Functional Ecology and Ecotoxicology of AgroEcosystems

Similarly to other European mountain areas, in Serra da Estrela the grazing pressure has been reducing due to social and economic drivers that have pushed shepherds and sheep to the foothill, or plainly out of the sector. Shrub encroachment on commons and other previously grazed land is one of the most tangible effects of pastoral abandonment in Serra de Estrela. The impacts of the resulting increase in landscape continuity and biomass availability were made clear in the severe fires of 2017 and 2022. As fire risk is likely to increase with climate change, it becomes urgent to understand what strategies can be deployed to keep fragmentation in these landscapes. Key actors such as shepherds should be involved in this discussion to understand their perceptions, points of view and reasons for abandoning upland pastures. In this study, we use fuzzy cognitive mapping to identify the key variables and mechanisms affecting the pastoral system according to local shepherds. In our study, we developed with local stakeholders a framework outlining the local pastoral system. Based on that, we carried out the fuzzy cognitive mapping collecting 14 questionnaires. We found that shepherds' income is a central issue, but that it is highly dependent on many factors. Increasing the Common Agricultural Policy payments alone is not enough to incentivise the use of upland pastures. More targeted strategies, such as more support for shrub clearing, and direct payments conditional to transhumance are more impactful. Despite a contentious discourse between conservation and shepherding values in Serra da Estrela, we find that shepherd's values are aligned with biodiversity conservation and a potential nature-based solution for minimizing fire risk through woody fuel management. This opens up possibilities for new governance strategies, that put Serra da Estrela's social, environmental and cultural values at its core.

Abstract The year 2022 saw record breaking temperatures in Europe during both summer and fall. Close to 30% of the European continent was under severe summer drought with a similarly large area affected (3.0 million km2) as during the recent 2018 drought, but now located in central and southeastern Europe. Multiple sets of observations suggest a reduction of net ecosystem carbon exchange in summer (57-62 TgC) over this area, and specific sites in France even showed a widespread summertime carbon release by forests, as well as wildfires. A warm fall with prolonged carbon uptake offered only partial compensation (up to 32%) for the carbon uptake lost due to drought. This severity of this second drought event in 5 years suggests these impacts to no longer be exceptional, and important to factor into Europe's developing plans for net-zero greenhouse gas emissions that rely on carbon sequestration by forests.

Abstract. Quantification of land surface-atmosphere fluxes of carbon dioxide (CO2) fluxes and their trends and uncertainties is essential for monitoring progress of the EU27+UK bloc as it strives to meet ambitious targets determined by both international agreements and internal regulation. This study provides a consolidated synthesis of fossil sources (CO2 fossil) and natural sources and sinks over land (CO2 land) using bottom-up (BU) and top-down (TD) approaches for the European Union and United Kingdom (EU27+UK), updating earlier syntheses (Petrescu et al., 2020, 2021b). Given the wide scope of the work and the variety of approaches involved, this study aims to answer essential questions identified in the previous syntheses and understand the differences between datasets, particularly for poorly characterized fluxes from managed ecosystems. The work integrates updated emission inventory data, process-based model results, data-driven sectoral model results, and inverse modeling estimates, extending the previous period 1990–2018 to the year 2020 to the extent possible. BU and TD products are compared with European National Greenhouse Gas Inventories (NGHGIs) reported by Parties including the year 2019 under the United Nations Framework Convention on Climate Change (UNFCCC). The uncertainties of the EU27+UK NGHGI were evaluated using the standard deviation reported by the EU Member States following the guidelines of the Intergovernmental Panel on Climate Change (IPCC) and harmonized by gap-filling procedures. Variation in estimates produced with other methods, such as atmospheric inversion models (TD) or spatially disaggregated inventory datasets (BU), originate from within-model uncertainty related to parameterization as well as structural differences between models. By comparing NGHGIs with other approaches, key sources of differences between estimates arise primarily in activities. System boundaries and emission categories create differences in CO2 fossil datasets, while different land use definitions for reporting emissions from Land Use, Land Use Change and Forestry (LULUCF) activities result in differences for CO2 land. The latter has important consequences for atmospheric inversions, leading to inversions reporting stronger sinks in vegetation and soils than are reported by the NGHGI. For CO2 fossil emissions, after harmonizing estimates based on common activities and selecting the most recent year available for all datasets, the UNFCCC NGHGI for the EU27+UK accounts for 3392 ± 49 Tg CO2 yr-1 (926 ± 13 Tg C yr-1), while eight other BU sources report a mean value of 3340 [3238,3401] [25th,75th percentile] Tg CO2 yr-1 (948 [937,961] Tg C yr-1). The sole top-down inversion of fossil emissions currently available accounts for 3800 Tg CO2 yr-1 (1038 Tg C yr-1), a value close to that of the NGHGI, but for which uncertainty estimates are not yet available. For the net CO2 land fluxes, during the most recent five-year period including the NGHGI estimates, the NGHGI accounted for -91 ± 32 Tg C yr-1 while six other BU approaches reported a mean sink of -62 [-117,-49] Tg C yr-1 and a 15-member ensemble of dynamic global vegetation models (DGVMs) reported -69 [-152,-5] Tg C yr-1. The five-year mean of three TD regional ensembles combined with one non-ensemble inversion of -73 Tg C yr-1 has a slightly smaller spread (0th–100th percentile of [-135,45] Tg C yr-1), and was calculated after removing land-atmosphere CO2 fluxes caused by lateral transport of carbon (crops, wood trade and inland waters) resulting in increased agreement with the the NGHGI and bottom-up approaches. Results at the sub-sector level (Forestland, Cropland, Grassland) show generally good agreement between the NGHGI and sub-sector-specific models, but results for a DGVM are mixed. Overall, for both CO2 fossil and net CO2 land fluxes, we find current independent approaches are consistent with the NGHGI at the scale of the EU27+UK. We conclude that CO2 emissions from fossil sources have decreased over the past 30 years in the EU27+UK, while large uncertainties on net uptake of CO2 by the land surface prevent trend identification. In addition, a gap on the order of 1000 Tg C yr-1 between CO2 fossil emissions and net CO2 uptake by the land exists regardless of the type of approach (NGHGI, TD, BU), falling well outside all available estimates of uncertainties. However, uncertainties in top-down approaches to estimate CO2 fossil emissions remain uncharacterized and are likely substantial. The data used to plot the figures are available at https://doi.org/10.5281/zenodo.7365863.

Zwitterionic, cationic, and anionic per- and polyfluoroalkyl substances (PFAS) are increasingly reported in terrestrial and aquatic environments, but their inputs to agricultural lands are not fully understood. Here, we characterized PFAS in 47 organic waste products (OWP) applied in agricultural fields of France, including historical and recent materials. Overall, 160 PFAS from 42 classes were detected from target screening and homologue-based nontarget screening. Target PFAS were low in agriculture-derived wastes such as pig slurry, poultry manure, or dairy cattle manure (median ∑46PFAS: 0.66 μg/kg dry matter). Higher PFAS levels were reported in urban and industrial wastes, paper mill sludge, sewage sludge, or residual household waste composts (median ∑46PFAS: 220 μg/kg). Historical municipal biosolids and composts (1976-1998) were dominated by perfluorooctanesulfonate (PFOS), N-ethyl perfluorooctanesulfonamido acetic acid (EtFOSAA), and cationic and zwitterionic electrochemical fluorination precursors to PFOS. Contemporaneous urban OWP (2009-2017) were rather dominated by zwitterionic fluorotelomers, which represented on average 55% of ∑160PFAS (max: 97%). The fluorotelomer sulfonamidopropyl betaines (X:2 FTSA-PrB, median: 110 μg/kg, max: 1300 μg/kg) were the emerging class with the highest occurrence and prevalence in contemporary urban OWP. They were also detected as early as 1985. The study informs for the first time that urban sludges and composts can be a significant repository of zwitterionic and cationic PFAS.

Abstract. Changes in soil organic carbon (SOC) stocks are a major source of uncertainty for the evolution of atmospheric CO2 concentration during the 21st century. They are usually simulated by models dividing SOC into conceptual pools with contrasted turnover times. The lack of reliable methods to initialize these models, by correctly distributing soil carbon amongst their kinetic pools, strongly limits the accuracy of their simulations. Here, we demonstrate that PARTYsoc, a machine-learning model based on Rock-Eval® thermal analysis optimally partitions the active and stable SOC pools of AMG, a simple and well validated SOC dynamics model, accounting for effects of soil management history. Furthermore, we found that initializing the SOC pool sizes of AMG using machine-learning strongly improves its accuracy when reproducing the observed SOC dynamics in nine independent French long-term agricultural experiments. Our results indicate that multi-compartmental models of SOC dynamics combined with a robust initialization can simulate observed SOC stock changes with excellent precision. We recommend exploring their potential before a new generation of models of greater complexity becomes operational. The approach proposed here can be easily implemented on soil monitoring networks, paving the way towards precise predictions of SOC stock changes over the next decades.

Letter to the Editor of the European Journal of Soil Science as a reaction to the Russell Review by Phillipe Baveye “Bypass and hyperbole in soil research: worrisome practices critically reviewed through examples” and to his follow‐up Invited Opinion paper “Bypass and hyperbole in soil research: a personal view on plausible causes and possible remedies” and the subsequent Letter to the Editor by Johan Bouma “Soil challenges beyond publication issues”

Over the last two decades, the sequestration of carbon in soils has often been advocated as a solution to mitigate the steady increase in the concentration of CO2 in the atmosphere, one of the most commonly mentioned causes of climate change. A large body of literature, as well as sustained efforts to attract funding for the research on soil organic matter, have focused on the soil carbon sequestration – climate change nexus. However, because CO2 is not the only greenhouse gas released by soils, and given the fact that the feasibility of large-scale carbon sequestration in soils remains controversial, this approach does not appear optimal to convince policy makers to invest in soils. In this perspective article, we argue that a far better strategy revolves around the effect of climate change on functions/services that soils render. In particular, since climatologists forecast less frequent but more intense rainfall events in the future, which may lead to food shortages, catastrophic flooding, and soil erosion if soils are not able to cope, a more suitable focus of the research would be to increase soil organic matter content so as to strengthen the water regulation function of soils. The different conceptual and methodological shifts that this new focus will require are discussed in detail.

<p>Soil texture and microorganisms are key drivers controlling the fate of organic matter (OM) originating from decaying plant litter, and thus the stabilization of soil organic matter (SOM). However, the understanding of the mutual interactions between microbial litter decay and soil structure formation controlled by different soil textures remains incomplete. We monitored the fate of litter-derived OM (using <sup>13</sup>C isotopic enrichment) from decaying litter (shredded maize leaves) to microorganisms and SOM in two differently textured soils (sand and loam). The two soils were incubated with litter mixed in the top layer in microcosms for 95 days during which regular CO<sub>2</sub> and <sup>13</sup>CO<sub>2</sub> measurements were conducted. After the incubation, each microcosm was divided in three to separate a top, center and bottom layer. Using a physical soil fractionation scheme, we assessed the fate of litter-derived OM to free and occluded particulate OM (POM), as well as mineral associated OM (MAOM). All SOM fractions were analysed with respect to their mass distribution, C, N, and <sup>13</sup>C contents, and for their chemical composition using compound-specific <sup>13</sup>C-CPMAS NMR spectroscopy. The effects of contrasting textures on the total microbial community structure were studied using phospholipid fatty acids (PLFA) and the incorporation of litter-derived C into individual PLFAs was assessed via <sup>13</sup>C-PLFA. Lastly, scanning electron microscopy and nano scale secondary ion mass spectroscopy (NanoSIMS) analysis of free POM of both textures enabled qualitative insights directly at the biogeochemical interface of the microbial hot spot of decaying plant litter.</p><p>We were able to clearly demonstrate higher contents of litter-derived OM still residing as free POM in the loamy textured soil after the 95 day-incubation, while higher contents were found in occluded and MAOM in the sandy textured soil. This indicated that the overall litter decomposition was refrained in the finer-textured soil, whereas microbial alteration and allocation of litter-derived compounds was promoted in the coarser textured soil. This was further corroborated by higher respiration and higher amounts of respired litter-derived CO<sub>2</sub>-C in the sandy soil. The PLFA analysis showed a coherent pattern between the textures, with similar community structures in all treatments and significant increases in microbial abundance in the top layers induced by litter addition. This increase was found most pronounced in fungal biomarkers, which was in line with the <sup>13</sup>C-PLFA measurements revealing over 90% of fungal biomarkers to be of litter-origin (compared to 30-40% in the other microbial groups). The labelled PLFA profiles also confirmed the importance of fungi as a vector for litter-derived OM into deeper layers of the soil columns, with significantly higher litter-derived fungal markers also in center and bottom layers. The NanoSIMS measurements verified the high <sup>13</sup>C enrichment in fungal hyphae and further revealed clay minerals embedded in enriched microbial-derived extracellular polymeric substances and intertwined with hyphae directly on top of the POM. Based on this comprehensive data, we highlight that regardless of the texture, plant litter in association with microbial-derived products represent a hot spot for soil structure formation by harbouring a core for aggregation and MAOM formation.</p>

<p>Bioenergy crops are expected to provide biomass to replace fossil resources and reduce greenhouse gas emissions. In this context, their effect on soil carbon sequestration is of primary importance. There is a wide range of candidate crops including perennial C4 crops or annual crops but their impact on soil organic carbon (SOC) stocks remain very uncertain as shown by the wild variability in published experimental results.</p><p>In this study, we measured the changes in SOC stocks under perennial (miscanthus and switchgrass), semi-perennial (fescue and alfalfa) and annual (triticale and sorghum or maize) bioenergy crops managed with two N fertilisation rates. The experiment called “Biomass & Environment” is located in northern France on a deep loamy soil (Haplic Luvisol) and was set up in 2006. The soil was sampled at the start of the experiment, in 2011-2012 and again in 2018 (0-60 cm, 5 layers). SOC stocks were calculated at equivalent soil mass and δ<sup>13</sup>C was systematically measured and used to calculate changes in new and old SOC stocks. In 2018, the SOC distribution in different soil particle-size fractions was also characterized for some treatments.</p><p>After 12 years, there was a large increase in SOC concentration (+7.6 g kg<sup>-1</sup> on average) under perennial crops in the surface layer (≈ 0-5 cm) but a slight decrease in deeper layers. Changes in δ<sup>13</sup>C also showed that more than half of the new SOC accumulated in the surface layer. In addition, the additional SOC storage in the first layer was found in coarse organic fractions (50-200 and 200-2000 μm) but also in the more stabilised 0-50 μm fraction. SOC concentration under semi-perennial crops increased in the two first layers (≈ 0-20 cm), from 10.2 g kg<sup>-1</sup> in 2006 to 11.6 g kg<sup>-1</sup> in 2018 on average and slightly decreased below. Under annual crops, a decrease in SOC concentration was observed in all layers and particularly in the third layer (≈ 20-33 cm). There was no significant effect of the N fertilisation. Over the old ploughed layer (≈ 0-33 cm), SOC stocks increased between 2006 and 2018 under perennial and semi-perennial bioenergy crops (by 3 and 2 t C ha<sup>-1</sup> on average respectively) and decreased by 7 t C ha<sup>-1</sup> on average under annual crops.</p><p>This study show that different bioenergy crops can have contrasted impacts on SOC stocks but also on SOC distribution in the soil profile.</p>