Résumé
Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens is missing. We evaluate the diversity of soft rot Pectobacteriaceae (SRP) of the genera Dickeya and Pectobacterium over two years in a temperate, mixed use watershed. The abundance of isolated strains correlates with the agricultural gradient along the watershed with a positive correlation found with temperature, nitrate and dissolved organic carbon water concentration. We characterized 582 strains by amplification and sequencing of the gapA gene. MLSA analysis performed with 3 housekeeping genes for 99 strains and core genome analysis of 38 sequenced strains confirmed for all the strains but one the taxonomic assignation obtained with the sole gapA sequence. Pectobacterium spp. (549 isolates) were far more abundant than Dickeya spp. (33 isolates). Dickeya spp. were only observed in the lower part of the river when water temperature was above 19°C and we experimentally confirmed a decreased fitness of several Dickeya spp. at 8°C in river water. D. oryzae dominates the Dickeya spp. P. versatile and P. aquaticum dominate the Pectobacterium spp. but their repartition along the watershed was different, P. versatile being the only species regularly recovered all along the watershed. Excepting P. versatile, Dickeya and Pectobacterium spp. responsible for disease outbreak on crops were less abundant or rarely detected. This work sheds light on the various ecological behaviours of different SRP in stream water and indicates that SRP occupation is geographically structured.
Auteurs, date et publication :
Auteurs Hajar Ben Moussa , Claire Bertrand , Emma Rochelle-Newall , Sarah Fiorini , Jacques Pédron , Marie-Anne Barny
Publication : Phytopathology
Date : 2022
Catégorie(s)
#CNRS #Ecotron IleDeFrance #ENS #PLANAQUAAuteurs, date et publication :
Auteurs Isabelle Braud , Chloé Martin , Isabelle Charpentier , Jean-François Le Gaillard
Date : 2022
Catégorie(s)
#CNRS #Ecotron IleDeFrance #ENSRésumé
Pyrogenic organic matter (PyOM) is a product of incomplete combustion during wildfires and an important pool of soil organic carbon (SOC). The dynamics of PyOM and SOC in boreal and permafrost-affected soils are largely unknown, while storing large amounts of global carbon and being vulnerable to climate change. Here, we traced the vertical mobility, allocation in soil fractions and decomposition losses of highly 13C-labeled PyOM and its precursor ryegrass organic matter (grass OM) after two years of in-situ incubation in soil cores installed in the upper 10 cm of continuous (northern sites) and discontinuous to sporadic (southern sites) permafrost-affected forest soils in Northern Canada. At the northern sites, up to three times more PyOM was lost by decomposition (39% of initial) compared to the southern sites (11% of initial). Losses of grass OM were substantial (69–84% of initial) and larger in southern soils. The vertical incorporation was limited and >90% of recovered PyOM and grass OM were found at the applied depth (0–3 cm). The PyOM strongly interacted with mineral surfaces, as indicated by around 40% recovered in the mineral-associated heavy density fractions (<63 μm). Microscale analyses by SEM and NanoSIMS showed that PyOM was mainly allocated towards the fine fraction in a particulate and aggregated form, highlighting the importance of abiotic processes for the incorporation of PyOM in permafrost-affected soils. The grass OM was mainly recovered in the mineral fractions at southern soils with enhanced allocation towards mineral surfaces as well as increased distribution at the microscale after initial decomposition, while it remained as particulate OM in northern soils. Our results highlight that permafrost-affected boreal forest soils are sensitive to fresh PyOM and OM inputs with substantial losses. Especially PyOM persistence depended on site and soil specific properties and not solely on its physico-chemical persistence. The responses are decoupled for PyOM and non-pyrolyzed OM and require a better understanding to evaluate carbon feedbacks of high-latitude soils with global warming and associated shifts in vegetation and wildfire regimes.
Auteurs, date et publication :
Auteurs Marcus Schiedung , Severin-Luca Bellè , Carmen Hoeschen , Steffen A. Schweizer , Samuel Abiven
Publication : Soil Biology and Biochemistry
Date : 2023
Volume : 178
Pages : 108959
Catégorie(s)
#CNRS #Ecotron IleDeFrance #ENSAuteurs, date et publication :
Auteurs Marcus Schiedung , Philippa Ascough , Severin-Luca Bellè , Robert G. Hilton , Carmen Hoeschen , Steffen A. Schweizer , Samuel Abiven
Date : 2023
Catégorie(s)
#CNRS #Ecotron IleDeFrance #ENSRésumé
Increasing soil organic carbon contents contributes to global climate change mitigation. However, new plant inputs can enhance the mineralization of native soil organic carbon by the positive priming effect, which may counterbalance the sequestration of new carbon. Here we use soils from a 20 year chronosequence of inverted pasture soils (reciprocal translocation of topsoil and subsoil to >1 m) to study the dynamics of soil organic carbon in topsoils and subsoils. We evaluated the root-induced priming effect by differentiating native soil organic carbon from 13C root-derived carbon in a 6 month incubation experiment. We found that the addition of fresh root-derived carbon caused positive priming of native soil organic carbon in new topsoils (109 ± 27% additional respiration compared with controls without roots) and subsoils (331 ± 84%) after inversion. This effect was temporary for new topsoils as they accumulated soil organic carbon and adapted to high carbon inputs within a few years, leading to no priming in the long term. In contrast, buried topsoils became more sensitive to root carbon inputs over time, demonstrating how the legacy of high carbon inputs mediates the magnitude of priming (50% to 390% after 20 years of inversion). Overall, carbon losses with priming never exceeded new root-derived carbon inputs. We conclude that priming is a temporary reaction to additional carbon, which attenuates when soils adapt to high carbon inputs within a few years to decades.
Auteurs, date et publication :
Auteurs Marcus Schiedung , Axel Don , Michael H. Beare , Samuel Abiven
Publication : Nature Geoscience
Date : 2023
Volume : 16
Issue : 10
Pages : 909-914
Catégorie(s)
#CNRS #Ecotron IleDeFrance #ENSRésumé
Peatlands are an important carbon (C) reservoir storing one-third of global soil organic carbon (SOC), but little is known about the fate of these C stocks under climate change. Here, we examine the impact of warming and 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. We further observed increasing root-derived inputs (suberin) and declining leaf/needle-derived inputs (cutin) into SOC under warming and 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.
Auteurs, date et publication :
Auteurs Nicholas O. E. Ofiti , Michael W. I. Schmidt , Samuel Abiven , Paul J. Hanson , Colleen M. Iversen , Rachel M. Wilson , Joel E. Kostka , Guido L. B. Wiesenberg , Avni Malhotra
Publication : Nature Communications
Date : 2023
Volume : 14
Issue : 1
Pages : 7533
Catégorie(s)
#CNRS #Ecotron IleDeFrance #ENSRésumé
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.
Auteurs, date et publication :
Auteurs Valerie R. Milici , Samuel Abiven , Hannes H. Bauser , Lily G. Bishop , Rebecca G. W. Bland , Jon Chorover , Katerina M. Dontsova , Kielah Dyer , Linus Friedman , Matthew J. Rusek-Peterson , Scott Saleska , Katrina M. Dlugosch
Publication : Geobiology
Date : 2025
Volume : 22
Issue : 6
Pages : e70004
Catégorie(s)
#CNRS #Ecotron de Montpellier #Ecotron IleDeFrance #ENSAuteurs, date et publication :
Auteurs Antoine Sobaga , Florence Habets , Samuel Abiven , Pierre Faure-Catteloin
Date : 2025
Catégorie(s)
#CNRS #Ecotron IleDeFrance #ENSRésumé
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.
Auteurs, date et publication :
Auteurs Marion Maceiras , Marie Arnaud , Catherine Lovelock , Alex Pearse , Huyen Dang , Sarah Robin , Cyril Marchand , Axel Felbacq , Samuel Abiven , Johanne Lebrun Thauront , Nicolas Bottinelli , Amrit kumar Mishra , Syed Hilal Farooq , Tuhin Bhadra , Cornelia Rumpel
Date : 2024
Pages : 8023
Catégorie(s)
#CNRS #Ecotron IleDeFrance #ENSRésumé
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.
Auteurs, date et publication :
Auteurs Gabriel Portzer , Albert Marchiol , Olivier Stab , Jean-Alain Fleurisson , Samuel Abiven , Simon Chollet , Yara Maalouf , Nicole Khoueiry , Neda Yadari , Neda Yadari
Date : 2024