Samuel Abiven

Mangroves are carbon dense ecosystems. Their root exudates could remobilise buried soil organic matter in the form of CO2 emission, notably by stimulating organic matter decay indirectly via an exudate sugar-driven and microbially mediated pathway, or directly by the breakage of organo-mineral bonds. Here, we used a manipulative laboratory incubation to test the effect of root exudate type on CO2 emission in two contrasting mangrove soils: a peat soil with mostly particulate organic matter (Dumbea, New Caledonia, France) and a mineral soil dominated by organo-mineral associations (Can Gio, Vietnam). Using a custom-made 20 cm long needle with a side-port near the tip,we spiked two exudates types, oxalic acid and glucose, into the mineral and organic mangrove soils. The soil CO2 emission was quantified with a gas analyser over time. Iron and pH were mapped at high spatial resolution using two-dimensional Diffusive Equilibrium Thin-films (2D-DET) gels. The root exudate inputs significantly increased the CO2 emission in both mangroves (by an order of magnitude; p< 0.01). The organic rich and mineral mangrove soil CO2 emission responded similarly to both root exudate types. There was no difference in soil CO2 emission between glucose and oxalic acid treatment. Oxalic acid reduced the soil pH consistently across the vertical soil profile in the mineral mangrove soil, while in the peat soil there was a sharp pH decrease in the few top millimetres of soil. For both soil types, the iron concentration was multiplied by an order of magnitude under oxalic acid treatment with a peak in the soil surface, and was slightly increased under glucose treatment. Our results reveal that root exudation could be a major driver of carbon, pH, and iron dynamics in mangrove soils. These findings highlight the importance of understanding root-soil interaction to constrain mangrove carbon budgets.

Mangrove forests store significant amounts of blue carbon, mainly as soil organic matter. Insights into mangrove organic matter are limited, despite its importance for understanding blue carbon accumulation and vulnerability to global change. Here, we quantified soil organic matter preserved through chemical recalcitrance and association with the mineral phase, as key factors influencing blue carbon persistence. We found that the nature of the soil organic matter varied with mangrove geomorphic settings. Delta settings were dominated by presumably the most persistent soil organic matter associated with minerals, while open coast karstic settings contained mostly particulate soil organic matter, likely preserved due to low microbial activity. Across mangrove soil depths, there was little difference in soil organic matter pools. The soil organic matter pool across mangroves’ geomorphic settings exhibited greater variation than that observed across all terrestrial biomes. These findings underscore the need to tailor mangrove conservation and restoration to geomorphic settings.

Between March 2023 and September 2024, the Tara Europa expedition embarked 50 international scientists to systematically deploy over 60 protocols at 188 sites along the European coastline from Finland to Greece. Covering the waters of 19 countries, the teams on board Tara measured a suite of oceanographic (bio)physical parameters and recovered approximately 23,000 samples to characterize the mosaic of coastal aquatic ecosystems along the way, ranging from molecules to organisms and from viruses to animals. Tara Europa was the ocean part of a larger initiative, TREC - Traversing European Coastlines -, led by the European Molecular Biology Laboratory (EMBL), which aims to explore life across the basic components of the Earth system: soils, sediments, waters, and air. While Tara focused on sampling marine waters and aerosols, a fleet of EMBL mobile laboratories collected data from shallow waters, sediments, soils, and air. Overall, TREC involved 90 institutions across 30 countries, systematically collecting over 70,000 samples from 115 land-to-sea gradients. The sampling strategy was designed to encompass various habitats and geomorphologies (open coasts or estuaries), including areas impacted by human activity (agriculture, urbanization), as well as pristine environments and sharp climate gradients—ranging from brackish waters in the Baltic Sea to hyper-saline warm waters in the Mediterranean. In addition to a comprehensive suite of cutting-edge meta-omics techniques (metagenomics, metatranscriptomics, metabarcoding, metametabolomics, metaproteomics, metamorphomics), we measured key contextual (bio)physical and biogeochemical parameters, including trace metals and over 4,000 pollutants (pesticides, drugs, etc.). We also deployed state-of-the-arts imaging tools and novel phenogenomics protocols in the EMBL Advanced Mobile Laboratory, for systematic and much deeper understanding of interactions, functions, and processes at cellular and subcellular levels. All together, this expedition represents the largest consistent exploration of life across the dimensions and drivers of the Earth systems, including local and global anthropogenic impacts. Beyond uncovering a wealth of novel molecules, genes, and species, TREC will illuminate fundamental molecular and cellular mechanisms underlying the interactions occurring between taxa and ecosystems, from which emerge ecosystems and planetary functions and their adaptation and evolution. TREC also lays the groundwork for distributed yet integrative planetary biology research through foundational concepts, infrastructure, methods, and baseline datasets.

The need for continuous local and long-term observations in the vadose zone has been growing for many years, as they are essential for improving our understanding of the processes occurring in the vadose zone of the soil and enhancing seasonal forecasts from numerical models.Lysimeters and Ecotrons are the main tools to directly access water and nutrient transport over long periods of time. In France, with the impulsion of the ONEWATER project, a French lysimeter network is in development since April 2024, taking benefice of the existing structure.A workshop was organised to identify all the sites in France and to collect expectations. We considered about the major scientific questions that could be supported by such a network, and identifying the measurement systems and instruments that are compatible with our ambitions, as well as considering the management and diffusion of the data.In 2024, 32 lysimeter sites have been identified in France, with a total of 650 lysimeters. These sites are very heterogeneous : i) different type and size of devices : (columns, boxes, plates, mini-lysimeters, porous cells, Ecotrons, etc.); ii) different filling methods (undisturbed or reconstituted), iii) different measurements (probes, frequency…), iv) different atmospheric condition (natural or controlled)… Despite each site is unique and has specific scientific objectives, they all measure drainage.The site managers expect this network will help sharing experience in terms of device management, data valorisation and probe development, and to enable the data collected in the sites to be more used.A main issue with this heterogeneous network is to be able to compare and interprete each site. To do so several methods will be used, from in situ temporary experiment to numerical simulations. Additional, the individual sites would benefit from some upgrade, with the use of similar low-cost probes and effort will be done to share and valorize the lysimetric data.

Mangrove ecosystems are one of the most carbon dense ecosystems worldwide. Yet, the stabilization and recalcitrance of carbon (C) and organic matter (OM) are little understood in mangroves, especially across eco-geomorphological settings and depths. Here, we characterized the sediment C and OM of Indo-Pacific mangroves, located in four distinct eco-geomorphological settings (i.e., delta, estuary, non-carbonated open coast, carbonated open coast) and at two different depths (i.e., 0-20 cm and 80-100 cm). We quantified the fraction of C within (i) mineralized associated organic matter (MAOM), and (ii) within particulate organic matter (POM). We coupled these analyses with lignin quantity and composition, as well as stable C isotopes analysis in mangrove sediments.We found significant variation in the quantity of MAOM and POM across mangrove eco-geomorphological settings, but not across mangrove sediment depths. The terrigenous deltaic mangrove exhibited up to three times more MAOM than the carbonate open coast mangrove, which was dominated by POM. Mangroves of the carbonate coast type had higher C content than other eco-geomorphic types. The was not different across mangrove eco-geomorphologies, but was different across mangrove sediment depths. Regarding OM recalcitrance, the lignin content displayed strong variations across the different eco-geomorphologies, however, there was no clear pattern of lignin degradation stage across depths. Finally, an inverse correlation between sediment C recalcitrance (i.e., lignin content) and stabilization (MAOM) processes were determined across mangroves.Our findings suggest that the processes leading to OM preservation differ among mangroves in various eco-geomorphological settings. Those results have important implications to guide mangrove restoration for carbon persistence and to model carbon pools across mangrove areas.

This study focuses on the evolution of soil erosion rates on artificial covers for low level radioactive waste in the context of climate change. The objective is to test the impacts on erosion of (i) increasing rainfall intensities during storms and (ii) decreasing soil moisture content before storms. The “Centre de stockage de la Manche” (CSM) in Normandy, France, where Low-Level Nuclear waste are stored and monitored for the next centuries, is used as a reference case. There, climatic models anticipate an increase of temperature and seasonality (i.e., dryer Summers and wetter conditions from Fall to Spring) in the next centuries.First, the soils of the CSM are sampled to be characterized. The densities, moisture, grainsize distribution and organic content of the soil are measured. We find that these values are rather homogeneous at the scale of the CSM. Second, a series of experimental rainfall simulations is performed on the CSM soils, focusing of rates and distribution of erosion processes. We simulate rainfall events of decennial, centennial, millennial and decamillennial intensities on 18° slopes, corresponding to the steeper banks of the CSM. Using the capacities of the climatic chambers at the Ecotron Lab in Nemours, France, we further test several soil moistures, i.e., very wet, moderately wet and dry, before simulating rainfall events. Finally, each experiment is repeated several times to assess the “memory” effect of topography on erosion. We quantify erosion by measuring sediment concentrations in run-off water collected at the outlet of the model and using topographic acquisitions performed using photogrammetry.The experimental results are compared with estimations based on the Revised Universal Soil Loss Equation. Some propositions for upscaling, which could be used for assessing hypothetical future increase in soil loss in the CSM, are discussed.

Peatlands are an important global carbon (C) reservoir storing at least one-third of global soil organic carbon (SOC), but little is known about the stability of these vast C stocks under climate change. Here, we examine the impact of four years of warming (+0, +2.25, +4.5, +6.75, +9 °C) and two years of elevated atmospheric CO2 concentration (eCO2) on the molecular composition of SOC to infer SOC sources (microbe-, plant- and fire-derived) and stability in a boreal peatland. We show that while warming alone decreased plant- and microbe-derived SOC due to enhanced decomposition, warming combined with eCO2 increased plant-derived SOC compounds. Further, using biopolymers distinct to either leaf/needle (cutin) or root (suberin), we observed increasing root-derived inputs and declining leaf-derived C inputs into SOC under warming and eCO2. Unsurprisingly, SOC derived from historical pyrolysis (pyrogenic C) was unaffected by warming or eCO2. The decline in SOC compounds with warming and gains from new root-derived C under eCO2, suggest that warming and eCO2 may shift peatland C budget towards pools with faster turnover. Together, our results indicate that climate change may increase inputs and enhance decomposition of SOC potentially destabilising C storage in peatlands.

The importance of biota to soil formation and landscape development is widely recognized. As biotic complexity increases during early succession via colonization by soil microbes followed by vascular plants, effects of biota on mineral weathering and soil formation become more complex. Knowledge of the interactions among groups of organisms and environmental conditions will enable us to better understand landscape evolution. Here, we used experimental columns of unweathered granular basalt to investigate how early successional soil microbes, vascular plants (alfalfa; Medicago sativa), and soil moisture interact to affect both plant performance and mineral weathering. We found that the presence of soil microbes reduced plant growth rates, total biomass, and survival, which suggests that plants and microbes were competing for nutrients in this environment. However, we also found considerable genotype‐specific variation in plant–microbial interactions, which underscores the importance of within‐species genetic variation on biotic interactions. We also found that the presence of vascular plants reduced variability in pH and electrical conductivity, suggesting that plants may homogenize weathering reactions across the soil column. We also show that there is heterogeneity in the abiotic conditions in which microbes, plants, or their combination have the strongest effect on weathering, and that many of these relationships are sensitive to soil moisture. Our findings highlight the importance of interdependent effects of environmental and biotic factors on weathering during initial landscape formation.