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Peatland restoration and rehabilitation action has become more widely acknowledged as a necessary response to mitigating climate change risks and improving global carbon storage. Peatland ecosystems require restoration time spans of the order of decades and, thus, cannot be dependent upon the shorter-term monitoring often carried out in research projects. Hydrological assessments using geospatial tools provide the basis for planning restoration works as well as analysing associated environmental influences. “Restoration” encompasses applications to pre-restoration and post-restoration scenarios for both bogs and fens, across a range of environmental impact fields. The aim of this scoping review is to identify, describe, and categorize current process-based modelling uses in peatlands in order to investigate the applicability and appropriateness of ecohydrological and/or hydrological models for northern peatland restoration. Two literature searches were conducted using the entire Web of Science database in September 2022 and August 2023. Of the final 211 papers included in the review, models and their applications were categorized according to this review's research interests in seven distinct categories aggregating the papers' research themes and model outputs. Restoration site context was added by identifying 229 unique study site locations from the full database, which were catalogued and analysed against raster data for the Köppen–Geiger climate classification scheme. A majority of northern peatland sites were in temperate oceanic zones or humid continental zones that experienced snow. Over one in five models from the full database of papers were unnamed and likely intended for single use. Key themes emerging from topics covered by papers in the database included the following: modelling restoration development from a bog growth perspective, the prioritization of modelling greenhouse gas (GHG) emissions dynamics as a part of policymaking, the importance of spatial connectivity within or alongside process-based models to represent heterogeneous systems, and the increased prevalence of remote sensing and machine learning techniques to predict restoration progress with little physical site intervention. Models are presented according to their application to peatlands or broader ecosystem and organized from most to least complex. This review provides valuable context for the application of ecohydrological models in determining strategies for peatland restoration and evaluating post-intervention development over time.

This paper provides an overview and demonstration of emerging float-based methods for quantifying gross primary production (GPP) and net community production (NCP) using Biogeochemical-Argo (BGC-Argo) float data. Recent publications have described GPP methods that are based on the detection of diurnal oscillations in upper-ocean oxygen or particulate organic carbon concentrations using single profilers or a composite of BGC-Argo floats. NCP methods rely on budget calculations to partition observed tracer variations into physical or biological processes occurring over timescales greater than 1 d. Presently, multi-year NCP time series are feasible at near-weekly resolution, using consecutive or simultaneous float deployments at local scales. Results, however, are sensitive to the choice of tracer used in the budget calculations and uncertainties in the budget parameterizations employed across different NCP approaches. Decadal, basin-wide GPP calculations are currently achievable using data compiled from the entire BGC-Argo array, but finer spatial and temporal resolution requires more float deployments to construct diurnal tracer curves. A projected, global BGC-Argo array of 1000 floats should be sufficient to attain annual GPP estimates at 10∘ latitudinal resolution if floats profile at off-integer intervals (e.g., 5.2 or 10.2 d). Addressing the current limitations of float-based methods should enable enhanced spatial and temporal coverage of marine GPP and NCP measurements, facilitating global-scale determinations of the carbon export potential, training of satellite primary production algorithms, and evaluations of biogeochemical numerical models. This paper aims to facilitate broader uptake of float GPP and NCP methods, as singular or combined tools, by the oceanographic community and to promote their continued development.

Ocean alkalinity enhancement (OAE) aims to transfer carbon dioxide (CO2) from the atmosphere to the ocean by increasing the capacity of seawater to store CO2. The potential effects of OAE-induced changes in seawater chemistry on marine biology must be assessed to understand if OAE, operated at a climate-relevant scale, would be environmentally sustainable. Here, we describe the design of the Ocean Alkalinity Enhancement Pelagic Impact Intercomparison Project (OAEPIIP) – a standardised OAE microcosm experiment with plankton communities to be conducted worldwide. OAEPIIP provides funding for participating laboratories to conduct OAE experiments in their local environments. This paper constitutes a detailed manual on the standardised methodology that shall be adopted by all OAEPIIP participants. The individual studies will provide new insights into how plankton communities respond to OAE. The synthesis of these standardised studies, without publication bias, will reveal common OAE-responses that occur across geographic and environmental gradients and are therefore particularly important to determine. The funding available to OAEPIIP and the resulting data will be shared to maximise their value and accessibility. The globally coordinated effort has potential to promote scientific consensus about the potential effects of OAE on diverse plankton communities. Such consensus, through inclusion of the global community, will provide a sounder base to facilitate political decision making as to whether OAE should be scaled up or not.

Achieving climate targets requires mitigation against climate change but also understanding of the response of land and ocean carbon systems. In this context, global soil carbon stocks and their response to environmental changes are key. This paper quantifies the global soil carbon feedbacks due to changes in atmospheric CO2, and the associated climate changes, for Earth system models (ESMs) in CMIP6. A standard approach is used to calculate carbon cycle feedbacks, defined here as soil carbon-concentration (βs) and carbon-climate (γs) feedback parameters, which are also broken down into processes which drive soil carbon change. The sensitivity to CO2 is shown to dominate soil carbon changes at least up to a doubling of atmospheric CO2. However, the sensitivity of soil carbon to climate change is found to become an increasingly important source of uncertainty under higher atmospheric CO2 concentrations.

In spring, the Mediterranean Sea, a well-stratified low-nutrient–low-chlorophyll region, receives atmospheric deposition by both desert dust from the Sahara and airborne particles from anthropogenic sources. Such deposition translates into a supply of new nutrients and trace metals for the surface waters that likely impact biogeochemical cycles. However, the relative impacts of the processes involved are still far from being assessed in situ. After summarizing the knowledge on dust deposition and its impact on the Mediterranean Sea biogeochemistry, we present in this context the objectives and strategy of the PEACETIME project and cruise. Atmospheric and marine in situ observations and process studies have been conducted in contrasted areas encountering different atmospheric deposition context, including a dust deposition event that our dedicated “fast-action” strategy allowed us to catch. Process studies also include artificial dust seeding experiments conducted on board in large tanks in three ecoregions of the open waters of the Mediterranean Sea for the first time. This paper summarizes the work performed at sea and the type of data acquired in the atmosphere, at the air–sea interface and in the water column. An overview of the results presented in papers of this special issue (and in some others published elsewhere) is presented.

In this paper, we quantify the CO2 and N2O emissions from denitrification over the Amazonian wetlands. The study concerns the entire Amazonian wetland ecosystem with a specific focus on three floodplain (FP) locations: the Branco FP, the Madeira FP and the FP alongside the Amazon River. We adapted a simple denitrification model to the case of tropical wetlands and forced it by open water surface extent products from the Soil Moisture and Ocean Salinity (SMOS) satellite. A priori model parameters were provided by in situ observations and gauging stations from the HYBAM Observatory. Our results show that the denitrification and the trace gas emissions present a strong cyclic pattern linked to the inundation processes that can be divided into three distinct phases: activation, stabilization and deactivation. We quantify the average yearly denitrification and associated emissions of CO2 and N2O over the entire watershed at 17.8 kgN ha−1 yr−1, 0.37 gC-CO2 m−2 yr−1 and 0.18 gN-N2O m−2 yr−1 respectively for the period 2011–2015. When compared to local observations, it was found that the CO2 emissions accounted for 0.01 % of the integrated ecosystem, which emphasizes the fact that minor changes to the land cover may induce strong impacts on the Amazonian carbon budget. Our results are consistent with the state of the art of global nitrogen models with a positive bias of 28 %. When compared to other wetlands in different pedoclimatic environments we found that the Amazonian wetlands have similar emissions of N2O with the Congo tropical wetlands and lower emissions than the temperate and tropical anthropogenic wetlands of the Garonne (France), the Rhine (Europe) and south-eastern Asia rice paddies. In summary our paper shows that a data-model-based approach can be successfully applied to quantify N2O and CO2 fluxes associated with denitrification over the Amazon basin. In the future, the use of higher-resolution remote sensing products from sensor fusion or new sensors like the Surface Water and Ocean Topography (SWOT) mission will permit the transposition of the approach to other large-scale watersheds in tropical environments.

Identifying the climate-induced variability in the condition of vegetation is particularly important in the context of recent climate change and plants' impact on the mitigation of climate change. In this paper, we present the coherence and time lags in the spectral response of three individual vegetation types in the European temperate zone to the influencing meteorological factors in the period 2002–2022. Vegetation condition in broadleaved forest, coniferous forest and pastures was measured with monthly anomalies of two spectral indices – normalised difference vegetation index (NDVI) and enhanced vegetation index (EVI). As meteorological elements we used monthly anomalies of temperature (T), precipitation (P), vapour pressure deficit (VPD), evapotranspiration (ETo), and the teleconnection indices North Atlantic Oscillation (NAO) and North Sea Caspian Pattern (NCP). Periodicity in the time series was assessed using the wavelet transform, but no significant intra- or interannual cycles were detected in both vegetation (NDVI and EVI) and meteorological variables. In turn, coherence between NDVI and EVI and meteorological elements was described using the methods of wavelet coherence and Pearson's linear correlation with time lag. In the European temperate zone analysed in this study, NAO produces strong coherence mostly for forests in a circa 1-year band and a weaker coherence in a circa 3-year band. For pastures these interannual patterns are hardly recognisable. The strongest relationships occur between conditions of the vegetation and T and ETo – they show high coherence in both forests and pastures. There is a significant cohesion with the 8–16-month (ca. 1-year) and 20–32-month (ca. 2-year) bands. More time-lagged significant correlations between vegetation indices and T occur for forests than for pastures, suggesting a significant lag in the forests' response to the changes in T.

Quantifying water vapor and carbon dioxide (CO2) exchange dynamics between the land and the atmosphere through observations and modeling is necessary in order to reproduce and project near-surface climate in coupled land–atmosphere models. The exchange of water and CO2 occurs at the leaf surface (leaf level) and in a net manner through exchanges at all the leaf surfaces composing the vegetation canopy and at the soil surface (canopy level). These exchanges depend on the meteorological forcings imposed by the overlying atmosphere (atmospheric boundary layer level). In this paper, we investigate the effect of four canopy environmental variables (photosynthetic active radiation (PAR), water vapor pressure deficit (VPD), air temperature (T), and atmospheric CO2 concentration (Ca)) on the local individual leaf exchange and canopy exchange of water and CO2 at hourly timescales. Additionally, we investigate the effect of atmospheric boundary layer (ABL) processes on the local exchange. To that end, we simultaneously investigated the exchanges of water and CO2 at leaf level and canopy level for an alfalfa field in northern Spain over 1 day in summer 2021. We used comprehensive observations ranging from stomatal conductance to ABL measurements collected during the Land Surface Interactions with the Atmosphere in the Iberian Semi-Arid Environment (LIAISE) experiment. To support the observational analysis, we used a coupled land–atmosphere model (CLASS model) that has representations at all levels considered. To relate how temporal changes of the four environmental variables modify the fluxes of water and CO2, we studied tendency equations of the leaf gas exchange. These mathematical expressions quantify the temporal evolution of the leaf gas exchange as a function of the temporal evolution of PAR, VPD, T, and Ca. To investigate the effects of ABL processes on the local exchange, we developed three modeling experiments that impose surface radiative perturbations by a cloud passage (which perturbed PAR, T, and VPD), entrainment of dry air from the free troposphere (which perturbed VPD), and advection of cold air (which perturbed T and VPD). The model results and observations matched the leaf gas exchange (r2 between 0.23 and 0.67) and canopy gas exchange (r2 between 0.90 and 0.95). The tendency equations of the modeled leaf gas exchange during the study day revealed that the temporal dynamics of PAR were the main contributor to the temporal dynamics of the leaf gas exchange, with atmospheric CO2 temporal dynamics being the least important contributor. From the three modeling experiments with ABL perturbations, the surface radiative changes induced by a cloud perturbed the CO2 exchange the most, whereas all of them perturbed the water exchange to a similar extent. Second-order effects on the dynamics of the leaf gas exchange were also identified using the tendency equations. For instance, the decrease in the net CO2 assimilation rate during the cloud passage caused by a decrease in surface radiation was further enhanced due to the decrease in air temperature also associated with the cloud. With this research we showcase that the proposed tendency equations can disentangle the effect of environmental variables on the leaf exchange of water and CO2 with the atmosphere, as represented in land–surface parameterization schemes. As such, this framework can become a useful tool with which to analyze these schemes in weather and climate models.

The assessment of cropland carbon and nitrogen (C and N) balances plays a key role in identifying cost-effective mitigation measures to combat climate change and reduce environmental pollution. In this paper, a biogeochemical modelling approach is adopted to assess all C and N fluxes in a regional cropland ecosystem of Thessaly, Greece. Additionally, the estimation and quantification of the modelling uncertainty in the regional inventory are realized through the propagation of parameter distributions through the model, leading to result distributions for modelling estimations. The model was applied to a regional dataset of approximately 1000 polygons, deploying model initializations and crop rotations for the five major crop cultivations and for a time span of 8 years. The full statistical analysis on modelling results (including the uncertainty ranges given as ± values) yields for the C balance carbon input fluxes into the soil of 12.4 ± 1.4 t C ha−1 yr−1 and output fluxes of 11.9 ± 1.3 t C ha−1 yr−1, with a resulting average carbon sequestration of 0.5 ± 0.3 t C ha−1 yr−1. The averaged N influx was 212.3 ± 9.1 kg N ha−1 yr−1, while outfluxes of 198.3 ± 11.2 kg N ha−1 yr−1 were estimated on average. The net N accumulation into the soil nitrogen pools was estimated to be 14.0 ± 2.1 kg N ha−1 yr−1. The N outflux consists of gaseous N fluxes composed of N2O emissions of 2.6 ± 0.8 kg N2O–N ha−1 yr−1, NO emissions of 3.2 ± 1.5 kg NO–N ha−1 yr−1, N2 emissions of 15.5 ± 7.0 kg N2–N ha−1 yr−1 and NH3 emissions of 34.0 ± 6.7 kg NH3–N ha−1 yr−1, as well as aquatic N fluxes (only nitrate leaching into surface waters) of 14.1 ± 4.5 kg NO3–N ha−1 yr−1 and N fluxes of N removed from the fields in yields, straw and feed of 128.8 ± 8.5 kg N ha−1 yr−1.

Predicting the responses of terrestrial ecosystem carbon to future global change strongly relies on our ability to model accurately the underlying processes at a global scale. However, terrestrial biosphere models representing the carbon and nitrogen cycles and their interactions remain subject to large uncertainties, partly because of unknown or poorly constrained parameters. Parameter estimation is a powerful tool that can be used to optimise these parameters by confronting the model with observations. In this paper, we identify sensitive model parameters from a recent version of the ORgainzing Carbon and Hydrology in Dynamic Ecosystems (ORCHIDEE) land surface model that includes the nitrogen cycle. These sensitive parameters include ones involved in parameterisations controlling the impact of the nitrogen cycle on the carbon cycle and, in particular, the limitation of photosynthesis due to leaf nitrogen availability. We optimise these ORCHIDEE parameters against carbon flux data collected on sites from the FLUXNET network. However, optimising against present-day observations does not automatically give us confidence in future projections of the model, given that environmental conditions are likely to shift compared to the present day. Manipulation experiments give us a unique look into how the ecosystem may respond to future environmental changes. One such type of manipulation experiment, the Free Air CO2 Enrichment (FACE) experiment, provides a unique opportunity to assess vegetation response to increasing CO2 by providing data under ambient and elevated CO2 conditions. Therefore, to better capture the ecosystem response to increased CO2, we add the data from two FACE sites to our optimisations, in addition to the FLUXNET data. We use data from both CO2 conditions of FACE, which allows us to gain extra confidence in the model simulations using this set of parameters. We find that we are able to improve the magnitude of modelled productivity. Although we are unable to correct the interannual variability fully, we start to simulate possible progressive nitrogen limitation at one of the sites. Using an idealised simulation experiment based on increasing atmospheric CO2 by 1 % yr−1 over 100 years, we find that optimising against only FLUXNET data tends to imply a large fertilisation effect, whereas optimising against FLUXNET and FACE data (with information about nutrient limitation and acclimation of plants) decreases it significantly.

At the land–sea interface, the benthic carbon cycle is strongly influenced by the export of terrigenous particulate material across the river–ocean continuum. Episodic flood events delivering massive sedimentary materials can occur, but their short-term impact on carbon cycling is poorly understood. In this paper, we use a coupled data–model approach to estimate the temporal variations in sediment–water fluxes, biogeochemical pathways and their reaction rates during these abrupt phenomena. We studied one episodic depositional event in the vicinity of the Rhône River mouth (NW Mediterranean Sea) during the fall–winter of 2021/22. The distributions of dissolved inorganic carbon (DIC), sulfate (SO42-) and methane (CH4) were measured in sediment porewaters collected every 2 weeks before and after the deposition of a 25 cm sediment layer during the main winter flood event. Significant changes in the distribution of DIC, SO42- and CH4 concentrations were observed in the sediment porewaters. The use of an early diagenetic model (FESDIA) to calculate biogeochemical reaction rates and fluxes revealed that this type of flood event can increase the total organic carbon mineralization rate in the sediment by 75 % a few days after deposition. In this period, sulfate reduction is the main process contributing to the increase in total mineralization relative to non-flood deposition. The model predicts a short-term decrease in the DIC flux out of the sediment from 100 to 55 mmolm-2d-1 after the deposition of the new sediment layer with a longer-term increase by 4 %, therefore implying an initial internal storage of DIC in the newly deposited layer and a slow release over relaxation of the system. Furthermore, examination of the stoichiometric ratios of DIC and SO42- as well as model output over this 5-month window shows a decoupling between the two modes of sulfate reduction following the deposition – organoclastic sulfate reduction (OSR) intensified in the newly deposited layer below the sediment surface, whereas anaerobic oxidation of methane (AOM) intensified at depth below the former buried surface. The bifurcation depth of sulfate reduction pathways, i.e., the sulfate–methane transition zone (SMTZ), is shifted deeper by 25 cm in the sediment column following the flood deposition. Our findings highlight the significance of short-term transient biogeochemical processes at the seafloor and provide new insights into the benthic carbon cycle in the coastal ocean.

Vegetation productivity is a critical indicator of global ecosystem health and is impacted by human activities and climate change. A wide range of optical sensing platforms, from ground-based to airborne and satellite, provide spatially continuous information on terrestrial vegetation status and functioning. As optical Earth observation (EO) data are usually routinely acquired, vegetation can be monitored repeatedly over time, reflecting seasonal vegetation patterns and trends in vegetation productivity metrics. Such metrics include gross primary productivity, net primary productivity, biomass, or yield. To summarize current knowledge, in this paper we systematically reviewed time series (TS) literature for assessing state-of-the-art vegetation productivity monitoring approaches for different ecosystems based on optical remote sensing (RS) data. As the integration of solar-induced fluorescence (SIF) data in vegetation productivity processing chains has emerged as a promising source, we also include this relatively recent sensor modality. We define three methodological categories to derive productivity metrics from remotely sensed TS of vegetation indices or quantitative traits: (i) trend analysis and anomaly detection, (ii) land surface phenology, and (iii) integration and assimilation of TS-derived metrics into statistical and process-based dynamic vegetation models (DVMs). Although the majority of used TS data streams originate from data acquired from satellite platforms, TS data from aircraft and unoccupied aerial vehicles have found their way into productivity monitoring studies. To facilitate processing, we provide a list of common toolboxes for inferring productivity metrics and information from TS data. We further discuss validation strategies of the RS data derived productivity metrics: (1) using in situ measured data, such as yield; (2) sensor networks of distinct sensors, including spectroradiometers, flux towers, or phenological cameras; and (3) inter-comparison of different productivity metrics. Finally, we address current challenges and propose a conceptual framework for productivity metrics derivation, including fully integrated DVMs and radiative transfer models here labelled as “Digital Twin”. This novel framework meets the requirements of multiple ecosystems and enables both an improved understanding of vegetation temporal dynamics in response to climate and environmental drivers and enhances the accuracy of vegetation productivity monitoring.

Coastal marsh survival relies on the ability to increase elevation and offset sea level rise. It is therefore important to realistically model sediment fluxes between marshes, tidal channels, and bays as sediment availability controls accretion. Traditionally, numerical models have been calibrated and validated using in situ measurements at a few locations within the domain of interest. These datasets typically provide temporal information but lack spatial variability. This paper explores the potential of coupling numerical models with high-resolution remote sensing imagery. Products from three sensors from the NASA Delta-X airborne mission are used. Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) provides vertical water level change on the marshland and was used to adjust the bathymetry and calibrate water fluxes over the marsh. AirSWOT yields water surface elevation within bays, lakes, and channels, and was used to calibrate the Chezy bottom friction coefficient. Finally, imagery from AVIRIS-NG provides maps of total suspended solids (TSS) concentration that were used to calibrate sediment parameters of settling velocity and critical shear stress for erosion. Three numerical models were developed at different locations along coastal Louisiana using Delft3D. The coupling enabled a spatial evaluation of model performance that was not possible using simple point measurements. Overall, the study shows that calibration of numerical models and their general performance will greatly benefit from remote sensing.

In peatlands drained for forestry, the soil carbon (C) or carbon dioxide (CO2) balance is affected by both (i) higher heterotrophic CO2-C release from faster decomposing soil organic matter (SOM) and (ii) higher plant litter C input from more vigorously growing forests. This balance and other greenhouse gas (GHG) sinks and sources in managed lands are annually reported by national GHG inventories to the United Nations Climate Change Convention. In this paper, we present a revised, fully dynamic method for reporting the CO2 balance of drained peatland forest soils in Finland. Our method can follow temporal changes in tree biomass growth, tree harvesting and climatic parameters, and it is built on empirical regression models of SOM decomposition and litter input in drained peatland forests. All major components of aboveground and belowground litter input from ground vegetation as well as live trees and trees that died naturally are included, supplemented by newly acquired turnover rates of woody plant fine roots. Annual litter input from harvesting residues is calculated using national statistics of logging and energy use of trees. Leaching, which also exports dissolved C from drained peatlands, is not included. The results are reported as time series from 1990–2021 following the practice in the GHG inventory. Our revised method produces an increasing trend of annual emissions from 0.2 to 2.1 t CO2 ha−1 yr−1 for the period 1990–2021 in Finland (equal to a trend from 1.4 to 7.9 Mt CO2 yr−1 for the entire 4.3 Mha of drained peatland forests), with a statistically significant difference between the years 1990 and 2021. Across the period 1990–2021, annual emissions are on average 1.5 t CO2 ha−1 yr−1 (3.4 Mt CO2 yr−1 for 2.2 Mha area) in warmer southern Finland and −0.14 t CO2 ha−1 yr−1 (−0.3 Mt CO2 yr−1 for 2.1 Mha area) in cooler northern Finland. When combined with data on the CO2 sink created by the growing tree stock, in 2021 the drained peatland forest ecosystems were a source of 1.0 t CO2 ha−1 yr−1 (2.3 Mt CO2 yr−1) in southern Finland and a sink of 1.2 t CO2 ha−1 yr−1 (2.5 Mt CO2 yr−1) in northern Finland. We compare these results to those produced by the semi-dynamic method used earlier in the Finnish GHG inventory and discuss the strengths and vulnerabilities of the new revised method in comparison to more static emission factors.

The overall goal of OUTPACE (Oligotrophy to UlTra-oligotrophy PACific Experiment) was to obtain a successful representation of the interactions between planktonic organisms and the cycle of biogenic elements in the western tropical South Pacific Ocean across trophic and N2 fixation gradients. Within the context of climate change, it is necessary to better quantify the ability of the oligotrophic ocean to sequester carbon through biological processes. OUTPACE was organized around three main objectives, which were (1) to perform a zonal characterization of the biogeochemistry and biological diversity of the western tropical South Pacific during austral summer conditions, (2) to study the production and fate of organic matter (including carbon export) in three contrasting trophic regimes (increasing oligotrophy) with a particular emphasis on the role of dinitrogen fixation, and (3) to obtain a representation of the main biogeochemical fluxes and dynamics of the planktonic trophic network. The international OUTPACE cruise took place between 18 February and 3 April 2015 aboard the RV L'Atalante and involved 60 scientists (30 onboard). The west–east transect covered ∼ 4000 km from the western part of the Melanesian archipelago (New Caledonia) to the western boundary of the South Pacific gyre (French Polynesia). Following an adaptive strategy, the transect initially designed along the 19° S parallel was adapted along-route to incorporate information coming from satellite measurements of sea surface temperature, chlorophyll a concentration, currents, and diazotroph quantification. After providing a general context and describing previous work done in this area, this introductory paper elucidates the objectives of OUTPACE, the implementation plan of the cruise and water mass and climatological characteristics and concludes with a general overview of the other papers that will be published in this special issue.

Measurement of the exchange of energy and mass between the surface and the atmospheric boundary-layer by the eddy covariance technique has undergone great change in the last 2 decades. Early studies of these exchanges were confined to brief field campaigns in carefully controlled conditions followed by months of data analysis. Current practice is to run tower-based eddy covariance systems continuously over several years due to the need for continuous monitoring as part of a global effort to develop local-, regional-, continental- and global-scale budgets of carbon, water and energy. Efficient methods of processing the increased quantities of data are needed to maximise the time available for analysis and interpretation. Standardised methods are needed to remove differences in data processing as possible contributors to observed spatial variability. Furthermore, public availability of these data sets assists with undertaking global research efforts. The OzFlux data path has been developed (i) to provide a standard set of quality control and post-processing tools across the network, thereby facilitating inter-site integration and spatial comparisons; (ii) to increase the time available to researchers for analysis and interpretation by reducing the time spent collecting and processing data; (iii) to propagate both data and metadata to the final product; and (iv) to facilitate the use of the OzFlux data by adopting a standard file format and making the data available from web-based portals. Discovery of the OzFlux data set is facilitated through incorporation in FLUXNET data syntheses and the publication of collection metadata via the RIF-CS format. This paper serves two purposes. The first is to describe the data sets, along with their quality control and post-processing, for the other papers of this Special Issue. The second is to provide an example of one solution to the data collection and curation challenges that are encountered by similar flux tower networks worldwide.

The vehicles that fly the satellite into a model of the Earth system are observation operators. They provide the link between the quantities simulated by the model and the quantities observed from space, either directly (spectral radiance) or indirectly estimated through a retrieval scheme (biogeophysical variables). By doing so, observation operators enable modellers to properly compare, evaluate, and constrain their models with the model analogue of the satellite observations. This paper provides the formalism and a few examples of how observation operators can be used in combination with data assimilation techniques to better ingest satellite products in a manner consistent with the dynamics of the Earth system expressed by models. It describes commonalities and potential synergies between assimilation and classical retrievals. This paper explains how the combination of observation operators and their derivatives (linearizations) form powerful research tools. It introduces a technique called automatic differentiation that greatly simplifies both the development and the maintenance of code for the evaluation of derivatives. Throughout this paper, a special focus lies on applications to the carbon cycle.

This paper describes the operational methods to achieve and measure both deep-soil heating (0–3 m) and whole-ecosystem warming (WEW) appropriate to the scale of tall-stature, high-carbon, boreal forest peatlands. The methods were developed to allow scientists to provide a plausible set of ecosystem-warming scenarios within which immediate and longer-term (1 decade) responses of organisms (microbes to trees) and ecosystem functions (carbon, water and nutrient cycles) could be measured. Elevated CO2 was also incorporated to test how temperature responses may be modified by atmospheric CO2 effects on carbon cycle processes. The WEW approach was successful in sustaining a wide range of aboveground and belowground temperature treatments (+0, +2.25, +4.5, +6.75 and +9 °C) in large 115 m2 open-topped enclosures with elevated CO2 treatments (+0 to +500 ppm). Air warming across the entire 10 enclosure study required ∼ 90 % of the total energy for WEW ranging from 64 283 mega Joules (MJ) d−1 during the warm season to 80 102 MJ d−1 during cold months. Soil warming across the study required only 1.3 to 1.9 % of the energy used ranging from 954 to 1782 MJ d−1 of energy in the warm and cold seasons, respectively. The residual energy was consumed by measurement and communication systems. Sustained temperature and elevated CO2 treatments were only constrained by occasional high external winds. This paper contrasts the in situ WEW method with closely related field-warming approaches using both aboveground (air or infrared heating) and belowground-warming methods. It also includes a full discussion of confounding factors that need to be considered carefully in the interpretation of experimental results. The WEW method combining aboveground and deep-soil heating approaches enables observations of future temperature conditions not available in the current observational record, and therefore provides a plausible glimpse of future environmental conditions.

Oxygen availability is a pivotal factor for ecosystem functioning and the resistance of organisms to the effect of climate change in aquatic habitats. Although extensive work has been done to assess the effect of oxygen on marine and freshwater biota, many studies have not captured the ecological importance of oxygen variations. Overlooking the fluctuating nature of oxygen may cause potential biases in the design and implementation of management policies for aquatic habitats. Conceptual perspectives on the dynamic nature of oxygen fluctuations have been raised in the scientific community in order to enhance the understanding of the effect of oxygen on the physiology and the ecology of aquatic species as well as the biogeochemical functioning of their ecosystems. A growing number of empirical work has been outlining a novel conceptual framework that considers the magnitude of oxygen fluctuation as a key variable that explains adaptation to stress conditions. Oxygen in productive aquatic habitats shows large fluctuations at the diel scale, exposing aquatic species to conditions ranging from extreme supersaturation to anoxia. Recent research has indicated that such a fluctuation tunes the physiological plasticity of the animal in response to thermal stresses. In this paper, we provide compelling evidence based on current research that the fluctuating oxygen landscape, here defined as “oxyscape”, has an important role in aquatic animal physiology and adaptation as well as the ecosystem biogeochemistry. We propose that the oxyscape should be considered in the modelling and managing policies of aquatic ecosystems.

The oceans are losing oxygen (O2), and oxygen minimum zones are expanding due to climate warming (lower O2 solubility) and eutrophication related to agriculture. This trend is challenging for most marine taxa that are not well adapted to O2 depletion. For other taxa this trend might be advantageous because they can withstand low O2 concentrations or thrive under O2-depleted or even anoxic conditions. Benthic foraminifera are a group of protists that include taxa with adaptations to partly extreme environmental conditions. Several species possess adaptations to O2 depletion that are rare amongst eukaryotes, and these species might benefit from ongoing ocean deoxygenation. In addition, since some foraminifera can calcify even under anoxic conditions, they are important archives for paleoceanographic reconstruction in O2-depleted environments. This paper reviews the current state of knowledge about foraminifera from low-O2 environments. Recent advances in our understanding of specific survival strategies of foraminifera to withstand O2 depletion are summarized and discussed. These adaptations include an anaerobic metabolism, heterotrophic denitrification, symbiosis with bacteria, kleptoplasty and dormancy and have a strong impact on their preferred microhabitat in the sediments, especially the ability of some benthic foraminiferal species to denitrify. Benthic foraminifera also differ regarding their trophic strategies, which has an additional impact on the selection of their microhabitat. For example, some species are strict herbivores that feed exclusively on fresh phytodetritus and live close to the sediment surface, while some species are non-selective detrivores that occupy intermediate to deep infaunal habitats. There is evidence that foraminifers have the capacity to undergo phagocytosis, even under anoxia, and some foraminiferal species which can withstand low-O2 conditions seem to prey on meiofauna. Also, due to their high abundances in O2-depleted environments and their metabolic adaptations, benthic foraminifera are key players in marine nutrient cycling, especially within the marine N and P cycles. This review summarizes the denitrification rates for the species that are known to denitrify and the intracellular nitrate concentrations of the species that are known to intracellularly store nitrate. Finally, equations are provided that can be used to estimate the intracellular nutrient storage and denitrification rates of foraminifera and might be integrated into biogeochemical models.

OzFlux is the regional Australian and New Zealand flux tower network that aims to provide a continental-scale national research facility to monitor and assess trends, and improve predictions, of Australia's terrestrial biosphere and climate. This paper describes the evolution, design, and current status of OzFlux as well as provides an overview of data processing. We analyse measurements from all sites within the Australian portion of the OzFlux network and two sites from New Zealand. The response of the Australian biomes to climate was largely consistent with global studies except that Australian systems had a lower ecosystem water-use efficiency. Australian semi-arid/arid ecosystems are important because of their huge extent (70 %) and they have evolved with common moisture limitations. We also found that Australian ecosystems had a similar radiation-use efficiency per unit leaf area compared to global values that indicates a convergence toward a similar biochemical efficiency. The two New Zealand sites represented extremes in productivity for a moist temperate climate zone, with the grazed dairy farm site having the highest GPP of any OzFlux site (2620 gC m−2 yr−1) and the natural raised peat bog site having a very low GPP (820 gC m−2 yr−1). The paper discusses the utility of the flux data and the synergies between flux, remote sensing, and modelling. Lastly, the paper looks ahead at the future direction of the network and concludes that there has been a substantial contribution by OzFlux, and considerable opportunities remain to further advance our understanding of ecosystem response to disturbances, including drought, fire, land-use and land-cover change, land management, and climate change, which are relevant both nationally and internationally. It is suggested that a synergistic approach is required to address all of the spatial, ecological, human, and cultural challenges of managing the delicately balanced ecosystems in Australasia.

Hydrophilic surfaces influence the structure of water close to them and may thus affect the isotope composition of water. Such an effect should be relevant and detectable for materials with large surface areas and low water contents. The relationship between the volumetric solid : water ratio and the isotopic fractionation between adsorbed water and unconfined water was investigated for the materials silage, hay, organic soil (litter), filter paper, cotton, casein and flour. Each of these materials was equilibrated via the gas phase with unconfined water of known isotopic composition to quantify the isotopic difference between adsorbed water and unconfined water. Across all materials, isotopic fractionation was significant (p<0.05) and negative (on average −0.91 ± 0.22 ‰ for 18∕16O and −20.6 ± 2.4 ‰ for 2∕1H at an average solid : water ratio of 0.9). The observed isotopic fractionation was not caused by solutes, volatiles or old water because the fractionation did not disappear for washed or oven-dried silage, the isotopic fractionation was also found in filter paper and cotton, and the fractionation was independent of the isotopic composition of the unconfined water. Isotopic fractionation became linearly more negative with increasing volumetric solid : water ratio and even exceeded −4 ‰ for 18∕16O and −44 ‰ for 2∕1H. This fractionation behaviour could be modelled by assuming two water layers: a thin layer that is in direct contact and influenced by the surface of the solid and a second layer of varying thickness depending on the total moisture content that is in equilibrium with the surrounding vapour. When we applied the model to soil water under grassland, the soil water extracted from 7 and 20 cm depth was significantly closer to local meteoric water than without correction for the surface effect. This study has major implications for the interpretation of the isotopic composition of water extracted from organic matter, especially when the volumetric solid : water ratio is larger than 0.5 or for processes occurring at the solid–water interface.

On the global scale, N2 fixation provides the major external source of reactive nitrogen to the surface ocean, surpassing atmospheric and riverine inputs, and sustains ∼ 50 % of new primary production in oligotrophic environments. The main goal of the VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific (VAHINE) project was to study the fate of nitrogen newly fixed by diazotrophs (or diazotroph-derived nitrogen) in oceanic food webs, and how it impacts heterotrophic bacteria, phytoplankton and zooplankton dynamics, stocks and fluxes of biogenic elements and particle export. Three large-volume ( ∼ 50 m3) mesocosms were deployed in a tropical oligotrophic ecosystem (the New Caledonia lagoon, south-eastern Pacific) and intentionally fertilized with ∼ 0.8 µM of dissolved inorganic phosphorus (DIP) to stimulate diazotrophy and follow subsequent ecosystem changes. VAHINE was a multidisciplinary project involving close collaborations between biogeochemists, molecular ecologist, chemists, marine opticians and modellers. This introductory paper describes in detail the scientific objectives of the project as well as the implementation plan: the mesocosm description and deployment, the selection of the study site (New Caledonian lagoon), and the logistical and sampling strategy. The main hydrological and biogeochemical conditions of the study site before the mesocosm deployment and during the experiment itself are described, and a general overview of the papers published in this special issue is presented.

Afforestation and reduction of fossil fuel emissions are two major components of climate mitigation policies. However, their effects on the Earth's climate are different because a reduction of fossil fuel emissions directly alters the biogeochemical cycle of the climate system and modifies the physics of the atmosphere via its impact on radiation and the energy budget, while afforestation causes biophysical changes in addition to changes in the biogeochemical cycle. In this paper, we compare the climate and carbon cycle consequences of carbon removal by afforestation and an equivalent fossil fuel emission reduction using simulations from an intermediate complexity Earth system model. We performed two major sets of idealized simulations in which fossil fuel emissions follow extended Shared Socioeconomic Pathway (SSP) scenarios (SSP2-4.5, 3-7.0, and 5-8.5), and equal amounts of carbon are removed by afforestation in one set and by a reduction in fossil fuel emissions in another set. Our simulations show that the climate is cooler by 0.36, 0.47, and 0.42 ∘C in the long term (2471–2500) in the case of reduced fossil fuel emissions compared to the case with afforestation when the emissions follow the SSP2-4.5, SSP3-7.0, and SSP5-8.5 scenarios, respectively. The global mean surface temperature is cooler in the reduced fossil fuel emissions case compared to the afforestation case because the net biophysical effect of warming from afforestation partly offsets the biogeochemical cooling effect of afforestation. Thus, in terms of climate benefits, reducing fossil fuel emissions could be relatively more beneficial than afforestation for the same amount of carbon removed from the atmosphere. However, a robust understanding of the processes that govern the biophysical effects of afforestation should be improved before considering our results for climate policy.

In this paper, soil carbon, nitrogen and phosphorus concentrations and stocks were investigated in agricultural and natural areas in 17 plot-level paired sites and in a regional survey encompassing more than 100 pasture soils In the paired sites, elemental soil concentrations and stocks were determined in native vegetation (forests and savannas), pastures and crop–livestock systems (CPSs). Nutrient stocks were calculated for the soil depth intervals 0–10, 0–30, and 0–60 cm for the paired sites and 0–10, and 0–30 cm for the pasture regional survey by sum stocks obtained in each sampling intervals (0–5, 5–10, 10–20, 20–30, 30–40, 40–60 cm). Overall, there were significant differences in soil element concentrations and ratios between different land uses, especially in the surface soil layers. Carbon and nitrogen contents were lower, while phosphorus contents were higher in the pasture and CPS soils than in native vegetation soils. Additionally, soil stoichiometry has changed with changes in land use. The soil C : N ratio was lower in the native vegetation than in the pasture and CPS soils, and the carbon and nitrogen to available phosphorus ratio (PME) decreased from the native vegetation to the pasture to the CPS soils. In the plot-level paired sites, the soil nitrogen stocks were lower in all depth intervals in pasture and in the CPS soils when compared with the native vegetation soils. On the other hand, the soil phosphorus stocks were higher in all depth intervals in agricultural soils when compared with the native vegetation soils. For the regional pasture survey, soil nitrogen and phosphorus stocks were lower in all soil intervals in pasture soils than in native vegetation soils. The nitrogen loss with cultivation observed here is in line with other studies and it seems to be a combination of decreasing organic matter inputs, in cases where crops replaced native forests, with an increase in soil organic matter decomposition that leads to a decrease in the long run. The main cause of the increase in soil phosphorus stocks in the CPS and pastures of the plot-level paired site seems to be linked to phosphorus fertilization by mineral and organics fertilizers. The findings of this paper illustrate that land-use changes that are currently common in Brazil alter soil concentrations, stocks and elemental ratios of carbon, nitrogen and phosphorus. These changes could have an impact on the subsequent vegetation, decreasing soil carbon and increasing nitrogen limitation but alleviating soil phosphorus deficiency.

Ocean alkalinity enhancement (OAE) has recently gained attention as a potential method for carbon dioxide removal (CDR) at gigatonne (Gt) scale, with near-coast OAE operations being economically favorable due to proximity to mineral and energy sources. In this paper we study critical questions which determine the scale and viability of OAE. Which coastal locations are able to sustain a large flux of alkalinity at minimal pH and ΩArag (aragonite saturation) changes? What is the interference distance between adjacent OAE projects? How much CO2 is absorbed per unit of alkalinity added? How quickly does the induced CO2 deficiency equilibrate with the atmosphere? Choosing relatively conservative constraints on ΔpH or ΔOmega, we examine the limits of OAE using the ECCO LLC270 (0.3∘) global circulation model. We find that the sustainable OAE rate varies over 1–2 orders of magnitude between different coasts and exhibits complex patterns and non-local dependencies which vary from region to region. In general, OAE in areas of strong coastal currents enables the largest fluxes and depending on the direction of these currents, neighboring OAE sites can exhibit dependencies as far as 400 km or more. At these steady state fluxes most regional stretches of coastline are able to accommodate on the order of 10s to 100s of megatonnes of negative emissions within 300 km of the coast. We conclude that near-coastal OAE has the potential to scale globally to several Gt CO2 yr−1 of drawdown with conservative pH constraints, if the effort is spread over the majority of available coastlines. Depending on the location, we find a diverse set of equilibration kinetics, determined by the interplay of gas exchange and surface residence time. Most locations reach an uptake efficiency plateau of 0.6–0.8 mol CO2 per mol of alkalinity after 3–4 years, after which there is only slow additional CO2 uptake. Regions of significant downwelling (e.g., around Iceland) should be avoided by OAE deployments, as in such locations up to half of the CDR potential of OAE can be lost to bottom waters. The most ideal locations, reaching a molar uptake ratio of around 0.8, include North Madagascar, California, Brazil, Peru and locations close to the Southern Ocean such as Tasmania, Kerguelen and Patagonia, where the gas exchange appears to occur faster than the surface residence time. However, some locations (e.g., Hawaii) take significantly longer to equilibrate (up to 8–10 years) but can still eventually achieve high uptake ratios.

High-quality ocean colour observations are increasingly accessible to support various monitoring and research activities for water quality measurements. In this paper, we present a newly developed regional total suspended solids (TSSs) empirical model using MODIS Aqua's Rrs(530) and Rrs(666) reflectance bands to investigate the spatial and temporal variation in TSS dynamics along the southwest coast of Sarawak, Borneo, with the application of the Open Data Cube (ODC) platform. The performance of this TSS retrieval model was evaluated using error metrics (bias = 1.0, MAE = 1.47, and RMSE = 0.22, in milligrams per litre) with a log10 transformation prior to calculation as well as using a k-fold cross-validation technique. The temporally averaged map of the TSS distribution, using daily MODIS Aqua satellite datasets from 2003 until 2019, revealed that large TSS plumes were detected – particularly in the Lupar and Rajang coastal areas – on a yearly basis. The average TSS concentration in these coastal waters was in the range of 15–20 mg L−1. Moreover, the spatial map of the TSS coefficient of variation (CV) indicated strong TSS variability (approximately 90 %) in the Samunsam–Sematan coastal areas, which could potentially impact nearby coral reef habitats in this region. Study of the temporal TSS variation provides further evidence that monsoonal patterns drive the TSS release in these tropical water systems, with distinct and widespread TSS plume variations observed between the northeast and southwest monsoon periods. A map of relative TSS distribution anomalies revealed strong spatial TSS variations in the Samunsam–Sematan coastal areas, while 2010 recorded a major increase (approximately 100 %) and widespread TSS distribution with respect to the long-term mean. Furthermore, study of the contribution of river discharge to the TSS distribution showed a weak correlation across time at both the Lupar and Rajang river mouth points. The variability in the TSS distribution across coastal river points was studied by investigating the variation in the TSS pixels at three transect points, stretching from the river mouth into territorial and open-water zones, for eight main rivers. The results showed a progressively decreasing pattern of nearly 50 % in relation to the distance from shore, with exceptions in the northeast regions of the study area. Essentially, our findings demonstrate that the TSS levels on the southwest coast of Sarawak are within local water quality standards, promoting various marine and socio-economic activities. This study presents the first observation of TSS distributions in Sarawak coastal systems with the application of remote sensing technologies and aims at enhancing coastal sediment management strategies for the sustainable use of coastal waters and their resources.

Boreal forests are particularly vulnerable to climate warming, which increases the occurrence of natural disturbances, such as fires and insect outbreaks. It is therefore essential to better understand climate-induced changes in boreal vegetation dynamics. This requires accurate estimates of variations in biomass across regions and time. This remains challenging in the extensive larch forests of northeast Siberia because of the paucity of allometric equations and physical properties of woody debris needed for quantifying aboveground biomass pools from field surveys. Our study is the first to present values of mean squared diameter (MSD) and specific gravity that can be used to calculate fine dead and downed woody debris loads in Cajander larch (Larix cajanderi) forests using the line-intersect sampling approach. These values were derived from field measurements collected in 25 forest stands in the Republic of Sakha, Russia, and compared with values reported for other prevalent boreal tree species. We developed allometric equations relating diameter at breast height (DBH, at 1.3 m) to stem wood, stem bark, branches, foliage, and aboveground biomass based on measurements of 63 trees retrieved from previous studies. Differences between our allometric models and existing equations were assessed in predicting larch aboveground biomass in 53 forest stands sampled in the Republic of Sakha. We found that using fine woody debris (FWD) parameters from other boreal tree species and allometric equations developed in other regions may result in significantly lower biomass estimates in larch-dominated forests of northeast Siberia. The FWD parameters and allometric equations presented in our paper can be used to refine estimates of aboveground biomass in Cajander larch forests in northeast Siberia.

Framboidal pyrite has been a matter of interest of many studies due to its abundance in a wide range of environments and being a marker of redox conditions. However, the clear origin of framboidal pyrite remains unresolved. Our studies are preliminary laboratory investigations on the influence of the shape and physicochemical properties of bacteriophages on the synthesis of framboid-like structures. This paper discusses the possible role of bacteriophages (bacterial viruses) in the precipitation of sulfide minerals (FeS and CuS) and their impact on the formation of framboid-like structures. Here, two bacteriophages (Escherichia phage P1 and Pseudomonas phage Φ6), which differ significantly in shape and physicochemical properties, were used. Our observations suggest that viruses may bind ions from the solution. Moreover, we showed that bacteriophages P1 can lead to the formation of finer mineral particles of FeS and CuS, whereas the framboid-like structures were found only in experiments with precipitation of FeS. However, the lipid-enveloped Pseudomonas phage Φ6 did not cause the formation of similar structures. It is assumed that Escherichia phage P1 can promote the formation of FeS-based framboid-like or spherical structures. The proposed four-step conceptualized mechanism facilitating the framboid-like structure synthesis via viruses is as follows: (i) binding of ions by capsids, (ii) bacteriophages behaving like a crystallization surface, (iii) destabilization of the colloid (ζ potential ± 0), and (iv) formation of fine agglomerates and subsequent formation of small crystallites. Further studies are required to find all factors that may be affected by bacteriophages during sulfide precipitation. In addition, it is important to consider viruses present in sedimentation environments, despite possible difficulties in laboratory culturing. The consideration of such viruses may make laboratory testing more valid in terms of sedimentation environments.

Soils account for the largest share of carbon found in terrestrial ecosystems, and their status is of considerable interest for the global carbon cycle budget and atmospheric carbon concentration. The decomposition of soil organic matter depends on environmental conditions and human activities, which raises the question of how permanent are these carbon storages under changing climate. One way to get insight into carbon decomposition processes is to analyse different carbon isotope concentrations in soil organic matter. In this paper we introduce a carbon-13-isotope-specific soil organic matter decomposition add-on into the Yasso soil carbon model and assess its functionality. The new 13C-dedicated decomposition is straightforward to implement and depends linearly on the default Yasso model parameters and the relative carbon isotope (13C/12C) concentration. The model modifications are based on the assumption that the heavier 13C atoms are not as reactive as 12C. The new formulations were calibrated using fractionated C, 13C and δ13 measurements from litterbags containing pine needles and woody material, which were left to decompose in natural environment for 4 years. The introduced model modifications considerably improve the model behaviour in a 100-year-long simulation, where modelled δ13 is compared against fractionated peat column carbon content. The work presented here is a proof of concept and enables 13C to be used as a natural tracer to detect changes in the underlying soil organic matter decomposition.

The ability to constrain the mechanisms that transport organic carbon into the deep ocean is complicated by the multiple physical, chemical, and ecological processes that intersect to create, transform, and transport particles in the ocean. In this paper we develop and parameterize a data-assimilative model of the multiple pathways of the biological carbon pump (NEMUROBCP). The mechanistic model is designed to represent sinking particle flux, active transport by vertically migrating zooplankton, and passive transport by subduction and vertical mixing, while also explicitly representing multiple biological and chemical properties measured directly in the field (including nutrients, phytoplankton and zooplankton taxa, carbon dioxide and oxygen, nitrogen isotopes, and 234Thorium). Using 30 different data types (including standing stock and rate measurements related to nutrients, phytoplankton, zooplankton, and non-living organic matter) from Lagrangian experiments conducted on 11 cruises from four ocean regions, we conduct an objective statistical parameterization of the model and generate 1 million different potential parameter sets that are used for ensemble model simulations. The model simulates in situ parameters that were assimilated (net primary production and gravitational particle flux) and parameters that were withheld (234Thorium and nitrogen isotopes) with reasonable accuracy. Model results show that gravitational flux of sinking particles and vertical mixing of organic matter from the euphotic zone are more important biological pump pathways than active transport by vertically migrating zooplankton. However, these processes are regionally variable, with sinking particles most important in oligotrophic areas of the Gulf of Mexico and California Current, sinking particles and vertical mixing roughly equivalent in productive coastal upwelling regions and the subtropical front in the Southern Ocean, and active transport an important contributor in the eastern tropical Pacific. We further find that mortality at depth is an important component of active transport when mesozooplankton biomass is high, but it is negligible in regions with low mesozooplankton biomass. Our results also highlight the high degree of uncertainty, particularly amongst mesozooplankton functional groups, that is derived from uncertainty in model parameters. Indeed, variability in BCP pathways between simulations for a specific location using different parameter sets (all with approximately equal misfit relative to observations) is comparable to variability in BCP pathways between regions. We discuss the implications of these results for other data-assimilation approaches and for studies that rely on non-ensemble model outputs.

Forest environments contain a wide variety of airborne biological particles (bioaerosols), including pollen, fungal spores, bacteria, viruses, plant detritus, and soil particles. Forest bioaerosol plays a number of important roles related to plant and livestock health, human disease and allergenicity, and forest and wider ecology and are thought to influence biosphere–atmosphere interactions via warm and cold cloud formation. Despite the importance of bioaerosols, there are few measurements of forest aerosol, and there is a lack of understanding of how climate change will affect forest bioaerosol in the future. We installed low-cost optical particle counters (OPCs) to measure particles in the size range between 1 and 10 µm (PM10–PM1) for a period of 2 months in autumn 2018 at the Birmingham Institute of Forest Research (BIFoR) free-air carbon dioxide enrichment (FACE) facility. In the paper, we propose that the PM10–PM1 (particulate matter) metric is a good proxy for bioaerosols because of the bioaerosol representative size range, the location of the study site (a woodland in a rural location), the field measurement taking place during the season of peak fungal activity, and the low hygroscopicity of the particles measured. The BIFoR FACE facility fumigates three 700 m2 areas of the forest with an additional 150 ppm CO2 above ambient levels with minimal impacts on other potential environmental drivers such as temperature, humidity, and wind. This experimental set-up enabled us to investigate the effect of environmental variables, including elevated CO2 (eCO2), on bioaerosol proxy concentrations and to evaluate the performance of the low-cost OPCs in a forested environment. Operating the low-cost OPCs during autumn 2018, we aimed to capture predominantly the fungal bioaerosol season. Across the experimental duration, the OPCs captured both temporal and spatial variation in bioaerosol concentrations. Aerosol concentrations were affected by changing temperatures and wind speeds but, contrary to our initial hypothesis, not by relative humidity. We detected no effect of the eCO2 treatment on total bioaerosol concentrations, but a potential suppression of high-concentration bioaerosol events was detected under eCO2. In-canopy atmospheric dispersion modelling indicates that the median spore dispersion distance is sufficiently small that there is little mixing between treatment and control experiments. Our data demonstrate the suitability of low-cost OPCs, interpreted with due caution, for use in forests and so opens the possibility of forest bioaerosol monitoring in a wider range of habitats to a wider range of researchers at a modest cost.

The mean test size of planktonic foraminifera (PF) is known to have increased especially during the last 12 Myr, probably in terms of an adaptive response to an intensification of the surface-water stratification. On geologically short timescales, the test size in PF is related to environmental conditions. In an optimal species-specific environment, individuals exhibit a greater maximum and average test size, while the size decreases the more unfavourable the environment becomes. An interesting case was observed in the late Neogene and Quaternary size evolution of Globorotalia menardii, which seems to be too extreme to be only explained by changes in environmental conditions. In the western tropical Atlantic Ocean (WTAO) and the Caribbean Sea, the test size more than doubles from 2.6 to 1.95 and 1.7 Ma, respectively, following an almost uninterrupted and successive phase of test-size decrease from 4 Ma. Two hypotheses have been suggested to explain the sudden occurrence of a giant G. menardii form: it was triggered by either (1) a punctuated, regional evolutionary event or (2) the immigration of specimens from the Indian Ocean via the Agulhas leakage. Morphometric measurements of tests from sediment samples of the Ocean Drilling Program (ODP) Leg 108 Hole 667A in the eastern tropical Atlantic Ocean (ETAO) show that the giant type already appears 0.1 Myr earlier at this location than in the WTAO, which indicates that the extreme size increase in the early Pleistocene was a tropical-Atlantic-Ocean-wide event. A coinciding change in the predominant coiling direction likely suggests that a new morphotype occurred. If the giant size and the uniform change in the predominant coiling direction are an indicator for this new type, the form already occurred in the eastern tropical Pacific Ocean at the Pliocene–Pleistocene boundary at 2.58 Ma. This finding supports the Agulhas leakage hypothesis. However, the hypothesis of a regional, punctuated evolutionary event cannot be dismissed due to missing data from the Indian Ocean. This paper presents the Atlantic Meridional Overturning Circulation (AMOC) and thermocline hypothesis in the ETAO, which possibly can be extrapolated for explaining the test-size evolution of the whole tropical Atlantic Ocean and the Caribbean Sea for the time interval between 2 and 8 Ma. The test-size evolution shows a similar trend with indicators for changes in the AMOC strength. The mechanism behind this might be that changes in the AMOC strength have a major influence on the thermal stratification of the upper water column and hence the thermocline, which is known to be the habitat of G. menardii.

The B/Ca ratio in calcareous marine species is informative of past seawater CO32- concentrations, but scarce data exist on B/Ca in coralline algae. Recent studies suggest influences of temperature and growth rates on B/Ca, the effect of which could be critical for the reconstructions of surface ocean pH and atmospheric pCO2. In this paper, we present the first laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analyses of Mg, Sr, Li, and B in the coralline alga Lithothamnion corallioides collected from different geographic settings and depths across the Mediterranean Sea and in the Atlantic Ocean. We produced the first data on putative temperature proxies (Mg/Ca, Li/Ca, Sr/Ca, Mg/Li) and B/Ca in a coralline algal species grown in different basins from across the photic zone (12, 40, 45, and 66 m depth). We tested the B/Ca correlation with temperature proxies and growth rates in order to evaluate their possible effect on B incorporation. Our results suggested a growth rate influence on B/Ca, which was evident in the sample with the lowest growth rate of 0.10 mm yr−1 (Pontian Isl., Italy; 66 m depth) and in Elba (Italy; 45 m depth), where the algal growth rate was the highest (0.14 mm yr−1). At these two sites, the measured B/Ca was the lowest at 462.8 ± 49.2 µmol mol−1 and the highest at 757.7 ± 75.5 µmol mol−1, respectively. A positive correlation between B/Ca and temperature proxies was found only in the shallowest sample from Morlaix (Atlantic coast of France; 12 m depth), where the amplitude of temperature variation (ΔT) was the highest (8.9 ∘C). Still, fluctuations in B/Ca did not mirror yearly seasonal temperature oscillations as for Mg/Ca, Li/Ca, and Sr/Ca. We concluded that growth rates, triggered by the different ΔT and light availability across depth, affect the B incorporation in L. corallioides.

The size-fractionated phytoplankton growth and microzooplankton grazing are crucial for the temporal change of community size structure, regulating not only trophic transfer but also the carbon cycle of the ocean. However, the size-dependent growth and grazing dynamics on a monthly or an annual basis are less addressed in the coastal ocean. In this paper, the seasonal responses of the size-fractionated phytoplankton growth and grazing to environmental change were examined over 1 year at a coastal site of the northern South China Sea. We found a nanophytoplankton-dominated community with strong seasonal variations in all size classes. Phytoplankton community growth rate was positively correlated to nutrients, with community grazing rate correlating to the total chlorophyll a at the station, reflecting a combined bottom-up and topdown effect on phytoplankton population dynamics. Further analyses suggested that the specific growth rate of microphytoplankton was significantly influenced by phosphate, and that of nanophytoplankton was influenced by light, although picophytoplankton growth was controlled by both nitrate and temperature. In addition, the specific grazing rate of nanophytoplankton was well correlated to phytoplankton standing stock, while that of micro- and pico-compartments was negatively influenced by ciliate abundance and salinity. Finally, a lower grazing impact for micro-cells (38 %) than nano- and pico-cells (72 % and 60 %, respectively) may support size-selective grazing of microzooplankton on small cells at this eutrophic system.

The uptake of carbonyl sulfide (COS) by terrestrial plants is linked to photosynthetic uptake of CO2 as these gases partly share the same uptake pathway. Applying COS as a photosynthesis tracer in models requires an accurate representation of biosphere COS fluxes, but these models have not been extensively evaluated against field observations of COS fluxes. In this paper, the COS flux as simulated by the Simple Biosphere Model, version 4 (SiB4), is updated with the latest mechanistic insights and evaluated with site observations from different biomes: one evergreen needleleaf forest, two deciduous broadleaf forests, three grasslands, and two crop fields spread over Europe and North America. We improved SiB4 in several ways to improve its representation of COS. To account for the effect of atmospheric COS mole fractions on COS biosphere uptake, we replaced the fixed atmospheric COS mole fraction boundary condition originally used in SiB4 with spatially and temporally varying COS mole fraction fields. Seasonal amplitudes of COS mole fractions are ∼50–200 ppt at the investigated sites with a minimum mole fraction in the late growing season. Incorporating seasonal variability into the model reduces COS uptake rates in the late growing season, allowing better agreement with observations. We also replaced the empirical soil COS uptake model in SiB4 with a mechanistic model that represents both uptake and production of COS in soils, which improves the match with observations over agricultural fields and fertilized grassland soils. The improved version of SiB4 was capable of simulating the diurnal and seasonal variation in COS fluxes in the boreal, temperate, and Mediterranean region. Nonetheless, the daytime vegetation COS flux is underestimated on average by 8±27 %, albeit with large variability across sites. On a global scale, our model modifications decreased the modeled COS terrestrial biosphere sink from 922 Gg S yr−1 in the original SiB4 to 753 Gg S yr−1 in the updated version. The largest decrease in fluxes was driven by lower atmospheric COS mole fractions over regions with high productivity, which highlights the importance of accounting for variations in atmospheric COS mole fractions. The change to a different soil model, on the other hand, had a relatively small effect on the global biosphere COS sink. The secondary role of the modeled soil component in the global COS budget supports the use of COS as a global photosynthesis tracer. A more accurate representation of COS uptake in SiB4 should allow for improved application of atmospheric COS as a tracer of local- to global-scale terrestrial photosynthesis.

The Indian Ocean presents two distinct climate regimes. The north Indian Ocean is dominated by the monsoons, whereas the seasonal reversal is less pronounced in the south. The prevailing wind pattern produces upwelling along different parts of the coast in both hemispheres during different times of the year. Additionally, dynamical processes and eddies either cause or enhance upwelling. This paper reviews the phenomena of upwelling along the coast of the Indian Ocean extending from the tip of South Africa to the southern tip of the west coast of Australia. Observed features, underlying mechanisms, and the impact of upwelling on the ecosystem are presented. In the Agulhas Current region, cyclonic eddies associated with Natal pulses drive slope upwelling and enhance chlorophyll concentrations along the continental margin. The Durban break-away eddy spun up by the Agulhas upwells cold nutrient-rich water. Additionally, topographically induced upwelling occurs along the inshore edges of the Agulhas Current. Wind-driven coastal upwelling occurs along the south coast of Africa and augments the dynamical upwelling in the Agulhas Current. Upwelling hotspots along the Mozambique coast are present in the northern and southern sectors of the channel and are ascribed to dynamical effects of ocean circulation in addition to wind forcing. Interaction of mesoscale eddies with the western boundary, dipole eddy pair interactions, and passage of cyclonic eddies cause upwelling. Upwelling along the southern coast of Madagascar is caused by the Ekman wind-driven mechanism and by eddy generation and is inhibited by the Southwest Madagascar Coastal Current. Seasonal upwelling along the East African coast is primarily driven by the northeast monsoon winds and enhanced by topographically induced shelf breaking and shear instability between the East African Coastal Current and the island chains. The Somali coast presents a strong case for the classical Ekman type of upwelling; such upwelling can be inhibited by the arrival of deeper thermocline signals generated in the offshore region by wind stress curl. Upwelling is nearly uniform along the coast of Arabia, caused by the alongshore component of the summer monsoon winds and modulated by the arrival of Rossby waves generated in the offshore region by cyclonic wind stress curl. Along the west coast of India, upwelling is driven by coastally trapped waves together with the alongshore component of the monsoon winds. Along the southern tip of India and Sri Lanka, the strong Ekman transport drives upwelling. Upwelling along the east coast of India is weak and occurs during summer, caused by alongshore winds. In addition, mesoscale eddies lead to upwelling, but the arrival of river water plumes inhibits upwelling along this coast. Southeasterly winds drive upwelling along the coast of Sumatra and Java during summer, with Kelvin wave propagation originating from the equatorial Indian Ocean affecting the magnitude and extent of the upwelling. Both El Niño–Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) events cause large variability in upwelling here. Along the west coast of Australia, which is characterized by the anomalous Leeuwin Current, southerly winds can cause sporadic upwelling, which is prominent along the southwest, central, and Gascoyne coasts during summer. Open-ocean upwelling in the southern tropical Indian Ocean and within the Sri Lanka Dome is driven primarily by the wind stress curl but is also impacted by Rossby wave propagations. Upwelling is a key driver enhancing biological productivity in all sectors of the coast, as indicated by enhanced sea surface chlorophyll concentrations. Additional knowledge at varying levels has been gained through in situ observations and model simulations. In the Mozambique Channel, upwelling simulates new production and circulation redistributes the production generated by upwelling and mesoscale eddies, leading to observations of higher ecosystem impacts along the edges of eddies. Similarly, along the southern Madagascar coast, biological connectivity is influenced by the transport of phytoplankton from upwelling zones. Along the coast of Kenya, both productivity rates and zooplankton biomass are higher during the upwelling season. Along the Somali coast, accumulation of upwelled nutrients in the northern part of the coast leads to spatial heterogeneity in productivity. In contrast, productivity is more uniform along the coasts of Yemen and Oman. Upwelling along the west coast of India has several biogeochemical implications, including oxygen depletion, denitrification, and high production of CH4 and dimethyl sulfide. Although weak, wind-driven upwelling leads to significant enhancement of phytoplankton in the northwest Bay of Bengal during the summer monsoon. Along the Sumatra and Java coasts, upwelling affects the phytoplankton composition and assemblages. Dissimilarities in copepod assemblages occur during the upwelling periods along the west coast of Australia. Phytoplankton abundance characterizes inshore edges of the slope during upwelling season, and upwelling eddies are associated with krill abundance. The review identifies the northern coast of the Arabian Sea and eastern coasts of the Bay of Bengal as the least observed sectors. Additionally, sustained long-term observations with high temporal and spatial resolutions along with high-resolution modelling efforts are recommended for a deeper understanding of upwelling, its variability, and its impact on the ecosystem.

This paper presents the measured active and passive fluxes of carbon (C), nitrogen (N), and phosphorus (P) and their response to seasonal and event-driven oceanographic changes in the northern South China Sea (NSCS). The total vertical flux of carbon (TFC) is defined as the sum of active and passive fluxes of biogenic carbon in the surface layer, which may be considered as the central part of marine carbon cycle. These active and passive fluxes of N and P were also considered to understand stoichiometric flux patterns and the roles of nutrients involved in the TFC. The magnitudes of total C, N, and P fluxes were, respectively, estimated to be 71.9–347 (mean ± SD, 163 ± 70) mgCm-2d-1, 13.0–30.5 (21.2.± 4.9) mgNm-2d-1, and 1.02–2.97 (1.94 ± 0.44) mgPm-2d-1, which were higher than most previously reported vertical fluxes in open oceans, likely because a quarter of the fluxes was contributed from active fluxes that were unaccounted for in vertical fluxes previously. Moreover, the passive fluxes dominated the total vertical fluxes and were estimated to be 65.3–255 (125 ± 64.9) mgCm-2d-1 (77 ± 52 % of total C flux), 11.9–23.2 (17.6 ± 4.2) mgNm-2d-1 (83 ± 28 % of total N flux), and 0.89–1.98 (1.44 ± 0.33) mgPm-2d-1 (74 ± 24 % of total P flux). Vertical fluxes of dissolved organic C, N, and P were small (< 5 %) relative to passive fluxes. The contrasting patterns of active and passive fluxes found between summer and winter could mainly be attributed to surface warming and stratification in summer and cooling and wind-induced turbulence for pumping nutrients into the euphotic zone in winter. In addition to seasonal variations, the impact of anticyclonic eddies and internal-wave events on enhancing active and passive fluxes was apparent in the NSCS. Both active and passive fluxes were likely driven by nutrient availability within the euphotic zone, which was ultimately controlled by the changes in internal and external forcings. The nutrient availability also determined the inventory of chlorophyll a and new production, thereby allowing the estimates of active and passive fluxes for unmeasured events. To a first approximation, the South China Sea (SCS) may effectively transfer 0.208 ± 0.089 Gt C yr−1 into the ocean's interior, accounting for approximately 1.89 ± 0.81 % of the global C flux. The internal forcing and climatic conditions are likely critical factors in determining the seasonal and event-driven variability of total vertical fluxes in the NSCS.

Lakes act as important sinks for inorganic and organic sediment components. However, investigations of sedimentary carbon budgets within glacial lakes are currently absent from Arctic Siberia. The aim of this paper is to provide the first reconstruction of accumulation rates, sediment and carbon budgets from a lacustrine sediment core from Lake Rauchuagytgyn, Chukotka (Arctic Siberia). We combined multiple sediment biogeochemical and sedimentological parameters from a radiocarbon-dated 6.5 m sediment core with lake basin hydroacoustic data to derive sediment stratigraphy, sediment volumes and infill budgets. Our results distinguished three principal sediment and carbon accumulation regimes that could be identified across all measured environmental proxies including early Marine Isotope Stage 2 (MIS2) (ca. 29–23.4 ka cal BP), mid-MIS2–early MIS1 (ca. 23.4–11.69 ka cal BP) and the Holocene (ca. 11.69–present). Estimated organic carbon accumulation rates (OCARs) were higher within Holocene sediments (average 3.53 g OC m−2 a−1) than Pleistocene sediments (average 1.08 g OC m−2 a−1) and are similar to those calculated for boreal lakes from Quebec and Finland and Lake Baikal but significantly lower than Siberian thermokarst lakes and Alberta glacial lakes. Using a bootstrapping approach, we estimated the total organic carbon pool to be 0.26 ± 0.02 Mt and a total sediment pool of 25.7 ± 1.71 Mt within a hydroacoustically derived sediment volume of ca. 32 990 557 m3. The total organic carbon pool is substantially smaller than Alaskan yedoma, thermokarst lake sediments and Alberta glacial lakes but shares similarities with Finnish boreal lakes. Temporal variability in sediment and carbon accumulation dynamics at Lake Rauchuagytgyn is controlled predominantly by palaeoclimate variation that regulates lake ice-cover dynamics and catchment glacial, fluvial and permafrost processes through time. These processes, in turn, affect catchment and within-lake primary productivity as well as catchment soil development. Spatial differences compared to other lake systems at a trans-regional scale likely relate to the high-latitude, mountainous location of Lake Rauchuagytgyn.

We report the distributions and stoichiometry of dissolved zinc (dZn) and cobalt (dCo) in sub-tropical and sub-Antarctic waters of the south-eastern Atlantic Ocean during austral spring 2010 and summer 2011/2012. In sub-tropical surface waters, mixed-layer dZn and dCo concentrations during early spring were 1.60 ± 2.58 nM and 30 ± 11 pM, respectively, compared with summer values of 0.14 ± 0.08 nM and 24 ± 6 pM. The elevated spring dZn concentrations resulted from an apparent offshore transport of elevated dZn at depths between 20–55 m, derived from the Agulhas Bank. In contrast, open-ocean sub-Antarctic surface waters displayed largely consistent inter-seasonal mixed-layer dZn and dCo concentrations of 0.10 ± 0.07 nM and 11 ± 5 pM, respectively. Trace metal stoichiometry, calculated from concentration inventories, suggests a greater overall removal for dZn relative to dCo in the upper water column of the south-eastern Atlantic, with inter-seasonally decreasing dZn / dCo inventory ratios of 19–5 and 13–7 mol mol−1 for sub-tropical surface water and sub-Antarctic surface water, respectively. In this paper, we investigate how the seasonal influences of external input and phytoplankton succession may relate to the distribution of dZn and dCo and variation in dZn / dCo stoichiometry across these two distinct ecological regimes in the south-eastern Atlantic.

The Indian Ocean Rim hosts many of the world's underdeveloped and emerging economies that depend on the ocean resources for the livelihoods of the populations of millions. Operational ocean information services cater to the requirements of managers and end-users to efficiently harness those resources and to ensure safety. Fishery information is not the only operational service that will be needed to empower such communities in the coming decades. Coral bleaching alerts, SCUBA (self-contained underwater breathing apparatus)-assisting advisories, conservation or ecotourism assisting services (e.g. TurtleWatch or WhaleWatch), poaching and/or by-catch reduction support and jellyfish, micro-plastic and oil spill watching to name a few, but not an exhaustive list, of the services that are needed operationally. This paper outlines the existing tools and explores the ongoing research that has potential to convert the findings into operational services in near- to midterm.

While there is agreement that global warming over the 21st century is likely to influence the biological pump, Earth system models (ESMs) display significant divergence in their projections of future new production. This paper quantifies and interprets the sensitivity of projected changes in new production in an idealized global ocean biogeochemistry model. The model includes two tracers that explicitly represent nutrient transport, light- and nutrient-limited nutrient uptake by the ecosystem (new production), and export via sinking organic particles. Globally, new production declines with warming due to reduced surface nutrient availability, as expected. However, the magnitude, seasonality, and underlying dynamics of the nutrient uptake are sensitive to the light and nutrient dependencies of uptake, which we summarize in terms of a single biological timescale that is a linear combination of the partial derivatives of production with respect to light and nutrients. Although the relationships are nonlinear, this biological timescale is correlated with several measures of biogeochemical function: shorter timescales are associated with greater global annual new production and higher nutrient utilization. Shorter timescales are also associated with greater declines in global new production in a warmer climate and greater sensitivity to changes in nutrients than light. Future work is needed to characterize more complex ocean biogeochemical models in terms of similar timescale generalities to examine their climate change implications.

The world map of anthropogenic atmospheric nitrogen deposition and its effects on natural ecosystems is not described with equal precision everywhere. In this paper, we report atmospheric nutrient, sulfate and spheroidal carbonaceous particle (SCP) deposition rates, based on snowpack analyses of a formerly unexplored Siberian mountain region. Then, we discuss their potential effects on lake phytoplankton biomass limitation. We estimate that the nutrient depositions observed in the late-season snowpack (40 ± 16 mg NO3-N m−2 and 0.58 ± 0.13 mg TP-P m−2; TP for total phosphorous) would correspond to yearly depositions lower than 119 ± 71 mg NO3-N m−2 yr−1 and higher than 1.71 ± 0.91 mg TP-P m−2 yr−1. These yearly deposition estimates would approximately fit the predictions of global deposition models and correspond to the very low nutrient deposition range, although they are still higher than world background values. In spite of the fact that such a low atmospheric nitrogen deposition rate would be enough to induce nitrogen limitation in unproductive mountain lakes, phosphorus deposition was also extremely low, and the resulting lake water N : P ratio was unaffected by atmospheric nutrient deposition. In the end, the studied lakes' phytoplankton appeared to be split between phosphorus and nitrogen limitation. We conclude that these pristine lakes are fragile sensitive systems exposed to the predicted climate warming, increased winter precipitation, enhanced forest fires and shifts in anthropogenic nitrogen emissions that could finally couple their water chemistry to that of atmospheric nutrient deposition and unlock temperature-inhibited responses of phytoplankton to nutrient shifts.

Can experimental studies on the behavioural impacts of ocean acidification be trusted? That question was raised in early 2020 when a high-profile paper failed to corroborate previously observed responses of coral reef fish to high CO2. New information on the methodologies used in the “replicated” studies now provides a plausible explanation: the experimental conditions were substantially different. High sensitivity to test conditions is characteristic of ocean acidification research; such response variability shows that effects are complex, interacting with many other factors. Open-minded assessment of all research results, both negative and positive, remains the best way to develop process-based understanding. As in other fields, replication studies in ocean acidification are most likely to contribute to scientific advancement when carried out in a spirit of collaboration rather than confrontation.

Continental shelf sediments are places of both rapid organic carbon turnover and accumulation, while at the same time increasingly subjected to human-induced disturbances. Recent research suggests that shelf sediments might have a role to play as a natural climate solution, e.g. by storing organic carbon if left undisturbed from anthropogenic activity. However, we have an incomplete understanding about the centres of organic carbon accumulation and storage on continental shelves. To better constrain the rate of accumulation and the mass of organic carbon that is stored in sediments, we developed and applied a spatial modelling framework that allows us to estimate those quantities from sparse observations and predictor variables known or suspected to influence the spatial patterns of these parameters. This paper presents spatial distribution patterns of organic carbon densities and accumulation rates in the North Sea and Skagerrak. We found that organic carbon stocks and accumulation rates are highest in the Norwegian Trough, while large parts of the North Sea are characterised by low stocks and zero net accumulation. The total stock of organic carbon that is stored in the upper 0.1 m of sediments amounted to 230.5 ± 134.5 Tg C, of which approximately 26 % is stored in the Norwegian Trough. Rates of organic carbon accumulation in the Norwegian Trough are comparable with those reported from nearby fjords. We provide baseline datasets that could be used in marine management, e.g. for the establishment of “carbon protection zones”. Additionally, we highlight the complex nature of continental shelves with zones of rapid carbon cycling and accumulation juxtaposed, which will require further detailed and spatially explicit analyses to constrain sedimentary organic carbon stocks and accumulation rates globally.

Jellyfish are increasingly recognised as important components of the marine ecosystem, yet their specific role is poorly defined compared to that of other zooplankton groups. This paper presents the first global ocean biogeochemical model that includes an explicit representation of jellyfish and uses the model to gain insight into the influence of jellyfish on the plankton community. The Plankton Type Ocean Model (PlankTOM11) model groups organisms into plankton functional types (PFTs). The jellyfish PFT is parameterised here based on our synthesis of observations on jellyfish growth, grazing, respiration and mortality rates as functions of temperature and jellyfish biomass. The distribution of jellyfish is unique compared to that of other PFTs in the model. The jellyfish global biomass of 0.13 PgC is within the observational range and comparable to the biomass of other zooplankton and phytoplankton PFTs. The introduction of jellyfish in the model has a large direct influence on the crustacean macrozooplankton PFT and influences indirectly the rest of the plankton ecosystem through trophic cascades. The zooplankton community in PlankTOM11 is highly sensitive to the jellyfish mortality rate, with jellyfish increasingly dominating the zooplankton community as its mortality diminishes. Overall, the results suggest that jellyfish play an important role in regulating global marine plankton ecosystems across plankton community structure, spatio-temporal dynamics and biomass, which is a role that has been generally neglected so far.

The biological cycle of rock-derived nutrients on the continents is a major component of element transfer between the Earth's surface compartments, but its magnitude currently remains elusive. The use of the stable isotope composition of rock-derived nutrients, which can be fractionated during biological uptake, provides a promising path forward with respect to quantifying biological cycling and its overall contribution to global element cycling. In this paper, we rely on the nutrient-like behaviour of the trace element barium (Ba) and use its elemental and stable isotope compositions in dissolved and sediment load river samples to investigate biological cycling in the Amazon Basin. From these measurements, we show that dissolved Ba mainly derives from silicate rocks, and a correlation between dissolved Ba and K abundances suggests that biological cycling plays a role in the Ba river budget. Furthermore, the isotope composition of Ba (δ138Ba) in the dissolved load was found to be significantly different from that of the parent silicate rocks, implying that dissolved Ba isotopic signatures are affected by (i) the precipitation of soil-forming secondary phases as well as (ii) biological uptake and release from dead organic matter. Results from an isotope mass balance method applied to the river dissolved load data indicate that, after its release to solution by rock weathering, Ba is partitioned between the river dissolved load, secondary weathering products (such as those found in soils and river sediments), and the biota. In most sub-catchments of the Amazon, river Ba abundances and isotope compositions are significantly affected by biological cycling. Relationships between estimates of Ba cycled through biota and independent metrics of ecosystem dynamics (such as gross primary production and terrestrial ecosystem respiration) allow us to discuss the role of environmental parameters such as climate or erosion rates on the biological cycling of Ba and, by extension, the role of major rock-derived nutrients. In addition, catchment-scale mass and isotope budgets of Ba show that the measured riverine export of Ba is lower than the estimated delivery of Ba to the Earth surface through rock alteration. This indicates the existence of a missing Ba component, which we attribute to the formation of Ba-bearing particulate organics (possibly accumulating as soil organic matter or currently growing biomass within the catchments) and to organic-bound Ba exported as “unsampled” river particulate organic matter. Given our findings on the trace element Ba, we explore whether the river fluxes of most major rock-derived nutrients (K, Mg, Ca) might also be significantly affected by biological uptake or release. A first-order correction of river-derived silicate weathering fluxes from biological cycling shows that the carbon dioxide (CO2) consumption by silicate weathering at the mouth of the Amazon could be several times higher than the previously reported value of 13 × 109 mol CO2 yr−1 (Gaillardet et al., 1997). Overall, our study clearly shows that the chemical and isotope compositions of rivers in the Amazon – and most likely in other large river basins – bear a biological imprint, thereby challenging common assumptions made in weathering studies.

The PEACETIME cruise (May–June 2017) was a basin-scale survey covering the Provencal, Algerian, Tyrrhenian, and Ionian basins during the post-spring bloom period and was dedicated to tracking the impact of Saharan dust deposition events on the Mediterranean Sea pelagic ecosystem. Two such events occurred during this period, and the cruise strategy allowed for the study of the initial phase of the ecosystem response to one dust event in the Algerian Basin (during 5 d at the so-called “FAST long-duration station”) as well as the study of a latter response to another dust event in the Tyrrhenian Basin (by sampling from 5 to 12 d after the deposition). This paper documents the structural and functional patterns of the zooplankton component during this survey, including their responses to these two dust events. The mesozooplankton were sampled at 12 stations using nets with two different mesh sizes (100 and 200 µm) that were mounted on a Bongo frame for vertical hauls within the depth layer from 0 to 300 m. The Algerian and Tyrrhenian basins were found to be quite similar in terms of hydrological and biological variables, which clearly differentiated them from the northern Provencal Basin and the eastern Ionian Basin. In general, total mesozooplankton showed reduced variations in abundance and biomass values over the whole area, with a noticeable contribution from the small size fraction (<500 µm) of up to 50 % with respect to abundance and 25 % with respect to biomass. This small size fraction makes a significant contribution (15 %–21 %) to the mesozooplankton fluxes (carbon demand, grazing pressure, respiration, and excretion), which is estimated using allometric relationships to the mesozooplankton size spectrum at all stations. The taxonomic structure was dominated by copepods, mainly cyclopoid and calanoid copepods, and was completed by appendicularians, ostracods, and chaetognaths. Zooplankton taxa assemblages, analyzed using multivariate analysis and rank frequency diagrams, slightly differed between basins, which is in agreement with recently proposed Mediterranean regional patterns. However, the strongest changes in the zooplankton community were linked to the abovementioned dust deposition events. A synoptic analysis of the two dust events observed in the Tyrrhenian and Algerian basins, based on the rank frequency diagrams and a derived index proposed by Mouillot and Lepretre (2000), delivered a conceptual model of a virtual time series of the zooplankton community responses after a dust deposition event. The initial phase before the deposition event (state 0) was dominated by small-sized cells consumed by their typical zooplankton filter feeders (small copepods and appendicularians). The disturbed phase during the first 5 d following the deposition event (state 1) then induced a strong increase in filter feeders and grazers of larger cells as well as the progressive attraction of carnivorous species, leading to a sharp increase in the zooplankton distribution index. Afterward, this index progressively decreased from day 5 to day 12 following the event, highlighting a diversification of the community (state 2). A 3-week delay was estimated for the index to return to its initial value, potentially indicating the recovery time of a Mediterranean zooplankton community after a dust event. To our knowledge, PEACETIME is the first in situ study that has allowed for the observation of mesozooplankton responses before and soon after natural Saharan dust depositions. The change in the rank frequency diagrams of the zooplankton taxonomic structure is an interesting tool to highlight short-term responses of zooplankton to episodic dust deposition events. Obviously dust-stimulated pelagic productivity impacts up to mesozooplankton in terms of strong but short changes in taxa assemblages and trophic structure, with potential implications for oligotrophic systems such as the Mediterranean Sea.

Soil organic matter (OM) represents a key C pool for climate regulation but also an essential component for soil functions and services. Scientific research in the 21st century has considerably improved our knowledge of soil organic matter and its dynamics, particularly under the pressure of the global disruption of the carbon cycle. This paper reviews the processes that control C dynamics in soil, the representation of these processes over time, and their dependence on variations in major biotic and abiotic factors. The most recent advanced knowledge gained on soil organic matter includes the following. (1) Most organic matter is composed of small molecules, derived from living organisms, without transformation via additional abiotic organic polymerization; (2) microbial compounds are predominant in the long term; (3) primary belowground production contributes more to organic matter than aboveground inputs; (4) the contribution of less biodegradable compounds to soil organic matter is low in the long term; (5) two major factors determine the soil organic carbon production “yield” from the initial substrates: the yield of carbon used by microorganisms and the association with minerals, particularly poorly crystalline minerals, which stabilize microbial compounds; (6) interactions between plants and microorganisms also regulate the carbon turnover time and therefore carbon stocks; (7) among abiotic and biotic factors that regulate the carbon turnover time, only a few are considered in current modeling approaches (i.e., temperature, soil water content, pH, particle size, and sometimes C and N interactions); and (8) although most models of soil C dynamics assume that the processes involved are linear, there are now many indications of nonlinear soil C dynamics processes linked to soil OM dynamics (e.g., priming). Farming practices, therefore, affect soil C stocks not only through carbon inputs but also via their effect on microbial and organomineral interactions, yet it has still not been possible to properly identify the main mechanisms involved in C loss (or gain). Greater insight into these mechanisms and their interdependencies, hierarchy and sensitivity to agricultural practices could provide future levers of action for C sequestration in soil.

Eastern boundary upwelling systems (EBUS) are among the most productive marine ecosystems on Earth. The production of organic material is fueled by upwelling of nutrient-rich deep waters and high incident light at the sea surface. However, biotic and abiotic factors can modify surface production and related biogeochemical processes. Determining these factors is important because EBUS are considered hotspots of climate change, and reliable predictions of their future functioning requires understanding of the mechanisms driving the biogeochemical cycles therein. In this field experiment, we used in situ mesocosms as tools to improve our mechanistic understanding of processes controlling organic matter cycling in the coastal Peruvian upwelling system. Eight mesocosms, each with a volume of ∼55 m3, were deployed for 50 d ∼6 km off Callao (12∘ S) during austral summer 2017, coinciding with a coastal El Niño phase. After mesocosm deployment, we collected subsurface waters at two different locations in the regional oxygen minimum zone (OMZ) and injected these into four mesocosms (mixing ratio ≈1.5 : 1 mesocosm: OMZ water). The focus of this paper is on temporal developments of organic matter production, export, and stoichiometry in the individual mesocosms. The mesocosm phytoplankton communities were initially dominated by diatoms but shifted towards a pronounced dominance of the mixotrophic dinoflagellate (Akashiwo sanguinea) when inorganic nitrogen was exhausted in surface layers. The community shift coincided with a short-term increase in production during the A. sanguinea bloom, which left a pronounced imprint on organic matter C : N : P stoichiometry. However, C, N, and P export fluxes did not increase because A. sanguinea persisted in the water column and did not sink out during the experiment. Accordingly, export fluxes during the study were decoupled from surface production and sustained by the remaining plankton community. Overall, biogeochemical pools and fluxes were surprisingly constant for most of the experiment. We explain this constancy by light limitation through self-shading by phytoplankton and by inorganic nitrogen limitation which constrained phytoplankton growth. Thus, gain and loss processes remained balanced and there were few opportunities for blooms, which represents an event where the system becomes unbalanced. Overall, our mesocosm study revealed some key links between ecological and biogeochemical processes for one of the most economically important regions in the oceans.