Articles | Volume 10, issue 1
https://doi.org/10.5194/soil-10-251-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/soil-10-251-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Original research article
| Highlight paper
| 
11 Apr 2024
Original research article | Highlight paper |
| 11 Apr 2024
| 11 Apr 2024
Unraveling biogeographical patterns and environmental drivers of soil fungal diversity at the French national scale
Christophe Djemiel
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Samuel Dequiedt
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Walid Horrigue
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Arthur Bailly
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Mélanie Lelièvre
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Julie Tripied
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Charles Guilland
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
present address: Novasol experts, 21000 Dijon, France
Solène Perrin
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Gwendoline Comment
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Nicolas P. A. Saby
INRAE, Info&Sols, 45075 Orléans, France
Claudy Jolivet
INRAE, Info&Sols, 45075 Orléans, France
Antonio Bispo
INRAE, Info&Sols, 45075 Orléans, France
Line Boulonne
INRAE, Info&Sols, 45075 Orléans, France
Antoine Pierart
ADEME, Service Agriculture et Forêt, 49004 Angers, France
Patrick Wincker
Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
Corinne Cruaud
Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
Pierre-Alain Maron
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Sébastien Terrat
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Lionel Ranjard
CORRESPONDING AUTHOR
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
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Amicie A. Delahaie, Lauric Cécillon, Marija Stojanova, Samuel Abiven, Pierre Arbelet, Dominique Arrouays, François Baudin, Antonio Bispo, Line Boulonne, Claire Chenu, Jussi Heinonsalo, Claudy Jolivet, Kristiina Karhu, Manuel P. Martin, Lorenza Pacini, Christopher Poeplau, Céline Ratié, Pierre Roudier, Nicolas P. A. Saby, Florence Savignac, and Pierre Barré
EGUsphere, https://doi.org/10.5194/egusphere-2024-197, https://doi.org/10.5194/egusphere-2024-197, 2024
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This manuscript compares the soil organic carbon fractions obtained from a new thermal fractionation scheme and a well-known physical fractionation scheme on an unprecedented dataset of French topsoil samples. For each fraction, we use a machine learning model to determine its environmental drivers (pedology, climate, and land cover). Our results suggest that these two fractionation schemes provide different fractions, which means they provide complementary information.
Amicie A. Delahaie, Pierre Barré, François Baudin, Dominique Arrouays, Antonio Bispo, Line Boulonne, Claire Chenu, Claudy Jolivet, Manuel P. Martin, Céline Ratié, Nicolas P. A. Saby, Florence Savignac, and Lauric Cécillon
SOIL, 9, 209–229, https://doi.org/10.5194/soil-9-209-2023, https://doi.org/10.5194/soil-9-209-2023, 2023
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We characterized organic matter in French soils by analysing samples from the French RMQS network using Rock-Eval thermal analysis. We found that thermal analysis is appropriate to characterize large set of samples (ca. 2000) and provides interpretation references for Rock-Eval parameter values. This shows that organic matter in managed soils is on average more oxidized and more thermally stable and that some Rock-Eval parameters are good proxies for organic matter biogeochemical stability.
Kenji Fujisaki, Tiphaine Chevallier, Antonio Bispo, Jean-Baptiste Laurent, François Thevenin, Lydie Chapuis-Lardy, Rémi Cardinael, Christine Le Bas, Vincent Freycon, Fabrice Bénédet, Vincent Blanfort, Michel Brossard, Marie Tella, and Julien Demenois
SOIL, 9, 89–100, https://doi.org/10.5194/soil-9-89-2023, https://doi.org/10.5194/soil-9-89-2023, 2023
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This paper presents a first comprehensive thesaurus for management practices driving soil organic carbon (SOC) storage. So far, a comprehensive thesaurus of management practices in agriculture and forestry has been lacking. It will help to merge datasets, a promising way to evaluate the impacts of management practices in agriculture and forestry on SOC. Identifying the drivers of SOC stock changes is of utmost importance to contribute to global challenges (climate change, food security).
Alexandre M. J.-C. Wadoux, Nicolas P. A. Saby, and Manuel P. Martin
SOIL, 9, 21–38, https://doi.org/10.5194/soil-9-21-2023, https://doi.org/10.5194/soil-9-21-2023, 2023
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We introduce Shapley values for machine learning model interpretation and reveal the local and global controlling factors of soil organic carbon (SOC) stocks. The method enables spatial analysis of the important variables. Vegetation and topography determine much of the SOC stock variation in mainland France. We conclude that SOC stock variation is complex and should be interpreted at multiple levels.
Claire Froger, Nicolas P. A. Saby, Claudy C. Jolivet, Line Boulonne, Giovanni Caria, Xavier Freulon, Chantal de Fouquet, Hélène Roussel, Franck Marot, and Antonio Bispo
SOIL, 7, 161–178, https://doi.org/10.5194/soil-7-161-2021, https://doi.org/10.5194/soil-7-161-2021, 2021
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Pollution of French soils by polycyclic aromatic hydrocarbons (PAHs), known as carcinogenic pollutants, was quantified in this work using an extended data set of 2154 soils sampled across France. The map of PAH concentrations in French soils revealed strong trends in regions with heavy industries and around cities. The PAH signatures indicated the influence of PAH emissions in Europe during the industrial revolution. Health risks posed by PAHs in soils were low but need to be considered.
Virginie Moreaux, Simon Martel, Alexandre Bosc, Delphine Picart, David Achat, Christophe Moisy, Raphael Aussenac, Christophe Chipeaux, Jean-Marc Bonnefond, Soisick Figuères, Pierre Trichet, Rémi Vezy, Vincent Badeau, Bernard Longdoz, André Granier, Olivier Roupsard, Manuel Nicolas, Kim Pilegaard, Giorgio Matteucci, Claudy Jolivet, Andrew T. Black, Olivier Picard, and Denis Loustau
Geosci. Model Dev., 13, 5973–6009, https://doi.org/10.5194/gmd-13-5973-2020, https://doi.org/10.5194/gmd-13-5973-2020, 2020
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The model GO+ describes the functioning of managed forests based upon biophysical and biogeochemical processes. It accounts for the impacts of forest operations on energy, water and carbon exchanges within the soil–vegetation–atmosphere continuum. It includes versatile descriptions of management operations. Its sensitivity and uncertainty are detailed and predictions are compared with observations about mass and energy exchanges, hydrological data, and tree growth variables from different sites.
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Soil biodiversity and soil health
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Only a minority of bacteria grow after wetting in both natural and post-mining biocrusts in a hyperarid phosphate mine
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Jing Sun, Xinrui Lu, Guoshuang Chen, Nana Luo, Qilin Zhang, and Xiujun Li
SOIL, 9, 261–275, https://doi.org/10.5194/soil-9-261-2023, https://doi.org/10.5194/soil-9-261-2023, 2023
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A field experiment was conducted to compare and analyze the effects of combined application of biochar and nitrogen fertilizer on soil aggregate stability mechanism, the dynamic characteristics of aggregate organic carbon, and the microbial community structure in northeast black soil. We provide a scientific basis for formulating effective strategies to slow down soil quality degradation and ensure the sustainable development of the agroecosystem.
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SOIL, 9, 231–242, https://doi.org/10.5194/soil-9-231-2023, https://doi.org/10.5194/soil-9-231-2023, 2023
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This paper evaluates bacterial growth in biocrusts after a large-scale mining disturbance in a hyperarid desert, using a stable isotope probing assay.
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Huaihai Chen, Kayan Ma, Yu Huang, Qi Fu, Yingbo Qiu, Jiajiang Lin, Christopher W. Schadt, and Hao Chen
SOIL, 8, 297–308, https://doi.org/10.5194/soil-8-297-2022, https://doi.org/10.5194/soil-8-297-2022, 2022
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By analyzing and generalizing microbial taxonomic and functional profiles, we provide strong evidence that the degree of soil microbial functional redundancy differs significantly between “broad” and “narrow” functions across the globe. Future sequencing efforts will likely increase our confidence in comparative metagenomes and provide time-series information to further identify to what extent microbial functional redundancy regulates dynamic ecological fluxes across space and time.
Anne Daebeler, Eva Petrová, Elena Kinz, Susanne Grausenburger, Helene Berthold, Taru Sandén, Roey Angel, and the high-school students of biology project groups I, II, and
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SOIL, 8, 163–176, https://doi.org/10.5194/soil-8-163-2022, https://doi.org/10.5194/soil-8-163-2022, 2022
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Soil quality is important for functioning of the agricultural ecosystem to sustain productivity. It is combination of several physical, chemical, and biological attributes. In the present work, we developed a soil biological quality index, a sub-set of the soil quality index (SBQI) using six important biological variables. These variables were computed from long-term manurial experimental soils and transformed into a unitless 10-scaled SBQI. This will provide constraints of soil processes.
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Via anthropogenic input, microplastics (MPs) today represent a part of the soil organic matter. We analyzed studies on passive translocation, active ingestion, bioaccumulation and adverse effects of MPs on multicellular soil faunal life. These studies on a wide range of soil organisms found a recurring pattern of adverse effects on motility, growth, metabolism, reproduction, mortality and gut microbiome. However, the shape and type of the experimental MP often did not match natural conditions.
Marshall D. McDaniel and A. Stuart Grandy
SOIL, 2, 583–599, https://doi.org/10.5194/soil-2-583-2016, https://doi.org/10.5194/soil-2-583-2016, 2016
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Executive editor
This is one of the first surveys of soil fungal diversity across land uses at the national scale.
Short summary
The fungal kingdom has been diversifying for more than 800 million years by colonizing a large number of habitats on Earth. Based on a unique dataset (18S rDNA meta-barcoding), we described the spatial distribution of fungal diversity at the scale of France and the environmental drivers by tackling biogeographical patterns. We also explored the fungal network interactions across land uses and climate types.
The fungal kingdom has been diversifying for more than 800 million years by colonizing a large...
