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The nitrogen (N) cycle contains two different processes of dissimilatory nitrate (NO3−) reduction, denitrification and dissimilatory NO3− reduction to ammonium (DNRA). While there is general agreement that the denitrification process takes place in many soils, the occurrence and importance of DNRA is generally not considered. Two approaches have been used to investigate DNRA in soil, (1) microbiological techniques to identify soil microorganisms capable of DNRA and (2) 15N tracing to elucidate the occurrence of DNRA and to quantify gross DNRA rates. There is evidence that many soil bacteria and fungi have the ability to perform DNRA. Redox status and C/NO3− ratio have been identified as the most important factors regulating DNRA in soil. 15N tracing studies have shown that gross DNRA rates can be a significant or even a dominant NO3− consumption process in some ecosystems. Moreover, a link between heterotrophic nitrification and DNRA provides an alternative pathway of ammonium (NH4+) production to mineralisation. Numerical 15N tracing models are particularly useful when investigating DNRA in the context of other N cycling processes. The results of correlation and regression analyses show that highest gross DNRA rates can be expected in soils with high organic matter content in humid regions, while its relative importance is higher in temperate climates. With this review we summarise the importance and current knowledge of this often overlooked NO3− consumption process within the terrestrial N cycle. We strongly encourage considering DNRA as a relevant process in future soil N cycling investigations.

Anthropogenic nitrogen inputs cause major negative environmental impacts, including emissions of the important greenhouse gas N₂O. Despite their importance, shifts in terrestrial N loss pathways driven by global change are highly uncertain. Here we present a coupled soil-atmosphere isotope model (IsoTONE) to quantify terrestrial N losses and N₂O emission factors from 1850-2020. We find that N inputs from atmospheric deposition caused 51% of anthropogenic N₂O emissions from soils in 2020. The mean effective global emission factor for N₂O was 4.3 ± 0.3% in 2020 (weighted by N inputs), much higher than the surface area-weighted mean (1.1 ± 0.1%). Climate change and spatial redistribution of fertilisation N inputs have driven an increase in global emission factor over the past century, which accounts for 18% of the anthropogenic soil flux in 2020. Predicted increases in fertilisation in emerging economies will accelerate N₂O-driven climate warming in coming decades, unless targeted mitigation measures are introduced.

Quantifying soil carbon dynamics is of utmost relevance in the context of global change because soils play an important role in land–atmosphere gas exchange. Our current understanding of both present and future carbon dynamics is limited because we fail to accurately represent soil processes across temporal and spatial scales, partly because of the paucity of data on the relative importance and hierarchical relationships between microbial, geochemical and climatic controls. Here, using observations from a 3,000-kyr-old soil chronosequence preserved in alluvial terrace deposits of the Merced River, California, we show how soil carbon dynamics are driven by the relationship between short-term biotic responses and long-term mineral weathering. We link temperature sensitivity of heterotrophic respiration to biogeochemical soil properties through their relationship with microbial activity and community composition. We found that soil mineralogy, and in particular changes in mineral reactivity and resulting nutrient availability, impacts the response of heterotrophic soil respiration to warming by altering carbon inputs, carbon stabilization, microbial community composition and extracellular enzyme activity. We demonstrate that biogeochemical alteration of the soil matrix (and not short-term warming) controls the composition of microbial communities and strategies to metabolize nutrients. More specifically, weathering first increases and then reduces nutrient availability and retention, as well as the potential of soils to stabilize carbon.

The terrestrial carbon (C) cycle has received increasing interest over the past few decades, however, there is still a lack of understanding of the fate of newly assimilated C allocated within plants and to the soil, stored within ecosystems and lost to the atmosphere. Stable carbon isotope studies can give novel insights into these issues. In this review we provide an overview of an emerging picture of plant-soil-atmosphere C fluxes, as based on C isotope studies, and identify processes determining related C isotope signatures. The first part of the review focuses on isotopic fractionation processes within plants during and after photosynthesis. The second major part elaborates on plant-internal and plant-rhizosphere C allocation patterns at different time scales (diel, seasonal, interannual), including the speed of C transfer and time lags in the coupling of assimilation and respiration, as well as the magnitude and controls of plant-soil C allocation and respiratory fluxes. Plant responses to changing environmental conditions, the functional relationship between the physiological and phenological status of plants and C transfer, and interactions between C, water and nutrient dynamics are discussed. The role of the C counterflow from the rhizosphere to the aboveground parts of the plants, e.g. via CO2 dissolved in the xylem water or as xylem-transported sugars, is highlighted. The third part is centered around belowground C turnover, focusing especially on above- and belowground litter inputs, soil organic matter formation and turnover, production and loss of dissolved organic C, soil respiration and CO2 fixation by soil microbes. Furthermore, plant controls on microbial communities and activity via exudates and litter production as well as microbial community effects on C mineralization are reviewed. A further part of the paper is dedicated to physical interactions between soil CO2 and the soil matrix, such as CO2 diffusion and dissolution processes within the soil profile. Finally, we highlight state-of-the-art stable isotope methodologies and their latest developments. From the presented evidence we conclude that there exists a tight coupling of physical, chemical and biological processes involved in C cycling and C isotope fluxes in the plant-soil-atmosphere system. Generally, research using information from C isotopes allows an integrated view of the different processes involved. However, complex interactions among the range of processes complicate or currently impede the interpretation of isotopic signals in CO2 or organic compounds at the plant and ecosystem level. This review tries to identify present knowledge gaps in correctly interpreting carbon stable isotope signals in the plant-soil-atmosphere system and how future research approaches could contribute to closing these gaps.

The study of soil N cycling processes has been, is, and will be at the centre of attention in soil science research. The importance of N as a nutrient for all biota; the ever-increasing rates of its anthropogenic input in terrestrial (agro)ecosystems; its resultant losses to the environment; and the complexity of the biological, physical, and chemical factors that regulate N cycling processes all contribute to the necessity of further understanding, measuring, and altering the soil N cycle. Here, we review important insights with respect to the soil N cycle that have been made over the last decade, and present a personal view on the key challenges of future research. We identify three key challenges with respect to basic N cycling processes producing gaseous emissions: 1. quantifying the importance of nitrifier denitrification and its main controlling factors; 2. characterizing the greenhouse gas mitigation potential and microbiological basis for N2O consumption; 3. characterizing hotspots and hot moments of denitrification Furthermore, we identified a key challenge with respect to modelling: 1. disentangling gross N transformation rates using advanced 15N / 18O tracing models Finally, we propose four key challenges related to how ecological interactions control N cycling processes: 1. linking functional diversity of soil fauna to N cycling processes beyond mineralization; 2. determining the functional relationship between root traits and soil N cycling; 3. characterizing the control that different types of mycorrhizal symbioses exert on N cycling; 4. quantifying the contribution of non-symbiotic pathways to total N fixation fluxes in natural systems We postulate that addressing these challenges will constitute a comprehensive research agenda with respect to the N cycle for the next decade. Such an agenda would help us to meet future challenges on food and energy security, biodiversity conservation, water and air quality, and climate stability.

Polyunsaturated fatty acids (PUFA) are essential compounds that can limit the productivity of primary consumers in aquatic food webs, where the efficiency in energy transfer at the plant–animal interface has been related to food quality in terms of fatty acids (FA). At this interface, copepods play a pivotal role both as consumers of primary production and as a food source for higher trophic levels. Understanding the role of grazing copepods in the transfer of FA is therefore essential for our knowledge on the overall functioning of marine ecosystems. The harpacticoid copepodMicroarthridion littoralegrazed for 9 d on13C labelled diatoms and bacteria in the laboratory and was then subjected to FA-specific stable isotope analysis. The objective of this analysis was to inspect the copepod’s ability to bioconvert short-chain FA (SC-PUFA, <20 carbons) into long-chain PUFA (LC-PUFA, ≥20 carbons) and the FA involved in the potential bioconversion pathways. Diatoms and bacteria were chosen as test diets because of their different FA composition, i.e. docosahexaenoic acid (DHA; 22:6ω3) was absent in the bacteria, and eicosapentaenoic acid (EPA; 20:5ω3) was <5% of the total FA weight of bacteria. The presence of labelled DHA in copepods feeding on bacteria showed that this PUFA must have been converted from other FA, possibly EPA. The FA composition of copepods in the laboratory was different from that of field copepods, which suggests the availability of more food sources in the field than those offered in the experiment. The weight proportion of C18 FA decreased in copepods feeding on either bacteria or diatoms relative to field copepods, while the proportion of both EPA and DHA increased. In contrast to planktonic calanoid copepods that have limited ability to bioconvert FA, benthic harpacticoid copepods apparently developed the ability to elongate FA and to exploit niches with poor quality food. Moreover, by improving the quality of the food they graze upon, especially in terms of EPA and DHA, harpacticoid copepods upgrade the nutritive value of food available to the higher trophic levels in marine food webs.

The role of eroding landscapes in organic carbon stabilization operating as C sinks or sources has been frequently discussed, but the underlying mechanisms are not fully understood. Our analysis aims to clarify the effects of soil redistribution on physical and biogeochemical soil organic carbon (SOC) stabilization mechanisms along a hillslope transect. The observed mineralogical differences seem partly responsible for the effectiveness of geochemical and physical SOC stabilization mechanisms as the mineral environment along the transect is highly variable and dynamic. The abundance of primary and secondary minerals and the weathering status of the investigated soils differ drastically along this transect. Extractable iron and aluminum components are generally abundant in aggregates, but show no strong correlation to SOC, indicating their importance for aggregate stability but not for SOC retention. We further show that pyrophosphate extractable soil components, especially manganese, play a role in stabilizing SOC within non-aggregated mineral fractions. The abundance of microbial residues and measured 14C ages for aggregated and non-aggregated SOC fractions demonstrate the importance of the combined effect of geochemical and physical protection to stabilize SOC after burial at the depositional site. Mineral alteration and the breakdown of aggregates limit the protection of C by minerals and within aggregates temporally. The 14C ages of buried soil indicate that C in aggregated fractions seems to be preserved more efficiently while C in non-aggregated fractions is released, allowing a re-sequestration of younger C with this fraction. Old 14C ages and at the same time high contents of microbial residues in aggregates suggest either that microorganisms feed on old carbon to build up microbial biomass or that these environments consisting of considerable amounts of old C are proper habitats for microorganisms and preserve their residues. Due to continuous soil weathering and, hence, weakening of protection mechanisms, a potential C sink through soil burial is finally temporally limited.

Drained organic forest soils represent a hotspot for nitrous oxide (N 2 O) emissions, which are directly related to soil fertility, with generally higher emissions from N-rich soils. Highest N 2 O emissions have been observed in organic forest soils with low pH. The mechanisms for these high emissions are not fully understood. Therefore, the present study was conducted to gain a deeper insight into the underlying mechanisms that drive high N 2 O emissions from acid soils. Specifically, we investigated the microbial community structure, by phospholipid fatty acid analysis, along a natural pH gradient in an organic forest soil combined with measurements of physico-chemical soil properties. These were then statistically related to site-specific estimates of annual N 2 O emissions along the same natural pH gradient. Our results indicate that acidic locations with high N 2 O emissions had a microbial community with an increased fungal dominance. This finding points to the importance of fungi for N 2 O emissions from acid soils. This may either be directly via fungal N 2 O production or indirectly via the effect of fungi on the N 2 O production by other microorganisms (nitrifiers and denitrifiers). The latter may be due to fungal mediated N mineralization, providing substrate for N 2 O production, or by creating favourable conditions for the bacterial denitrifier community. Therefore, we conclude that enhanced N 2 O emission from acid forest soil is related, in addition to the known inhibitory effect of low pH on bacterial N 2 O reduction, to a soil microbial community with increased fungal dominance. Further studies are needed to reveal the exact mechanisms.

Inadequate or lack of prudent soil fertility management by cocoa farmers leads to nutrient depletion in cocoa production fields. The objective of this study was to assess current soil fertility status of cocoa farms from six cocoa growing regions in Ghana and to derive an integrated soil quality index (SQI). Composite soil samples from 0 to 30 cm depth were collected from 100 selected farms covering the six cocoa regions. Soil pH, %C, %N, total and available P, cation exchange capacity (CEC), and exchangeable cations (Ca, Mg, K) were measured. These parameters were analyzed using principal component analysis, normalized, and integrated into a weighted-additive SQI. Soil pH of majority (59.0%) of the farms was within 5.6–7.2, suitable for cocoa production. Available soil-P in most (82%) of the farms was < 20 mg kg−1. Soil quality in most farms was generally low, with an average SQI of 0.41 ± 0.14. Soil quality in Western region farms was relatively high, followed by farms in Brong Ahafo and Volta regions. Farms in Eastern, Central and Ashanti regions had the least soil quality. Soil pH, CEC and available P showed great influence on SQI. Given the latter observation, diagnostic yield response experiments should be conducted, which include: application of locally generated liming materials, organic residues and agro-mineral base fertilizers such as phosphate rock and dolomite.

Agricultural intensification and forest conservation are often seen as incompatible. Agricultural interventions can help boost food security for poor rural communities but in certain cases can exacerbate deforestation, known as the rebound effect. We tested whether coupling agricultural interventions with participatory forest zoning could improve food security and promote forest conservation in the Democratic Republic of the Congo. Simple agricultural interventions led to a >60% increase in cassava yields and a spill-over effect of improved cassava variety uptake in non-intervention zones. Household surveys conducted at the end of the 8 year project implementation period revealed that households that received agricultural interventions had more favorable attitudes toward forest zoning and conservation. The surveys also showed that farmers in the intervention domain practiced less land-intensive field and fallow management strategies compared to those practiced in the non-intervention domain. However, an 18 year time series analysis of Landsat satellite data revealed that agricultural expansion persisted in areas both with and without intervention assistance, and there is risk of a rebound effect. Approximately 70% of the tree cover loss that occurred outside of the agricultural areas was located within a 3 km buffer zone surrounding the outermost edges of the agricultural areas, which suggested that the majority of tree cover loss was caused by agricultural expansion. Within that 3 km buffer, average annual tree cover loss during the post-intervention period was higher in the intervention domain compared to the non-intervention domain (0.17% yr −1 compared to 0.11% yr −1 respectively, p < 0.001), suggesting risk of a rebound effect. The disconnection between household perceptions of zoning adherence and actual behavior indicates the importance of strengthening governance structures for community-based monitoring and enforcement.