# Changes, interactions and drivers of soil chemical, physical and biological properties after repeated application of organic waste products in two contrasted long-term field experiments in France

Haotian Chen, Florent Levavasseur, Pierre Barré, François Baudin, Sophie Sadet-Bourgeteau, Camille Chauvin, Nathalie Cheviron, Christian Mougin, Amicie Delahaie, Safya Menasseri-Aubry, et al.

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Haotian Chen, Florent Levavasseur, Pierre Barré, François Baudin, Sophie Sadet-Bourgeteau, et al. Changes, interactions and drivers of soil chemical, physical and biological properties after repeated application of organic waste products in two contrasted long-term field experiments in France. Environmental Research Letters, 2025, 10.1088/1748-9326/ae16bb. hal-05332759

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# Changes, interactions and drivers of soil chemical, physical and biological properties after repeated application of organic waste products in two contrasted long-term field experiments in France

Haotian Chen<sup>1,2,*</sup> <sup>ID</sup>, Florent Levavasseur<sup>1</sup> <sup>ID</sup>, Pierre Barré<sup>3</sup> <sup>ID</sup>, François Baudin<sup>4,5</sup> <sup>ID</sup>, Sophie Sadet-Bourgeteau<sup>1</sup> <sup>ID</sup>, Camille Chauvin<sup>6</sup>, Nathalie Cheviron<sup>1,7</sup> <sup>ID</sup>, Christian Mougin<sup>1,7</sup> <sup>ID</sup>, Amicie Delahaie<sup>3</sup> <sup>ID</sup>, Safya Menasseri-Aubry<sup>8</sup> <sup>ID</sup>, Cécile Villenave<sup>6</sup> <sup>ID</sup> and Sabine Houot<sup>1</sup> <sup>ID</sup>

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16 June 2025

REVISED

15 September 2025

ACCEPTED FOR PUBLICATION

23 October 2025

PUBLISHED

11 November 2025

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E-mail: chenhaotian@caas.cn

**Keywords:** soil biology, long-term field experiment, soil quality, organic wastes products

Supplementary material for this article is available [online](#)

<figure><img src="image_3.png" /></figure>

Abstract

Recycling organic waste products (OWPs) is known to influence soil physical, chemical, and bio-
logical properties, yet few studies have compared the long-term effects of different OWP type
across multiple sites. This study examined the impacts of repeated OWP application on soil prop-
erties in two French long-term field experiments: QualiAgro and PROspective (20 and 18 years,
respectively). The OWP included dehydrated urban sewage sludge (SLU), green waste and SLU
compost, biowaste compost from source-separated municipal organic waste co-composted with
green waste, municipal solid waste compost, farmyard manure from a dairy cow farm (FYM), and
composted FYM from open-air composting on a concrete platform. The application of OWP led
to increased soil nutrient levels and trace element availability, and stimulated microbial biomass
and enzyme activities, while the response of nematode varied depending on site and OWP type.
Biological properties were less affected than physico-chemical properties, though the OWP applic-
ation enhanced soil microbial biomass and specific enzyme activities. The impact on soil nematode
communities varied depending on OWP type and site. Strong correlations were observed among
soil property changes, with exogenous carbon and nutrient inputs from OWP identified as key
drivers. Larger changes were noted in QualiAgro, where OWP application rates were higher and
initial soil quality lower. These findings highlight that OWP applications, depending on their type,
rate, and initial soil conditions, can significantly alter soil properties.

1. Introduction

Organic waste (OW) is increasingly generated world-
wide due to population growth, urbanization, and
intensified industrial activities, with current estimates
exceeding 2.2 billion tons of municipal solid waste
(MSW), 13 billion tons of livestock manure, and 53
million tons of dry sewage sludge (SLU) annually,

and further increases projected (Nanda and Berruti
2021, Feng et al 2023). The growing volume of OW
products (OWP) offers significant opportunities for
sustainable agriculture, as its application can sus-
tain crop productivity by supplying nutrients while
reducing the environmental impacts of mineral fer-
tilizers (Chen et al 2022). While OWP enhance soil
organic matter, improve the availability of major

<footnote n="1">¹ INRAE, AgroParisTech, Université Paris-Saclay, UMR ECOSYS, 91120 Palaiseau, France</footnote>

<footnote n="2">² Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs of China, Beijing 100081, People's Republic of China</footnote>

<footnote n="3">³ Laboratoire de Géologie, UMR 8538, École normale supérieure, CNRS, Université PSL, IPSL, 75005 Paris, France</footnote>

<footnote n="4">⁴ Agroécologie, INRAE, Institute Agro Dijon, University Bourgogne, University Bourgogne Franche-Comté, F-21000 Dijon, France</footnote>

<footnote n="5">⁵ Sorbonne Université, CNRS, ISTE, 75005 Paris, France</footnote>

<footnote n="6">⁶ ELISOL environnement, ZA des Tourels, 10 avenue du midi, 30111 Congénies, France</footnote>

<footnote n="7">⁷ INRAE, Plateforme Biochem-Env, UMR ECOSYS, 91120 Palaiseau, France</footnote>

<footnote n="8">⁸ INRAE, Institute Agro, SAS, Rennes 35000, France</footnote>

<footnote>* Author to whom any correspondence should be addressed.</footnote>
nutrients (*N*, *P*, *K*), and promote soil aggregate stability (Diacono and Montemurro 2010, Peltre *et al* 2017), they may also introduce trade-offs such as increased trace element accumulation and leaching (Araújo *et al* 2019, Chen *et al* 2025), highlighting the need for comprehensive evaluation of their impacts on soil health and ecosystem functions.

Soil biological indicators, including microbial communities, enzymes, and nematodes, are supposed to be more sensitive to environmental changes than physico-chemical properties and play crucial roles in nutrient cycling and soil ecosystem functions (Böhme *et al* 2005, Lazarova *et al* 2021). Numerous studies from various regions have confirmed that soil biological indicators are greatly influenced by fertilization management (Nahar *et al* 2006, Chang *et al* 2007, Li *et al* 2008, Puissant *et al* 2021). Assessing the dynamics of soil biological and physico-chemical properties under OWP application provides valuable insights into ecosystem responses to agricultural practices and ensures the preservation of soil ecosystem services (Garbuz *et al* 2021).

The benefits of OWP vary with type, application rate, climate conditions, and initial soil properties (Gómez-Muñoz *et al* 2017, Sharma *et al* 2019). However, few studies have systematically assessed how different OWP types and application rates jointly affect soil biological and physico-chemical properties over the long term across contrasting soils. Understanding these effects is critical for optimizing nutrient recycling, enhancing soil fertility, and minimizing risks such as trace element accumulation. This study analyzes two long-term field experiments in contrasting soils in France to quantify the impacts of repeated OWP applications on soil chemical, physical, and biological properties. By linking cumulative OWP fluxes with observed soil responses, the study identifies both site-specific and generalizable effects, providing actionable guidance for sustainable OWP recycling and soil management.

## 2. Material and methods

### 2.1. Field experiments

This study utilized soil samples from two French long-term field experiments within the SOERE-PRO network: PROspective (Colmar, northeastern France, established in 2000) and QualiAgro (Feucherolles, northwestern France, established in 1998). PROspective features Calcic Cambisol (IUSS Working Group WRB 2014) with a semicontinental climate and a maize-wheat-sugarbeet-barley rotation. QualiAgro comprises Horthic Luvisol soil with an oceanic climate. Crop rotation is based on various cereals (wheat, barley, rye) and maize rotation in half of the experiment (QUAΔN), while leguminous crops (alfa alfa, faba bean) are also used in the other

half (QUAΔLEG) since 2014. Both sites implemented annual plowing (28 cm depth). All crop residues were incorporated in PROspective, while cereal straw were harvested until 2013 in QualiAgro. Although the two sites differ in location, climate, soil type, and crop rotation, their inclusion offers complementary contexts for evaluating the long-term effects of OWP under contrasting agro-environmental conditions.

The PROspective experiment comprised a control without OWP application (CON) and five OWP treatments: dehydrated urban SLU, green waste and SLU compost (GWS), biowaste compost (BIO), farmyard manure (FYM), composted FYM (FYMC). All OWP were applied every 2 years since 2000 at the same nitrogen rate per application (170 kg N ha⁻¹) and combined with two mineral nitrogen supplementation levels: (1) no mineral nitrogen (COLΔN⁻) and (2) optimal mineral nitrogen (COLΔN⁺). The QualiAgro experiment comprised a CON and four OWP treatments: BIO, GWS, FYM, and MSW compost, which were applied since 1998 every 2 years at the same C amount per application (4 t C ha⁻¹), with two fertilization levels: (1) optimal mineral nitrogen (QUAΔN) and (2) low mineral nitrogen (QUAΔLEG). Both experiments were arranged in a randomized block design with four replicates, with each block containing all OWP treatments and the corresponding control (CON) (figure S1). Changes in the experimental designs occurred in 2014, with detailed descriptions of management and the implemented modifications available in the supplementary material and cited (Cambier *et al* 2019, Chen *et al* 2022, 2024).

Specifically, at the PROspective site, SLU, FYM and FYMC had significantly higher C content than GWS and BIO (370, 399, 348, 291 and 258 g kg⁻¹ DM, respectively) (table S3). SLU had also a significantly higher total N content compared to other OWP (60 g kg⁻¹ DM and 24 g kg⁻¹ DM for SLU and the mean of the four other OWP, respectively). SLU and GWS had significantly higher P content compared to other OWP, while FYM and FYMC had significantly higher K content.

At the QualiAgro site, MSW and FYM had significantly higher C content than GWS and BIO (314, 327, 266 and 227 g kg⁻¹ respectively). GWS had also a significantly higher N and P content, while FYM was more enriched in N and K, compared to BIO and MSW. Detailed physicochemical properties and application rates of the OWP are provided in the supplementary material (tables S1–S5).

### 2.2. Soil analysis

Detailed soil analysis methodologies are available in supplementary material. In brief, composite soil samples were collected from the 0–28 cm (plow layer) in both sites, with sampling conducted in March at the PROspective site and in April at the QualiAgro
site. For each composite sample, at least five individual cores were collected randomly using an auger and homogenized. Chemical properties, including pH, total C and N, cation exchange capacity (CEC), Olsen-P (AP), and exchangeable K (EK), were analyzed using ISO standard methods. In PROspective, soil organic carbon (SOC) was specifically measured instead of total carbon (Chen et al 2022). Active and stable SOC proportions were determined using the PARTYsoc v2.0 model (Cécillon et al 2021) based on thermal analysis performed with Rock-Eval® 6 (Vinci Technologies, France). Extractable trace elements (Cd, Cr, Cu, Ni, Pb, Zn) were analyzed using EDTA chelated, as they better reflect soil quality and toxicity concerns (Gupta and Sinha 2007).

As physical soil properties, soil aggregate stability was assessed through fast wetting, wet stirring, and mechanical breakdown tests (Le Bissonnais 1996).

Concerning biological properties, enzymatic activities (phosphatase, arylsulfatase, β-glucosidase, urease, arylamidase) were measured per ISO 20130 and expressed as mU g⁻¹ corresponding to nanomoles of product released per minute per gram of dry soil (Cheviron et al 2022). Microbial diversity (bacteria and fungi) was analyzed using DNA sequencing. Microbial DNA was extracted following the standardized procedure ISO 11063 (Plassart et al 2012), and the DNA concentrations were used as estimates of soil microbial biomass (Dequiedt et al 2011). Bacterial and fungal diversity was characterized by OTUs richness, evenness, and Shannon index (Constancias et al 2015). Soil nematodes were extracted by Oostenbrink elutriation coupled with cotton-wool filter method (extraction ISO 23611-4) and identified by morphological identification under light microscope into: (1) bacterial feeders, (2) fungal feeders, (3) omnivore-predators, and (4) plant feeders following Yeates et al (1993). Enrichment index, structure index, maturity index, plant parasite index, nematode channel ratio and Shannon index were calculated to assess the nematode community (Ferris et al 2001, Yeates 2003).

## 2.3. Data analysis and statistical analysis

The statistical differences between each OWP treatment and its CON within the four experiments (COLΔN-, COLΔN+, QUAΔN, and QUAΔLEG) were evaluated using one-way ANOVA followed by Duncan's test. Prior to analysis, data were checked for normality (Shapiro-Wilk test) and homogeneity of variance (Levene's test); non-parametric alternatives were employed if the assumptions were violated. To reduce spatial heterogeneity, OWP treatment was compared with the CON within the same block, and Pearson correlation coefficients were calculated based on these differences to explore interrelationships among variables.

The gradient boosting model (GBM) was applied to evaluate the influence of OWP on soil characteristics. GBM is an ensemble machine-learning method that builds multiple regression trees sequentially and combines them to improve prediction accuracy. It captures nonlinear relationships and interactions among variables without requiring strict distributional assumptions (Friedman 2001). The cumulative budget of C, N, P, and K (ΔCΔbudget, ΔNΔbudget, ΔPΔbudget, ΔKΔbudget) between the OWP treatment and the CON within the same block were included as predictors, while the relative changes in soil properties served as response variables. The cumulative budgets were calculated as the difference between inputs (OWP, mineral fertilizers, and residues) and outputs (crop uptake and harvested residues). Other potential outputs, such as gaseous emissions and leaching, were not included due to the lack of the measurements and their relatively smaller magnitude compared with fertilization and crop uptake (Kros et al 2011, Welikhe et al 2023). An individual GBM model was calibrated for each soil property to specifically assess its response to the nutrient budgets. Hyperparameters were optimized via grid search using cross-validation with RMSE as the selection metric, while model performance was ultimately evaluated through cross-validated (CV-R²). All analyses were implemented using the 'caret' and 'GBM' packages in R (v.4.2.1). Detailed statistical methodologies are available in supplementary material.

## 3. Results and discussion

Long-term OWP application significantly influenced soil chemical, physical and biological properties at both sites compared to controls (figure 1). OWP application significantly increased the TC, TN, AP, EK, CEC, trace elements and alter soil pH in most treatments, aligning with numerous previous studies (Maillard and Angers 2014, Gross and Glaser 2021). For example, TC increased by a maximum of 73.0% with GWSΔLEG and TN of 71.6% with GWSΔN in QUA. Both active and stable C increased after OWP application, except for certain specific treatments, with a more pronounced rise in active C. Such an increase led to a decrease in the proportion of stable C, particularly at QUA, where reductions ranged from 16.7% to 29.9%, reflecting the stronger effect of OWP on labile C pools. This likely reflects OWP enhancing active C by providing labile C and stimulating microbial activity to convert plant residue into active C (Poirier et al 2013, Li et al 2018).

The increase in aggregate stability was limited compared to previous studies (Zhang et al 2014, He et al 2018, Chen et al 2021), particularly the findings by Annabi et al (2011) at site QUA. This discrepancy may be attributed to the revised experimental protocol implemented at QUA, which involved the
<figure><img src="image_4.png" /></figure>

incorporation of all crop residues into the soil since 2014. Crop residue return is widely recognized to enhance aggregate stability by increasing organic matter inputs, stimulating microbial activity, and improving soil structure, which may have masked or diluted the contribution of OWP application (Baloch et al 2025). Additionally, aggregate stability is highly sensitive to seasonal moisture fluctuations (Algayer et al 2014). Treatment contrasts are typically more evident when soil water content is close to field capacity (Bottinelli et al 2017). Since the sampling in this study was conducted in early spring, when soil water content and water repellency were relatively low, potential differences among treatments may have been obscured by variations in soil water content. These results indicate that the response of aggregate stability to OWP application is dynamic, shaped by interactions among climate, management, temporal factors, and OWP inputs. Selecting the optimal sampling time is inherently challenging, as it requires a compromise between capturing the distinct seasonal dynamics of various soil properties (Wuest 2015). Consequently, the findings should be interpreted within the specific environmental and temporal context of the study.

Despite the significant increased microbial biomass, bacterial and fungal diversity remained largely

unaffected, with the exception of a 37.8% decrease in fungal richness under FYMΔN- at COL. Enzyme activities, including β-glucosidase, urease, and arylamidase, were significantly enhanced by OWP treatments, with larger increases observed at QUA. Phosphatase activity increased only at QUA under GWS treatments, with rises of 35.4% and 46.7% observed in GWSΔN and GWSΔLEG, respectively. These results highlight the role of OWP in supplying labile C and modulating enzymatic functions (Tejada et al 2006). Nematode communities showed site- and OWP type-specific responses, and no significant changes for nematode-related indicators under COLΔN+. Bacterial-feeding nematodes increased under BIOΔN and FYMΔN in QUA, while fungal-feeding nematodes decreased by 51.8% under SLUΔN- in COL. Overall, nematode indices in COL remained largely stable, with maturity index, structure index, enrichment index, and Shannon index showing minimal variation. Notably, under FYMΔN in QUA, the enrichment index and Shannon index increased by 23.0% and 9.4%, respectively, while the maturity index declined slightly by 11.0%, suggesting that FYM application promotes a well-structured and complex soil nematode community (Liu et al 2016). Overall, most nematode indicators did not show significant responses to OWP application, partly due to
<figure><img src="image_5.png" /></figure>

high spatial variability. In Contrast, maturity index declined by 20.8%–24.3% in the QUAΔLEG experiment, accompanied by an average 89.2% reduction in the abundance of omnivorous-predatory nematodes while enrichment index increase (+40.7% in average). These results suggest that nutrient recycling function, especially nitrogen, is stimulated in this soil. This result is consistent with the presence of a legume crop on the plot at sampling time (DuPont et al 2009, Villenave and Chauvin et al 2018).

In general, more significant changes were observed in QUA than in COL (figure 2(a)), with the significant effects mainly occurred in soil chemical properties (85.7% of measured indicators changed at QUA), while changes in soil biological indicators and aggregate stability were less pronounced. The stronger effects in QUA likely resulted from its higher OWP input (4 t C ha⁻¹ vs. ~2 t C ha⁻¹ in COL), supplying more exogenous carbon, while crop residue export further emphasized OWP as the main carbon source. Additionally, site-specific responses were influenced by native soil properties, such as soil C and pH. Soils in QUA, characterized by lower baseline soil C content, likely demonstrated greater sensitivity to changes in biological communities and structure, and the application of equal amounts of C from different OWP types further facilitated a clearer assessment of their impacts on soil biology and differentiation among OWP types (Yanardağ et al 2017,

Sadet-Bourgeteau et al 2018). In contrast, soils in COL was rich in calcium carbonate leading to an alkaline pH, which could influence microbial communities and therefore result in the different biological responses (Lejon et al 2007). For instance, OWP inputs increased arylsulfatase activities in COL whereas not in QUA, probably due to the critical role of calcium in regulating arylsulfatase activity (Chen et al 2019).

Changes in soil properties showed strong correlations (figure 2(b)). TN and TC were related to most of the soil biological properties. Notably, a significant positive correlation was observed between soil microbial biomass and active soil C, rather than stable C (figure 2(b)), highlighting active soil C serves as an energy source and a critical limiting factor for microbial growth and proliferation (Zhang et al 2022). Trace elements exhibited the strongest association with other soil properties (figure 2). This was likely primarily due to trace elements originating from OWP application, as the simultaneous increase with OWP input. However, contrary to previous reports suggesting that enzymatic activity diminishes with increasing trace elements concentrations and availability (Moreno et al 2003), our results indicated that trace elements did not negatively affect phosphatase, β-glucosidase, arylsulfatase, and urease, only arylamidase activities were negative correlated with trace elements availability (figure 2(b)), likely due to the concentration-dependent negative effects of
<figure><img src="image_6.png" /><figcaption>**Figure 3.** The R² of test dataset in GBM and the relative contributions (%) of predictive variables (total P, K, N, and C budgets) for the GBM model of (a) soil chemical characteristics (b) soil nematodes (c) soil enzyme activities and (d) soil microbial.</figcaption></figure>

trace elements being offset by the positive influence of OWP application (Albiach *et al* 2000).

The GBM model performance in predicting soil property changes based on element flux budgets and their relative contributions is shown in figure 3. While the model accurately predicted soil chemical properties, its performance was moderate to low for enzyme activities, microbial, and nematode indicators. This discrepancy likely reflects the more direct link between element flux budgets and soil chemical processes (Chen *et al* 2022). In contrast, biological indicators are shaped by a wider range of ecological and temporal factors, and therefore may not follow a single trend over time (Griffiths *et al* 2001, Chernov and Zhelezova 2020).

The C and N budgets were critical for predicting changes in soil chemical properties, explaining up to 87% of the variation in CEC and more than 50% of the variance in soil enzyme and nematode indices. Soil AP and EK were predominantly determined by the P and K budgets, respectively. For enzyme activities, the C and N budgets remained key factors: the C budget primarily influenced phosphatase and β-glucosidase, while the N budget was the major driver for urease and arylamidase. C and P budgets were the main explanatory factor for Shannon and Simpson's diversity indices of enzyme activities. The C budget also played a dominant role in determining the nematodes enrichment index, maturity index, and accounting for the vast majority of the variation in soil microbial biomass. However, microbial richness and diversity showed a different pattern. While C and N budgets strongly predicted soil physicochemical properties and enzymatic activities,

they accounted for little of the variance in bacterial richness and Shannon diversity. Instead, K and P budgets contributed more substantially to these microbial indicators, highlighting the nuanced nutrient dependencies across different soil biological domains.

## 4. Conclusions

Long-term OWP application significantly alters soil chemical, physical, and biological properties, with effects largely influenced by application rates, OWP types, and native soil conditions. While improvements in soil chemical properties were consistent, enhancements in biological properties and aggregate stability were more spatially variable and less statistically robust. Indicators of biological activity (enzyme activity, microbial biomass, nematodes abundance) were mostly improved by OWP application while indicators of biological diversity were less affected. This suggests that while OWP provides resources for soil organisms, it may not sufficiently improve habitat conditions to enhance biodiversity. Therefore, complementary practices such as no tillage and crop diversification are likely needed to promote soil structure and biological diversity. Element flux budgets of OWP effectively explained shifts in soil chemical properties, though the improvement effect of OWP was limited in soils with high initial SOM, particularly when crop residues were also incorporated. Despite being a common concern, the increased availability of trace elements still resulted in low concentrations that did not adversely affect soil biological activity.
## Data availability statement

The data that support the findings of this study are
openly available at the following URL/DOI: https://
doi.org/10.5281/zenodo.15584379.

## Acknowledgment

We thank the technicians responsible of the
QualiAgro and PROspective experiment manage-
ment. The QualiAgro and PROspective field exper-
iment is part of the SOERE-PRO (network of long-
term experiments dedicated to the study of impacts
of organic waste product recycling) integrated as a
service of the ‘Investment in the Future’ infrastruc-
ture AnaEE-France, overseen by the French National
Research Agency (ANR-11-INBS-0001). This work
benefited of the use of the Biochem-Env platform
(DOI 10.15454/HA6V6Y, UMR 1402 ECOSYS,
INRAE IdF Versailles-Saclay centre), granted by the
French government by the Agence Nationale de la
Recherche under the France 2030 program, reference
‘ANR-24-INBS-0001’ AnaEE France. The QualiAgro
experiment was founded and is still supported by
INRAE and Veolia R&I. The PROspective experi-
ment is supported by INRAE and SMRA68. This
work was funded by Ademe (Graine PROTERR pro-
ject). Haotian Chen gratefully acknowledged fin-
ancial support from the Postdoctoral Fellowship
Program of China Postdoctoral Science Foundation
(GZC20252642).

## Author contributions

Haotian Chen ID 0000-0001-7312-9006
Conceptualization (equal), Methodology (equal), Software (lead), Visualization (lead), Writing – original draft (lead)

Florent Levavasseur ID 0000-0002-2164-3334
Conceptualization (equal), Funding acquisition (equal), Investigation (equal), Methodology (equal), Supervision (equal), Writing – original draft (supporting)

Pierre Barré ID 0000-0002-0822-0556
Methodology (equal), Supervision (equal), Visualization (equal), Writing – review & editing (equal)

François Baudin ID 0000-0003-3180-459X
Methodology (equal), Supervision (equal),
Visualization (equal), Writing – review &
editing (equal)

Sophie Sadet-Bourgeteau ID 0000-0002-7533-4289
Investigation (equal), Methodology (equal),
Supervision (equal), Validation (equal), Writing –
review & editing (equal)

Camille Chauvin
Methodology (equal), Resources (equal),
Validation (equal), Writing – review &
editing (equal)

Nathalie Cheviron ID 0000-0003-4395-4229
Methodology (equal), Validation (equal), Writing – review & editing (equal)

Christian Mougin ID 0000-0003-1333-9049
Methodology (equal), Supervision (equal),
Validation (equal), Writing – review &
editing (equal)

Amicie Delahaie ID 0000-0002-5971-4900
Methodology (equal), Supervision (equal),
Validation (equal), Writing – review &
editing (equal)

Safya Menasseri-Aubry ID 0000-0002-0036-8994
Methodology (equal), Supervision (equal),
Validation (equal), Writing – review &
editing (equal)

Cécile Villenave ID 0000-0003-3624-0498
Investigation (equal), Methodology (equal),
Resources (equal), Validation (equal), Writing –
review & editing (equal)

Sabine Houot ID 0000-0001-7297-7038
Conceptualization (equal), Funding acquisition (equal), Project administration (equal),
Supervision (equal), Writing – original draft (equal),
Writing – review & editing (equal)

## References

Albiach R, Canet R, Pomares F and Ingelmo F 2000 Microbial biomass content and enzymatic activities after the application of organic amendments to a horticultural soil *Bioresour. Technol.* **75** 43–48

Algayer B, Le Bissonnais Y and Darboux F 2014 Short-term dynamics of soil aggregate stability in the field *Soil Sci. Soc. Am. J.* **78** 1168–76

Annabi M, Le Bissonnais Y, Le Villio-Poitrenaud M and Houot S 2011 Improvement of soil aggregate stability by repeated applications of organic amendments to a cultivated silty loam soil *Agric. Ecosyst. Environ.* **144** 382–9

Araújo E, Strawn D G, Morra M, Moore A and Ferracciú Alleoni L R 2019 Association between extracted copper and dissolved organic matter in dairy-manure amended soils *Environ. Pollut.* **246** 1020–6

Baloch S B *et al* 2025 Crop Residue Management for Soil Health and Environmental Sustainability: a Comprehensive Review *J. Soil Sci. Plant Nutr.* **25** 7808–28

Böhme L, Langer U and Böhme F 2005 Microbial biomass, enzyme activities and microbial community structure in two European long-term field experiments *Agric. Ecosyst. Environ.* **109** 141–52

Bottinelli N, Angers D A, Hallaire V, Michot D, Le Guillou C, Cluzeau D, Heddadj D and Menasseri-Aubry S 2017 Tillage and fertilization practices affect soil aggregate stability in a Humic Cambisol of Northwest France *Soil Tillage Res.* **170** 14–17

Cambier P, Michaud A, Paradelo R, Germain M, Mercier V, Guérin-Lebourg A, Revallier A and Houot S 2019 Trace metal availability in soil horizons amended with various
urban waste composts during 17 years—monitoring and modelling *Sci. Total Environ.* 651 2961–74

Cécillon L *et al* 2021 Partitioning soil organic carbon into its centennialily stable and active fractions with statistical models based on Rock-Eval® thermalanalysis (PARTYSOCv2.0 and PARTYSOCv2.0EU) (preprint) *Biogeosciences* 14 3879–98

Chang E-H, Chung R-S and Tsai Y-H 2007 Effect of different application rates of organic fertilizer on soil enzyme activity and microbial population *Soil Sci. Plant Nutr.* 53 132–40

Chen H, Levavasseur F and Houot S 2024 Substitution of mineral N fertilizers with organic wastes in two long-term field experiments: dynamics and drivers of crop yields *Soil Use Manage.* 40 e13079

Chen H, Levavasseur F, Montenach D, Lollier M, Morel C and Houot S 2022 An 18-year field experiment to assess how various types of organic waste used at European regulatory rates sustain crop yields and C, N, P, and K dynamics in a French calcareous soil *Soil Tillage Res.* 221 105415

Chen H, Liu J, Li D, Xiao K and Wang K 2019 Controls on soil arylsulfatase activity at a regional scale *Eur. J. Soil Biol.* 90 9–14

Chen H, Yang H, Shi X, Li H, Wang X, Ren Q, Deng A, Song Z and Zhang W 2025 A bibliometric review of research trends in exogenous organic amendments application and soil leaching (1964–2024) *J. Hazard. Mater. Adv.* 19 100801

Chen M, Zhang S, Liu L, Wu L and Ding X 2021 Combined organic amendments and mineral fertilizer application increase rice yield by improving soil structure, P availability and root growth in saline-alkaline soil *Soil Tillage Res.* 212 105060

Chernov T I and Zhelezova A D 2020 The dynamics of soil microbial communities on different timescales: a review *Eurasian Soil Sci.* 53 643–52

Cheviron N *et al* 2022 Inter-laboratory validation of an ISO test method for measuring enzyme activities in soil samples using colorimetric substrates *Environ. Sci. Pollut. Res.* 29 29348–57

Constancias F *et al* 2015 Mapping and determinism of soil microbial community distribution across an agricultural landscape *MicrobiologyOpen* 4 505–17

Dequiedt S, Saby N P A, Lelievre M, Jolivet C, Thioulouse J, Toutain B, Arrouays D, Bispo A, Lemanceau P and Ranjard L 2011 Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management *Glob. Ecol. Biogeogr.* 20 641–52

Diacono M and Montemurro F 2010 Long-term effects of organic amendments on soil fertility. A review *Agron. Sustain. Dev.* 30 401–22

DuPont S T, Ferris H and Van Horn M 2009 Effects of cover crop quality and quantity on nematode-based soil food webs and nutrient cycling *Appl. Soil Ecol.* 41 157–67

Feng J, Burke I T, Chen X and Stewart D I 2023 Assessing metal contamination and speciation in sewage sludge: implications for soil application and environmental risk *Rev. Environ. Sci. Biotechnol.* 22 1037–58

Ferris H, Bongers T and de Goede R G M 2001 A framework for soil food web diagnostics: extension of the nematode faunal analysis concept *Appl. Soil Ecol.* 18 13–29

Friedman J H 2001 Greedy function approximation: a gradient boosting machine *Ann. Stat.* 29 1189–232

Garbuz S, Mackay A, Camps-Arbestain M, DeVantier B and Minor M 2021 Biochar amendment improves soil physico-chemical properties and alters root biomass and the soil food web in grazed pastures *Agric. Ecosyst. Environ.* 319 107517

Gómez-Muñoz B, Magid J and Jensen L S 2017 Nitrogen turnover, crop use efficiency and soil fertility in a long-term field experiment amended with different qualities of urban and agricultural waste *Agric. Ecosyst. Environ.* 240 300–13

Griffiths B S, Bonkowski M, Roy J and Ritz K 2001 Functional stability, substrate utilisation and biological indicators of

soils following environmental impacts *Appl. Soil Ecol.* 16 49–61

Gross A and Glaser B 2021 Meta-analysis on how manure application changes soil organic carbon storage *Sci. Rep.* 11 5516

Gupta A K and Sinha S 2007 Assessment of single extraction methods for the prediction of bioavailability of metals to Brassica juncea L. Czern. (var. Vaibhav) grown on tannery waste contaminated soil *J. Hazard. Mater.* 149 144–50

He Y, Xu C, Gu F, Wang Y and Chen J 2018 Soil aggregate stability improves greatly in response to soil water dynamics under natural rains in long-term organic fertilization *Soil Tillage Res.* 184 281–90

IUSS Working Group WRB 2014 International soil classification system for naming soils and creating legends for soil maps *World Soil Resources Reports* vol 106 (FAO)

Kros J, Frumau K F A, Hensen A and de Vries W 2011 Integrated analysis of the effects of agricultural management on nitrogen fluxes at landscape scale *Environ. Pollut.* 159 3171–82 Assessment of Nitrogen Fluxes to Air and Water from Site Scale to Continental Scale

Lazarova S, Coyne D, G. Rodríguez M G, Peteira B and Ciancio A 2021 Functional diversity of soil nematodes in relation to the impact of agriculture—a review *Diversity* 13 64

Le Bissonnais Y 1996 Aggregate stability and assessment of soil crustability and erodibility: I. Theory and methodology *Eur. J. Soil Sci.* 47 425–37

Lejon D P H, Sebastia J, Lamy I, Chaussod R and Ranjard L 2007 Relationships between soil organic status and microbial community density and genetic structure in two agricultural soils submitted to various types of organic management *Microb. Ecol.* 53 650–63

Li J, Wen Y, Li X, Li Y, Yang X, Lin Z, Song Z, Cooper J M and Zhao B 2018 Soil labile organic carbon fractions and soil organic carbon stocks as affected by long-term organic and mineral fertilization regimes in the North China Plain *Soil Tillage Res.* 175 281–90

Li J, Zhao B, Li X, Jiang R and Bing S H 2008 Effects of long-term combined application of organic and mineral fertilizers on microbial biomass, soil enzyme activities and soil fertility *Agric. Sci. China* 7 336–43

Liu T, Chen X, Hu F, Ran W, Shen Q, Li H and Whalen J K 2016 Carbon-rich organic fertilizers to increase soil biodiversity: evidence from a meta-analysis of nematode communities *Agric. Ecosyst. Environ.* 232 199–207

Maillard É and Angers D A 2014 Animal manure application and soil organic carbon stocks: a meta-analysis *Glob. Change Biol.* 20 666–79

Moreno J L, García C and Hernández T 2003 Toxic effect of cadmium and nickel on soil enzymes and the influence of adding sewage sludge *Eur. J. Soil Sci.* 54 377–86

Nahar M S, Grewal P S, Miller S A, Stinner D, Stinner B R, Kleinhenz M D, Wszelaki A and Doohan D 2006 Differential effects of raw and composted manure on nematode community, and its indicative value for soil microbial, physical and chemical properties *Appl. Soil Ecol.* 34 140–51

Nanda S and Berruti F 2021 Municipal solid waste management and landfilling technologies: a review *Environ. Chem. Lett.* 19 1433–56

Peltre C, Gregorich E G, Bruun S, Jensen L S and Magid J 2017 Repeated application of organic waste affects soil organic matter composition: evidence from thermal analysis, FTIR-PAS, amino sugars and lignin biomarkers *Soil Biol. Biochem.* 104 117–27

Plassart P *et al* 2012 Evaluation of the ISO standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure *PLoS One* 7 e44279

Poirier V, Angers D A, Rochette P and Whalen J K 2013 Initial soil organic carbon concentration influences the short-term retention of crop-residue carbon in the fine fraction of a heavy clay soil *Biol. Fertil. Soils* 49 527–35
Puissant J, Villenave C, Chauvin C, Plassard C, Blanchart E and Trap J 2021 Quantification of the global impact of agricultural practices on soil nematodes: a meta-analysis *Soil Biol. Biochem.* **161** 108383

Sadet-Bourgeteau S et al 2018 Lasting effect of repeated application of organic waste products on microbial communities in arable soils *Appl. Soil Ecol.* **125** 278–87

Sharma B, Vaish B, Monika, Singh U K, Singh P and Singh R P 2019 Recycling of organic wastes in agriculture: an environmental perspective *Int. J. Environ. Res.* **13** 409–29

Tejada M, Hernandez M T and Garcia C 2006 Application of two organic amendments on soil restoration: effects on the soil biological properties *J. Environ. Qual.* **35** 1010–7

Villenave C, Chauvin C, Santune C, Cérémonie H and Schneider A 2018 L'effet des légumineuses sur le fonctionnement biologique du sol : une méta-analyse sur la nématofaune du sol *Innov. Agron.* **69** 47

Welikhe P et al 2023 Uncertainty in phosphorus fluxes and budgets across the US long-term agroecosystem research network *J. Environ. Qual.* **52** 873–85

Wuest S B 2015 Seasonal variation in soil bulk density, organic nitrogen, available phosphorus, and pH *Soil Sci. Soc. Am. J.* **79** 1188–97

Yanardağ I H, Zornoza R, Bastida F, Büyükkiliç-Yanardağ A, García C, Faz A and Mermut A R 2017 Native soil organic matter conditions the response of microbial communities to organic inputs with different stability *Geoderma* **295** 1–9

Yeates G W 2003 Nematodes as soil indicators: functional and biodiversity aspects *Biol. Fertil. Soils* **37** 199–210

Yeates G W, Bongers T, De Goede R G M, Freckman D W and Georgieva S S 1993 Feeding habits in soil nematode families and genera—an outline for soil ecologists *J. Nematol.* **25** 315–31 (available at: https://pmc.ncbi.nlm.nih.gov/articles/PMC2619405/)

Zhang X, Wu X, Zhang S, Xing Y, Wang R and Liang W 2014 Organic amendment effects on aggregate-associated organic C, microbial biomass C and glomalin in agricultural soils *CATENA* **123** 188–94

Zhang Y, Gao W, Luan H, Tang J, Li R, Li M, Zhang H and Huang S 2022 Effects of a decade of organic fertilizer substitution on vegetable yield and soil phosphorus pools, phosphatase activities, and the microbial community in a greenhouse vegetable production system *J. Integr. Agric.* **21** 2119–33