes) groups globally and in 12 major oceanographic basins. Global mean differences of all groups were within ~15% of an independent observation data base for both approaches except for satellite-derived chlorophytes. Diatoms and cyanobacteria concentrations were significantly (p < 0.05) correlated with the independent observation data base for both methods. Coccolithophore concentrations were only correlated with the in situ data for the model approach and the chlorophyte concentration was only significantly correlated to the in situ data for the satellite-derived approach. Using monthly means from 1998–2007, the seasonal variation from the satellite-derived approach and model were significantly correlated in 11 regions for diatoms and in 9 for coccolithophores but only in 3 and 2 regions for cyanobacteria and chlorophytes. Most disagreement on the seasonal variation of phytoplankton composition occurred in the North Pacific and Antarctic where, except for diatoms, no significant correlation could be found between the monthly mean concentrations derived from both approaches. In these two regions there was also an overestimate of diatom concentration by the model of ~60% whereas the satellite-derived approach was closer to in situ data (8-26% underestimate). Chlorophytes were the group for which both approaches differed most and that was furthest from the in situ data. These results highlight the strengths and weaknesses of both approaches and allow us to make some suggestions to improve our approaches to understanding phytoplankton dynamics and distribution. [ABSTRACT FROM AUTHOR]

To better predict how ocean acidification will affect coral reefs, it is important to understand how biogeochemical cycles on reefs alter carbonate chemistry over various temporal and spatial scales. This study quantifies the contribution of fresh groundwater discharge (as traced by radon) and shallow porewater exchange (as quantified from advective chamber incubations) to total alkalinity (TA) dynamics on a fringing coral reef lagoon along the southern Pacific island of Rarotonga over a tidal and diel cycle. Benthic alkalinity fluxes were affected by the advective circulation of water through permeable sediments, with net daily flux rates of carbonate alkalinity ranging from -1.55 to 7.76mmol m-2 d-1 , depending on the advection rate. Submarine groundwater discharge (SGD) was a source of TA to the lagoon, with the highest flux rates measured at low tide, and an average daily TA flux of 1080mmol m-2 d-1. Both sources of TA were important on a reef wide basis, although SGD acted solely as a delivery mechanism of TA to the lagoon, while porewater advection was either a sink or source of TA dependant on the time of day. On a daily basis, groundwater can contribute approximately 70% to 80% of the TA taken up by corals within the lagoon. This study describes overlooked sources of TA to coral reef ecosystems that can potentially alter water-column carbonate chemistry. We suggest that porewater and groundwater fluxes of TA should be taken into account in ocean acidification models in order to properly address changing carbonate chemistry within coral reef ecosystems. [ABSTRACT FROM AUTHOR]

The article presents a study that demonstrates the applications of the Biogeochemical Transport and Reactions (CLM4-BeTR) in regional and global biogeochemistry modeling and climate predictability. It outlines the functions of the model in which its transport code are evaluated through several analytical test cases. The study shows that the method provides detailed comparison between ecosystem observation and predictions.

During the oceanic anoxic event 2 (OAE 2) in the mid-Cretaceous widespread black shale (BS) formation occurred, reflecting perturbations in major biogeochemical cycles. Here we present geochemical and biomarker data of the OAE 2 from a shelf setting situated at about 100 to 150 water depth (Wunstorf, Germany). Our data support that processes inducing BS deposition were related to orbital cyclicity in Wunstorf and that they were not restricted to the time of the OAE 2 carbon isotope excursion. Correlations of total organic carbon (TOC) and δ15N and high relative abundances of functionalized hopanoids (incl. 2-methylated structures) suggest that BS were formed during times of imbalanced nutrients with high phosphorus inputs and increased (cyano)bacterial nitrogen fixation. Periods of BS formation were also characterized by enhanced growth of dinoflagellates and bacteriovorous ciliates, the latter supporting the presence of a stratified water body. The lack of biomarkers specific for green-sulfur bacteria excludes photic zone euxinia during OAE 2 in Wunstorf. Conflicting maturities and biomarker distributions in kerogen and extractable organic matter and, interestingly, a negative correlation of the diagenetically resistant 2-methyl hopane hydrocarbons with TOC indicate a complex depositional setting at Wunstorf. In Wunstorf this might have been induced by high continental run-off during BS formation and the accompanying mobilisation of refractory OM from the shelfs and near shore areas. [ABSTRACT FROM AUTHOR]

Due to their high biological productivity coastal upwelling regions are important for biogeochemical cycles in the ocean and for fisheries. Upwelled water is not only enriched in nutrients but also supersaturated with respect to atmospheric CO2 and N2O and undersaturated for O2. We present a novel approach to estimate carbon based net community production (NCP) using surface ocean data for CO2, O2 and N2O from three cruises to the Mauritanian upwelling region (Northwest Africa) that were conducted in different seasons. Through combination of the saturation patterns of CO2, O2 and N2O effects of air-sea gas exchange and NCP could be separated. NCP values ranges from 0.6±0.1gCm-2 d-1 during times of weak upwelling to 1.6±0.4gCm-2 d-1 during 10 strong upwelling. The estimated NCP values show a strong relationship with a wind derived upwelling index, which was used to estimate annual NCP. [ABSTRACT FROM AUTHOR]

The lagrangian progression of biogeochemical processes was followed in a filament of the Mauritanian upwelling system, North West Africa, during offshore advection. Inert duel tracers sulphur hexafluoride and helium-3 labelled a freshly upwelled patch of water that was mapped for 8 days. Changes in biological, physical and chemical characteristics were measured including phytoplankton productivity, nitrogen assimilation and regeneration. Freshly upwelled water contained high nutrient concentrations (NO3- = 9.0 ± 0.1 µmol L-1; PO43- = 0.7 ± 0.1 µmol L-1; Si = 2.7 ± 0.1 µmol L-1) but was depleted in N compared to Redfield stoichiometry (N:P = 13.9:1). A maximum primary productivity rate of 0.7 mol C m-2 d-1 was measured on the continental shelf, associated with N-assimilation rates of 43.8 nmol L-1 h-1 for NO3-, 32.8 nmol L-1 h-1 for NH4+ and a phytoplankton community dominated by diatoms and flagellates. Indicators of phytoplankton abundance and activity decreased as the labelled water mass transited the continental shelf slope into deeper water, possibly linked to the mixed layer depth exceeding the light penetration depth. By the end of the study, primary productivity rates of 0.1 mol C m-2 d-1 were measured, associated with N-assimilation rates of 3.9 nmol L-1 h-1 for NO3-, 6.1 nmol L-1 h-1 for NH4+ and lower nutrient concentrations (NO3- = 4.6 ± 0.3 µmol L-1; PO43- = 0.4 ± 0.1 µmol L-1; Si = 0.9 ± 0.1 µmol L-1). Nitrogen regeneration and assimilation took place simultaneously; NH4+ was regenerated at 9.4-85.0 nmol L-1 h-1; NH4+ was oxidised at 0.30-8.75 nmol L-1 h-1; NO2- was oxidised at 25.55-81.11 nmol L-1 h-1. Results highlight the importance of regenerated NH4+ in sustaining phytoplankton productivity and indicate that the upwelled NO3- pool contained an increasing fraction of regenerated NO3- as it advected offshore. By calculating this fraction and incorporating it into an f ratio formulation we estimated that of the 12.38 Tg C of annual regional production, 4.73 Tg C was exportable. [ABSTRACT FROM AUTHOR]

During the fifth phase of the Coupled Model Intercomparison Project (CMIP5) substantial efforts were carried out on the systematic assessment of the skill of Earth system models. One goal was to check how realistically representative marine biogeochemical tracer distributions could be reproduced by models. Mean-state assessments routinely compared model hindcasts to available modern biogeochemical observations. However, these assessments considered neither the extent of equilibrium in modeled biogeochemical reservoirs nor the sensitivity of model performance to initial conditions or to the spin-up protocols. Here, we explore how the large diversity in spin-up protocols used for marine biogeochemistry in CMIP5 Earth system models (ESM) contribute to model-to-model differences in the simulated fields. We take advantage of a 500 year spin-up simulation of IPSL-CM5A-LR to quantify the influence of the spin-up protocol on model ability to reproduce relevant data fields. Amplification of biases in selected biogeochemical fields (O2, NO3, Alk-DIC) is assessed as a function of spin-up duration. We demonstrate that a relationship between spin-up duration and assessment metrics emerges from our model results and is consistent when confronted against a larger ensemble of CMIP5 models. This shows that drift has implications on their performance assessment in addition to possibly aliasing estimates of climate change impact. Our study suggests that differences in spin-up protocols could explain a substantial part of model disparities, constituting a source of model-to-model uncertainty. This requires more attention in future model intercomparison exercices in order to provide realistic ESM results on marine biogeochemistry and carbon cycle feedbacks. [ABSTRACT FROM AUTHOR]

Despite the importance of soil processes for global biogeochemical cycles, our capability for predicting soil evolution over geological timescales is poorly constrained. We attempt to probe our understanding and predictive capability of this evolutionary process by developing a mechanistic soil evolution model, based on an existing model framework, and comparing the predictions with observations from soil chronosequences in Hawaii. Our soil evolution model includes the major processes of pedogenesis: mineral weathering, percolation of rainfall, leaching of solutes, surface erosion, bioturbation and vegetation interactions and can be applied to various bedrock compositions and climates. The specific properties the model simulates over timescales of tens to hundreds of thousand years are, soil depth, vertical profiles of elemental composition, soil solution pH and organic carbon distribution. We demonstrate with this model the significant role that vegetation plays in accelerating the rate of weathering and hence soil profile development. Comparisons with soils that have developed on Hawaiian basalts reveal a remarkably good agreement with Na, Ca and Mg profiles suggesting that the model captures well the key components of soil formation. Nevertheless, differences between modelled and observed K and P are substantial. The fact that these are important plant nutrients suggests that a process likely missing from our model is the active role of vegetation in selectively acquiring nutrients. This study therefore indirectly indicates the valuable role that vegetation can play in accelerating the weathering and thus release of these globally important nutrients into the biosphere. [ABSTRACT FROM AUTHOR]

Rising ocean temperatures will likely increase stratification of the water column and reduce nutrient input into the photic zone. This will increase the likelihood of nutrient limitation in marine microalgae, leading to changes in the abundance and composition of phytoplankton communities, which in turn will affect global biogeochemical cycles. Calcifying algae, such as coccolithophores, influence the carbon cycle by fixing CO2 into particulate organic carbon (POC) through photosynthesis and into particulate inorganic carbon (PIC) through calcification. As calcification produces a net release of CO2, the ratio of PIC/POC determines whether coccolithophores act as a source (PIC/POC > 1) or a sink (PIC/ POC < 1) of atmospheric CO2. We studied the effect of phosphorus (P-) limitation and temperature stress on the physiology and PIC/POC ratios of two subspecies of Coccolithus pelagicus. This large and heavily calcified species (PIC/POC generally > 1.5) is a major contributor to calcite export from the photic zone into deep-sea reservoirs. Phosphorus limitation did not influence exponential growth rates in either subspecies, but P-limited cells had significantly lower cellular P-content. A 5°C temperature increase did not affect exponential growth rates either, but nearly doubled cellular P-content under both high and low phosphate availability. The PIC/POC ratios did not differ between P-limited and nutrient-replete cultures, but at elevated temperature (from 10 to 15°C) PIC/POC ratios decreased by 40-60%. Our results suggest that elevated temperature may intensify P-limitation due to a higher P-requirement to maintain growth and POC production rates, possibly reducing abundances in a warmer ocean. Under such a scenario C. pelagicus may decrease its calcification rate relative to photosynthesis, resulting in PIC/POC ratios < 1 and favouring CO2-sequestration over release. Phosphorus limitation by itself is unlikely to cause changes in the PIC/POC ratio in this species. [ABSTRACT FROM AUTHOR]

Ocean acidification (OA) is the consequence of rising atmospheric CO2, and it is occurring in conjunction with global warming. Observational studies show that OA will impact ocean biogeochemical cycles. Here, we use a coupled carbon-climate Earth System Model under the RCP8.5 emission scenario to evaluate and quantify the first-order impacts of OA on marine biogeochemical cycles and the potential feedback on our future climate over this century. We find that OA impacts have only a small impact on the future atmospheric CO2 (less than 45 ppm) and future global warming (less than a 0.25 K) by 2100. While the climate change feedbacks are small, OA impacts may significantly alter the distribution of biological production and remineralization, which would alter the dissolved oxygen distribution in the ocean interior. Our results demonstrate that the consequences of OA will not be through its impact on climate change, but on how it impacts the flow of energy in marine ecosystems, which may significantly impact their productivity, composition and diversity. [ABSTRACT FROM AUTHOR]

Despite a multitude of studies, erosion rates as well as the contribution of different processes on Chinese Loess Plateau (CLP) remain uncertain. This makes it impossible to correctly assess the impact of conservation programs and the magnitude of the erosion-induced carbon sink. We used a novel approach, based on field evidence, to reassess erosion rates on the CLP before and after conservation measures were implemented. Our results show that the current average topsoil erosion rate is 3-9 times lower than earlier estimates suggested: most sediments are mobilised by gully erosion and/or landsliding. Under 2005 conditions, the combination of topsoil erosion, gully erosion and landslides mobilised 0.81 ±0.23Gt yr-1 of sediments and 4.77±1.96 Tg yr-1 of soil organic carbon (SOC): the latter number sets the maximum magnitude of the erosion-induced carbon sink, which is ca. 4 times lower than other recent estimates suggest. The sediment fluxes we calculate are consistent with sediment yields measured in the Yellow River. The conservation programs implemented from the 1950s onwards reduced topsoil erosion from 0.51 ±0.13 to 0.30±0.08 Gt yr-1 while SOC mobilisation was reduced from 7.63 ± 3.52 to 4.77 ± 1.96 Tg C. Prior to 1950, a geomorphological equilibrium existed whereby the amount of sediment and carbon exported to the Bohai sea was similar to the amount of sediment eroded on the CLP, so that the erosion-induced carbon sink nearly equalled the amount of mobilised SOC. Conservation efforts and reservoir construction have disrupted this equilibrium and most eroded sediments and carbon are now stored on land where part of the SOC may decompose, thereby potentially lowering the strength of the erosion-induced carbon sink. Despite the fact that average topsoil losses on the CLP are still relatively high, the current level of topsoil erosion on the CLP is no major threat to the agricultural productivity of the area, mainly because fertilizer application has dramatically increased since 1980. Assessing the human impact on agricultural ecosystems at larger scales requires a careful identification and quantification of the processes involved: by doing so for the CLP we have shown that current perceptions regarding the intensity of soil erosion and its effects (both negative and positive) need to be revised. [ABSTRACT FROM AUTHOR]

We studied the concurrence of methanogenesis and sulfate reduction in surface sediments (0-25 cm below sea floor, cmbsf) at six stations (70, 145, 253, 407, 770 and 1024 m) along the Peruvian margin (12°S). This oceanographic region is characterized by high carbon export to the seafloor, creating an extensive oxygen minimum zone (OMZ) on the shelf, both factors that could favor surface methanogenesis. Sediments sampled along the depth transect traversed areas of anoxic and oxic conditions in the bottom-near water. Net methane production (batch incubations) and sulfate reduction (35S-sulfate radiotracer incubation) were determined in the upper 0-25 cmbsf of multicorer cores from all stations, while deep hydrogenotrophic methanogenesis (> 30 cmbsf, 14C-bicarbonate radiotracer incubation) was determined in two gravity cores at selected sites (78 and 407 m). Furthermore, stimulation (methanol addition) and inhibition (molybdate addition) experiments were carried out to investigate the relationship between sulfate reduction and methanogenesis. Highest rates of methanogenesis and sulfate reduction in the surface sediments, integrated over 0-25 cmbsf, were observed on the shelf (70-253 m, 0.06-0.1 and 0.5-4.7 mmol m-2 d-1, respectively), while lowest rates were discovered at the deepest site (1024 m, 0.03 and 0.2 mmol m-2 d-1, respectively). The addition of methanol resulted in significantly higher surface methanogenesis activity, suggesting that the process was mostly based on non-competitive substrates, i.e., substrates not used by sulfate reducers. In the deeper sediment horizons, where competition was probably relieved due to the decline of sulfate, the usage of competitive substrates was confirmed by the detection of hydrogenotrophic activity in the sulfate-depleted zone at the shallow shelf station (70 m). Surface methanogenesis appeared to be correlated to the availability of labile organic matter (C/N ratio) and organic carbon degradation (DIC production), both of which support the supply of methanogenic substrates. A negative correlation of methanogenesis rates with dissolved oxygen in the bottom-near water was not obvious, however, anoxic conditions within the OMZ might be advantageous for methanogenic organisms at the sediment-water interface. Our results revealed a high relevance of surface methanogenesis on the shelf, where the ratio between surface to deep (below sulfate penetration) methanogenic activity ranged between 0.13 and 105. In addition, methane concentration profiles indicate a partial release of surface methane into the water column as well as a partial consumption of methane by anaerobic methane oxidation (AOM) in the surface sediment. The present study suggests that surface methanogenesis might play a greater role in ben-thic methane budgeting than previously thought, especially for fueling AOM above the sulfate-methane transition zone. [ABSTRACT FROM AUTHOR]

Wildfires are by far the largest contributor to global biomass burning and constitute a large global source of atmospheric traces gases and aerosols. Such emissions have a considerable impact on air quality and constitute a major health hazard. Biomass burning also influences the radiative balance of the atmosphere and is thus not only of societal, but also of significant scientific interest. There is a common perception that climate change will lead to an increase in emissions as hot and dry weather events that promote wildfire will become more common. However, even though a few studies have found that the inclusion of CO2 fertilization of photosynthesis and changes in human population patterns will tend to somewhat lower predictions of future wildfire emissions, no such study has included full ensemble ranges of both climate predictions and population projections, including the effect of different degrees of urbanisation. Here, we present a series of 124 simulations with the LPJ-GUESS-SIMFIRE global dynamic vegetation -wildfire model, including a semi-empirical formulation for the prediction of burned area based on fire weather, fuel continuity and human population density. The simulations comprise Climate Model Intercomparison Project 5 (CMIP5) climate predictions from eight Earth system models using two Representative Concentration Pathways (RCPs) and five scenarios of future human population density based on the series of Shared Socioeconomic Pathways (SSPs), sensitivity tests for the effect of climate and CO2, as well as a sensitivity analysis using two alternative parameteri-sations of the semi-empirical burned-area model. Contrary to previous work, we find no clear future trend of global wildfire emissions for the moderate emissions and climate change scenario based on the RCP 4.5. Only historical population change introduces a decline by around 15 % since 1900. Future emissions could either increase for low population growth and fast urbanisation, or continue to decline for high population growth and slow urbanisation. Only for high future climate change (RCP8.5), wildfire emissions start to rise again after ca. 2020 but are unlikely to reach the levels of 1900 by the end of the 21st century. We find that climate warming will generally increase the risk of fire, but that this is only one of several equally important factors driving future levels of wildfire emissions, which include population change, CO2 fertilisation causing woody thickening, increased productivity and fuel load, and faster litter turnover in a warmer climate. [ABSTRACT FROM AUTHOR]

D'Ortenzio and Ribera d'Alcalà (2009, DR09 hereafter) divided the Mediterranean Sea into "bioregions" based on the climatological seasonality (phenology) of phytoplank-ton. Here we investigate the interannual variability of this bioregionalization. Using 16 years of available ocean color observations (i.e. SeaWiFS and MODIS), we analyzed the spatial distribution of the DR09 trophic regimes on an annual basis. Additionally, we identified new trophic regimes, with seasonal cycles of phytoplankton biomass different from the DR09 climatological description and named "Anomalous". Overall, the classification of the Mediterranean phytoplankton phenology proposed by DR09 (i.e. "No Bloom", "Intermittently", "Bloom" and "Coastal"), is confirmed to be representative of most of the Mediterranean phytoplankton phenologies. The mean spatial distribution of these trophic regimes (i.e. bioregions) over the 16 years studied is also similar to the one proposed by DR09. But at regional scale some annual differences, in their spatial distribution and in the emergence of "Anomalous" trophic regimes, were observed compared to the DR09 description. These dissimilarities with the DR09 study were related to interannual variability in the sub-basin forcing: winter deep convection events, frontal instabilities, inflow of Atlantic or Black Sea Waters and river run-off. The large assortment of phytoplankton phenologies identified in the Mediterranean Sea is thus verified at interannual level, confirming the "sentinel" role of this basin to detect the impact of climate changes on the pelagic environment. [ABSTRACT FROM AUTHOR]

Woodlands represent highly significant carbon sinks globally, though could lose this function under future climatic change. Effective large-scale monitoring of these woodlands has a critical role to play in mitigating for, and adapting to, climate change. Mediterranean woodlands have low carbon densities, but represent important global carbon stocks due to their extensiveness and are particularly vulnerable because the region is predicted to become much hotter and drier over the coming century. Airborne lidar is already recognized as an excellent approach for high-fidelity carbon mapping, but few studies have used multi-temporal lidar surveys to measure carbon fluxes in forests and none have worked with Mediterranean woodlands. We use a multi-temporal (five year interval) airborne lidar dataset for a region of central Spain to estimate above-ground biomass (AGB) and carbon dynamics in typical mixed broadleaved/coniferous Mediterranean woodlands. Field calibration of the lidar data enabled the generation of grid-based maps of AGB for 2006 and 2011, and the resulting AGB change were estimated. There was a close agreement between the lidar-based AGB growth estimate (1.22 Mg ha-1 year-1) and those derived from two independent sources: the Spanish National Forest Inventory, and a tree-ring based analysis (1.19 and 1.13 Mg ha-1 year-1, respectively). We parameterised a simple simulator of forest dynamics using the lidar carbon flux measurements, and used it to explore four scenarios of fire occurrence. Under undisturbed conditions (no fire occurrence) an accelerating accumulation of biomass and carbon is evident over the next 100 years with an average carbon sequestration rate of 1.95 Mg C ha-1 year-1. This rate reduces by almost a third when fire probability is increased to 0.01, as has been predicted under climate change. Our work shows the power of multi-temporal lidar surveying to map woodland carbon fluxes and provide parameters for carbon dynamics models. Space deployment of lidar instruments in the near future could open the way for rolling out wide-scale forest carbon stock monitoring to inform management and governance responses to future environmental change. [ABSTRACT FROM AUTHOR]

To quantify the contribution of autotrophic microorganisms to organic matter formation (OM) in soils, we investigated natural CO22 vents (mofettes) situated in a wetland in NW Bohemia (Czech Republic). Mofette soils had higher SOM concentrations than reference soils due to restricted decomposition under high CO2 levels. We used radiocarbon (Δ14C) and stable carbon isotope ratios (δ13C) to characterize SOM and its sources in two moffetes and compared it with respective reference soils, which were not influenced by geogenic CO2. The geogenic CO2 emitted at these sites is free of radiocarbon and enriched in δ13C compared to atmospheric CO2. Together, these isotopic signals allow us to distinguish C fixed by plants from C fixed by autotrophic microorganisms using their differences in δ13C discrimination. We can then estimate that up to 27% of soil organic matter in the 0-10 cm layer of these soils was derived from microbially assimilated CO2. Isotope values of bulk SOM were shifted towards more positive d C and more negative Δ14C values in mofettes compared to reference soils, suggesting that geogenic CO2 emitted from the soil atmosphere is incorporated into SOM. To distinguish whether geogenic CO2 was fixed by plants or by CO2 assimilating microorganisms, we first used the proportional differences in radiocarbon and d C values to indicate the magnitude of discrimination of the stable isotopes in living plants. Deviation from this relationship was taken to indicate the presence of microbial CO2 fixation, as microbial discrimination should differ from that of plants. CO2-labelling experiments confirmed high activity of CO2 assimilating microbes in the top 10 cm, where δ13C values of SOM were shifted up to 2‰ towards more negative values. Uptake rates of microbial CO2 fixation ranged up to 1.59 ± 0.16 µg gdw-1 d-1. We inferred that the negative δ13C shift was caused by the activity of chemo-lithoautotrophic microorganisms, as indicated from quantification of cbbL/cbbM marker genes encoding for Rubis CO2 by quantitative polymerase chain reaction (qPCR) and by acetogenic and methanogenic microorganisms, shown present in the moffettes by previous studies. Combined Δ14C and δ13C isotope mass balances indicated that microbially derived carbon accounted for 8 to 27% of bulk SOM in this soil layer. The findings imply that autotrophic organisms can recycle significant amounts of carbon in wetland soils and might contribute to observed reservoir effects influencing radiocarbon signatures in peat deposits. [ABSTRACT FROM AUTHOR]

Stream channels in the McMurdo Dry Valleys are typically wide, incised, and stable. At typical flows, streams occupy a fraction of the oversized channels, providing habitat for algal mats. In January 2012, we discovered substantial channel erosion and subsurface thermomechanical erosion undercutting banks of Crescent Stream. We sampled stream water along the impacted reach and compared concentrations of solutes to the long-term data from this stream ( ~ 20 years of monitoring). Thermokarst-impacted stream water demonstrated higher electrical conductivity, and concentrations of chloride, sulfate, sodium, suspended sediments, and nitrate than the long-term medians. These results suggest that this mode of lateral permafrost degradation may substantially impact stream solute loads and potentially fertilize stream and lake ecosystems. The potential for sediment to scour or bury stream algal mats is yet to be determined, though it may offset impacts of associated increased nutrient loads to streams. [ABSTRACT FROM AUTHOR]

Stream networks were recently discovered as major but poorly constrained natural greenhouse gas (GHG) sources. A fundamental problem is that several measurement approaches have been used without cross comparisons. Flux chambers represent a potentially powerful methodological approach if robust and reliable ways 5 to use chambers on running water can be defined. Here we compare the use of anchored and freely drifting chambers on various streams having different flow velocities. The study clearly shows that (1) drifting chambers have a very small impact on the water turbulence under the chamber and thus generate more reliable fluxes, (2) anchored chambers enhance turbulence under the chambers and thus elevate fluxes, (3) the bias of the anchored chambers greatly depends on chamber design and sampling conditions, and (4) there is a promising method to reduce the bias from anchored chambers by using a flexible plastic foil seal to the water surface rather than having rigid chamber walls penetrating into the water. Altogether, these results provide novel guidance on how to apply flux chambers in running water, which will have important consequences for measurements to constrain the global GHG balances. [ABSTRACT FROM AUTHOR]

Benthic nitrogen (N2) fixation and sulfate reduction (SR) were investigated in the Peruvian oxygen minimum zone (OMZ). Sediment samples, retrieved by a multiple corer were taken at six stations (70-1025m) along a depth transect at 12° S, covering anoxic and hypoxic bottom water conditions. Benthic N2 fixation was detected at all sites, with high rates measured in OMZ mid-waters between the 70 and 253m and lowest N2 fixation rates below 253m down to 1025m water depth. SR rates were decreasing with increasing water depth, with highest rates at the shallow site. Benthic N2 fixation depth profiles largely overlapped with SR depth profiles, suggesting that both processes are coupled. The potential of N2 fixation by SR bacteria was verified by the molecular analysis of nifH genes. Detected nifH sequences clustered with SR bacteria that have been demonstrated to fix N2 in other benthic environments. Depth-integrated rates of N2 fixation and SR showed no direct correlation along the 12° S transect, suggesting that the benthic diazotrophs in the Peruvian OMZ are being controlled by additional various environmental factors. The organic matter availability and the presence of sulfide appear to be major drivers for benthic diazotrophy. It was further found that N2 fixation was not inhibited by high ammonium concentrations. N2 fixation rates in OMZ sediments were similar to rates measured in other organic-rich sediments. Overall, this work improves our knowledge on N sources in marine sediments and contributes to a better understanding of N cycling in OMZ sediments. [ABSTRACT FROM AUTHOR]

The outer Western Crimean Shelf of the Black Sea is a natural laboratory to investigate effects of stable oxic vs. varying hypoxic conditions on seafloor biogeochemical processes and benthic community structure. Bottom water oxygen concentrations varied between normoxic (175 μmol O2 L-1) and hypoxic (< 63 µmol O2 L-1) or even anoxic/sulfidic conditions within a few kilometres distance. Variations in oxygen concentrations between 160 and 10 µmol L-1 even occurred within hours close to the chemocline at 134 m water depth. Total oxygen uptake, including diffusive as well as fauna-mediated oxygen consumption, decreased from > 15 mmol m-2 d-1 in the oxic zone to < 9 mmol m-2 d-1 in the hypoxic zone, correlating with changes in macrobenthos composition. Benthic diffusive oxygen uptake rates, comprising microbial respiration plus reoxidation of inorganic products, were around 4.5 mmol m-2 d-1, but declined to 1.3 mmol m-2 d-1 at oxygen concentrations below 20 µmol L-1. Measurements and modelling of pore water profiles indicated that reoxidation of reduced compounds played only a minor role in the diffusive oxygen uptake, leaving the major fraction to aerobic degradation of organic carbon. Remineralization efficiency decreased from 100% in the oxic zone, to 50% in the oxic-hypoxic, to 10% in the hypoxic-anoxic zone. Overall the faunal remineralization rate was more important, but also more influenced by fluctuating oxygen concentrations than microbial and geochemical oxidation processes. [ABSTRACT FROM AUTHOR]

Global ocean biogeochemistry models currently employed in climate change projections use highly simplified representations of pelagic food webs. These food webs do not necessarily include critical pathways by which ecosystems interact with ocean biogeochemistry and climate. Here we present a global biogeochemical model which incorporates ecosystem dynamics based on the representation of ten plankton functional types (PFTs); six types of phytoplankton, three types of zooplankton, and heterotrophic bacteria. We improved the representation of zooplankton dynamics in our model through (a) the explicit inclusion of large, slow-growing zooplankton, and (b) the introduction of trophic cascades among the three zooplankton types. We use the model to quantitatively assess the relative roles of iron vs. grazing in determining phytoplankton biomass in the Southern Ocean High Nutrient Low Chlorophyll (HNLC) region during summer. When model simulations do not represent crustacean macrozooplankton grazing, they systematically overestimate Southern Ocean chlorophyll biomass during the summer, even when there was no iron deposition from dust. When model simulations included the developments of the zooplankton component, the simulation of phytoplankton biomass improved and the high chlorophyll summer bias in the Southern Ocean HNLC region largely disappeared. Our model results suggest that the observed low phytoplankton biomass in the Southern Ocean during summer is primarily explained by the dynamics of the Southern Ocean zooplankton community rather than iron limitation. This result has implications for the representation of global biogeochemical cycles in models as zooplankton faecal pellets sink rapidly and partly control the carbon export to the intermediate and deep ocean. [ABSTRACT FROM AUTHOR]

The chemical composition of the global ocean is governed by biological, chemical and physical processes. These processes interact with each other so that the concentrations of carbon dioxide, oxygen, nitrate and phosphate vary in constant proportions, referred to as the Redfield ratios. We build here the Generalized Total Least-Squares estimator of these ratios. The interest of our approach is twofold: it respects the hydrological characteristics of the studied areas, and it can be applied identically in any area where enough data are available. The tests performed on the Atlantic Ocean highlight a variability of the Redfield ratios, both with geographical location and with depth. This variability emphasizes the importance of local and accurate estimates of Redfield ratios. [ABSTRACT FROM AUTHOR]

Marine organisms precipitate 0.5-2.0 Gt of carbon as calcium carbonate (CaCO3) every year with a profound impact on global biogeochemical element cycles. Biotic calcification relies on calcium ions (Ca2+) and generally on bicarbonate ions (HCO3-) as CaCO3 substrates and can be inhibited by high proton (H+) concentrations. The seawater concentration of carbonate ions (CO32-) and the CO32-dependent CaCO3 saturation state (...) seem to be irrelevant in this production process. Nevertheless, calcification rates and the success of calcifying organisms in the oceans often correlate surprisingly well with these two carbonate system parameters. This study addresses this dilemma through rearrangement of carbonate system equations which revealed an important proportionality between [CO32-] or ... and the ratio of [HCO3- ] to [H+]. Due to this proportionality, calcification rates will always correlate equally well with [HCO3-] = [H+] as with [CO32-] or ... when temperature, salinity, and pressure are constant. Hence, [CO3- ] and ... may simply be very good proxies for the control by [HCO3-] = [H+] where [HCO3- ] would be the inorganic carbon substrate and [H+] would function as calcification inhibitor. If the "substrate-inhibitor ratio" (i.e. [HCO3- ] = [H+]) rather than [CO32- ] or ... controls CaCO3 formation then some of the most common paradigms in ocean acidification research need to be reviewed. For example, the absence of a latitudinal gradient in [HCO3- ] = [H+] in contrast to [CO32-] and ... could modify the common assumption that high latitudes are affected most severely by ocean acidification. [ABSTRACT FROM AUTHOR]

As high latitudes warm, vast stocks of carbon and nitrogen stored in permafrost will become available for transport to aquatic ecosystems. While there is a growing understanding of the potential effects of permafrost collapse (thermokarst) on aquatic biogeochemical cycles, neither the spatial extent nor temporal duration of these effects are known. To test hypotheses concerning patterns and persistence of elemental export from upland thermokarst, we sampled hydrologic outflow from 83 thermokarst features in various stages of development across the North Slope of Alaska. We hypothesized that an initial pulse of carbon and nutrients would be followed by a period of elemental retention during feature recovery, and that the duration of these stages would depend on feature morphology. Thermokarst caused substantial increases of dissolved organic carbon and other solute concentrations with a particularly large impact on inorganic nitrogen. Magnitude and duration of thermokarst effects on water chemistry differed by feature type and secondarily by landscape age. Most solutes returned to undisturbed concentrations after feature stabilization, but elevated dissolved carbon, inorganic nitrogen, and sulfate concentrations persisted through stabilization for some feature types, suggesting that aquatic disturbance by thermokarst for these solutes is long-lived. Dissolved methane decreased by 90% for most feature types, potentially due to high concentrations of sulfate and inorganic nitrogen. Spatial patterns of carbon and nutrient export from thermokarst suggest that upland thermokarst may be a dominant linkage transferring carbon and nutrients from terrestrial to aquatic ecosystems as the Arctic warms. [ABSTRACT FROM AUTHOR]

Burial of organic carbon in marine sediments has a profound influence in marine biogeochemical cycles, and provides a sink for greenhouse gases such as CO2 and CH4. However, tracing organic carbon from primary production sources as well as its transformations in the sediment record remains challenging. Here we examine a novel but growing tool for tracing biosynthetic origin of amino acid carbon skeletons, based on natural occurring stable carbon isotope patterns in individual amino acids (δ13CAA). We focus on two important aspects for δ13CAA utility in sedimentary paleoarchives: first, the fidelity of source diagnostic of algal δ13CAA patterns across different oceanographic growth conditions; and second, the ability of δ13CAA patterns to record the degree of subsequent microbial amino acid synthesis after sedimentary burial. Using the marine diatom Thalassiosira weissflogii, we tested under controlled conditions how δ13CAA patterns respond to changing environmental conditions, including light, salinity, temperature, and pH. Our findings show that while differing oceanic growth conditions can change macromolecular cellular composition, δ13CAA isotopic patterns remain largely invariant. These results underscore that δ13CAA patterns should accurately record biosynthetic sources across widely disparate oceanographic conditions. We also explored how δ13CAA patterns change as a function of age, total nitrogen and organic carbon content after burial, in a marine sediment core from a coastal upwelling area off Peru. Based on the four most informative amino acids for distinguishing between diatom and bacterial sources (i.e. isoleucine, lysine, leucine and tyrosine), bacterial derived amino acids ranged from 10-15% in the sediment layers from the last 5000 years to 35% during the last glacial period. The larger bacterial fractions in older sediments indicate that bacterial activity and amino acid resynthesis progressed, approximately as a function of sediment age, to a substantially larger degree than suggested by changes in total organic nitrogen and carbon content. Taken together, these culturing and sediment studies suggest that δ13CAA patterns in sediments represent a novel proxy for understanding both primary production sources, as well as direct bacterial role in the ultimate preservation of sedimentary organic matter. [ABSTRACT FROM AUTHOR]

Reflections about three influential environmental contaminants papers published in Ambio are presented. The PCB Story by Jensen in (1972) had a very important influence on environmental chemistry. This is captured by way of comments and personal anecdotes. Wania's and MacKay's (1993) paper highlights the physical chemistry underlying transport of PCBs and organochlorine pesticides from temperate zone ecosystems to Polar Regions. Their paper exemplifies how principles of chemistry and environmental processes informed understanding the biogeochemical cycles of chemicals of environmental concern (CEC). Mergler et al.'s (2007) paper reviews knowledge of methyl mercury exposure and impacts in humans and served as an example of how to approach exposure and human health concerns for all CECs. All great progress. Then, the question: "How we missed for two decades the importance of plastics in the environment identified in a paper published the same year as The PCB Story? Are we missing yet another important environmental contaminant now? [ABSTRACT FROM AUTHOR]