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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Benjamin Loubet, Nicolas P. Saby, Maryam Gebleh, Pauline Buysse, Jean-Philippe Chenu, Céline Ratie, Claudy Jolivet, Carmen Kalalian, Florent Levavasseur, Jose-Luis Munera-Echeverri, Sebastien Lafont, Denis Loustau, Dario Papale, Giacomo Nicolini, Bruna Winck, and Dominique Arrouays
EGUsphere, https://doi.org/10.5194/egusphere-2025-592, https://doi.org/10.5194/egusphere-2025-592, 2025
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Soil is a large pool of carbon storing globally from two to three times more carbon than the atmosphere and vegetation. We compute the soil stock evolution from 2005 to 2019 for a wheat-maize-barley-oilseed-rape crop rotation at a French crop site. The soil carbon stock decreased by around 70 ± 16 g C m-2 yr-1 over the period, leading to a total loss of around 8 % of the initial soil stock. This strong destocking is primarily explained by a decrease in the residue return to the site.
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 Martin, Lorenza Pacini, Christopher Poeplau, Céline Ratié, Pierre Roudier, Nicolas P. A. Saby, Florence Savignac, and Pierre Barré
SOIL, 10, 795–812, https://doi.org/10.5194/soil-10-795-2024, https://doi.org/10.5194/soil-10-795-2024, 2024
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This paper 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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Despite the massive use of soil storage, its impact on soil microbial parameters (SMPs) has been assessed in a very scattered way. I analysed 73 research articles dealing with the impact of storage practices on various SMPs. The results show significant effects of all storage practices on SMPs in a vast majority of cases. Storage practices should be carefully selected according to the conditions that prevail in the native soil environment and to the SMPs of interest.
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Soil health is of critical importance and many soils are threatened. Benchmarking sustainable soil management is a challenge as there is no comprehensive indicator set. Here, I introduce a novel conceptual approach to soil health, representing soil functions as complex and hard to measure variables. I outline a new methodology to study soil multifunctionality using latent variable models to represent soil functions. This is a new starting point for soil health research and ultimately monitoring.
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Forest conversion alters both bacterial and fungal soil networks: it reduces bacterial network complexity and enhances fungal network complexity. This is because forest conversion changes the soil pH and other soil properties, which alters the bacterial composition and subsequent network structure. Our study demonstrates the impact of forest conversion on soil network structure, which has important implications for ecosystem functions and the health of soil ecosystems in tropical regions.
Zijun Zhou, Zengqiang Li, Kun Chen, Zhaoming Chen, Xiangzhong Zeng, Hua Yu, Song Guo, Yuxian Shangguan, Qingrui Chen, Hongzhu Fan, Shihua Tu, Mingjiang He, and Yusheng Qin
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Straw mulching is not always combined with no-till systems during conservation tillage. We explored the effects of long-term straw mulching on soil attributes with soil depths under a no-till system. Compared to straw removal, straw mulching had various effects on soil properties at different depths, the biggest difference occurring at the topsoil depth. Overall, straw mulch is highly recommended for use under the no-till system because of its benefits to soil fertility and bacterial abundance.
Munawwar A. Khan and Shams T. Khan
SOIL, 6, 513–521, https://doi.org/10.5194/soil-6-513-2020, https://doi.org/10.5194/soil-6-513-2020, 2020
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Soil is a renewable resource for purposes ranging from agriculture to mineralization. Soil microbiome plays vital roles in facilitating process like providing nutrients to plants, or their mobilization for plant uptake, consequently improving plant growth and productivity. Therefore, understanding of these microbial communities and their role in soil is crucial for exploring the possibility of using microbial community inoculants for improving desert soil fertility and agricultural potential.
Selvaraj Aravindh, Chinnappan Chinnadurai, and Dananjeyan Balachandar
SOIL, 6, 483–497, https://doi.org/10.5194/soil-6-483-2020, https://doi.org/10.5194/soil-6-483-2020, 2020
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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.
Frederick Büks, Nicolette Loes van Schaik, and Martin Kaupenjohann
SOIL, 6, 245–267, https://doi.org/10.5194/soil-6-245-2020, https://doi.org/10.5194/soil-6-245-2020, 2020
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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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Modern agriculture is dominated by monoculture crop production, having negative effects on soil biology. We used a 12-year crop rotation experiment to examine the effects of increasing crop diversity on soil microorganisms and their activity. Crop rotations increased microbial biomass by up to 112 %, and increased potential ability to supply nitrogen as much as 58 %, compared to monoculture corn. Collectively, our findings show that soil health is increased when crop diversity is increased.
Karen A. Thompson, Bill Deen, and Kari E. Dunfield
SOIL, 2, 523–535, https://doi.org/10.5194/soil-2-523-2016, https://doi.org/10.5194/soil-2-523-2016, 2016
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Dedicated bioenergy crops are required for future energy production; however the effects of land use change from traditional crops to biofuel crops on soil microbial communities, which drive greenhouse gas production, are largely unknown. We used quantitative PCR to enumerate these microbial communities to assess the sustainability of different bioenergy crops, including miscanthus and corn. We found that miscanthus may be a suitable crop for bioenergy production in variable Ontario conditions.
Georgina Key, Mike G. Whitfield, Julia Cooper, Franciska T. De Vries, Martin Collison, Thanasis Dedousis, Richard Heathcote, Brendan Roth, Shamal Mohammed, Andrew Molyneux, Wim H. Van der Putten, Lynn V. Dicks, William J. Sutherland, and Richard D. Bardgett
SOIL, 2, 511–521, https://doi.org/10.5194/soil-2-511-2016, https://doi.org/10.5194/soil-2-511-2016, 2016
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Enhancing soil health is key to providing ecosystem services and food security. There are often trade-offs to using a particular practice, or it is not fully understood. This work aimed to identify practices beneficial to soil health and gaps in our knowledge. We reviewed existing research on agricultural practices and an expert panel assessed their effectiveness. The three most beneficial practices used a mix of organic or inorganic material, cover crops, or crop rotations.
Mohammed Ahmed, Melanie Sapp, Thomas Prior, Gerrit Karssen, and Matthew Alan Back
SOIL, 2, 257–270, https://doi.org/10.5194/soil-2-257-2016, https://doi.org/10.5194/soil-2-257-2016, 2016
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This review covers the history and advances made in the area of nematode taxonomy. It highlights the success and limitations of the classical approach to nematode taxonomy and provides reader with a bit of background to the applications of protein and DNA-based methods for identification nematodes. The review also outlines the pros and cons of the use of DNA barcoding in nematology and explains how DNA metabarcoding has been applied in nematology through next-generation sequencing.
E. Ashley Shaw, Karolien Denef, Cecilia Milano de Tomasel, M. Francesca Cotrufo, and Diana H. Wall
SOIL, 2, 199–210, https://doi.org/10.5194/soil-2-199-2016, https://doi.org/10.5194/soil-2-199-2016, 2016
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We investigated fire's effects on root decomposition and carbon (C) flow to the soil food web. We used 13C-labeled dead roots buried in microcosms constructed from two burn treatment soils (annual and infrequent burn). Our results showed greater root decomposition and C flow to the soil food web for the annual burn compared to infrequent burn treatment. Thus, roots are a more important C source for decomposers in annually burned areas where surface plant litter is frequently removed by fire.
E. Gagnarli, D. Goggioli, F. Tarchi, S. Guidi, R. Nannelli, N. Vignozzi, G. Valboa, M. R. Lottero, L. Corino, and S. Simoni
SOIL, 1, 527–536, https://doi.org/10.5194/soil-1-527-2015, https://doi.org/10.5194/soil-1-527-2015, 2015
M.-A. de Graaff, J. Adkins, P. Kardol, and H. L. Throop
SOIL, 1, 257–271, https://doi.org/10.5194/soil-1-257-2015, https://doi.org/10.5194/soil-1-257-2015, 2015
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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...
