This systematic review shows that thinning effects on soil fauna abundance and species richness vary with thinning strategy and methodological approach. Positive responses are due to improved resources and favorable microclimate conditions, whereas negative responses were mainly associated with unfavorable microclimate conditions. However, current evidence remains fragmented, highlighting the need for standardized, comprehensive experiments to draw robust conclusions and generalize management recommendations. As harvesting and reforestation expand to meet bio-economy and renewable energy demands, forests face increasing pressure from both unsustainable practices and climate change. Forest thinning, widely used across many regions, alters forest structure, vegetation and microclimate, leading to cascading effects on soil biodiversity. Yet, compared to microbial communities, soil fauna remains comparatively understudied despite their diversity and central role in ecosystem functioning. We conducted a systematic review to assess how forest thinning influences soil fauna. Only 41 articles were identified: 27 focused on macrofauna (170 observations), 20 on mesofauna (96), and 6 on microfauna (13). These experiments varied considerably in their forest thinning strategies, sampling methods and soil fauna metrics, making it difficult to conclude whether soil fauna abundance or species richness respond to thinning in a consistent way. Both positive and negative effects were reported. Reducing forest cover can lead to less favorable microclimatic conditions with cascading negative effects on soil fauna. Conversely, the resulting increase in understory vegetation biomass and diversity caused by forest opening can create more heterogeneous microhabitats and resources with cascading positive effects on soil fauna. The observed variability in research approaches limits our mechanistic understanding of soil fauna response to thinning. We therefore emphasized recommendations for future research to improve methodological consistency and the robustness of findings.

Agroforestry is promoted as a sustainable agricultural practice that enhances biodiversity and ecosystem services, including natural pest control. However, its effects on arthropod communities, particularly across different trophic groups and seasonal dynamics, remain poorly understood. In this study, we assessed the impact of a Mediterranean alley-cropping agroforestry system on the abundance, diversity, and community composition of eight arthropod trophic groups, in Southern France. Using pan traps and pitfall traps, we sampled arthropods in agroforestry alleys and tree rows at three dates in spring 2023 (April, March and May), comparing them to monocultures and tree plantations. After identification, invertebrate taxa were classified into eight trophic groups based on current ecological knowledge. Agroforestry influenced arthropod abundance and diversity, though responses varied among trophic groups. Community composition, as reflected through a Principal Coordinates Analysis, was primarily structured by phenology rather than habitat type, with pronounced seasonal shifts across most trophic groups. Effect size analysis showed that tree rows supported a higher abundance of certain beneficial arthropods, emphasizing their role in agroforestry system function. Further research on multi-trophic interactions and long-term dynamics is needed to optimize agroforestry as a strategy for ecological intensification.

Home-Field Advantage (HFA) theory-positing that litter decomposes faster at its site of origin-allows us to disentangle the respective influences of litter quality, soil biota composition, and microclimate on shifts in litter decomposition following land use conversion. However, HFA remains poorly understood in tropical ecosystems with nutrient-poor soils. We conducted a full in situ litterbag transplant experiment across land use conversion driven by agricultural expansion in Madagascar: secondary natural forests, two stages of slash-and-burn fallows, and Eucalyptus plantations. Litter mass loss, HFA and Functional Breadth (FB)-defined as the capacity of soil biota to decompose different litter types with varying properties at similar rates-was assessed to distinguish the influence of the whole soil food web (coarse mesh) versus micro- and mesofauna-driven processes (fine mesh). These indicators were compared across land uses in relation to soil properties, litter quality, and soil biota composition. Forested land uses had lower microbial alpha-diversity but a higher proportion of specialist taxa than fallows. Natural forests showed markedly higher nematode and macrofauna alpha-diversity, as well as a greater proportion of omnivores and predator taxa, than all the other land uses. Litter decomposition was higher in natural forests, for both litterbag mesh sizes, during the early stage of decomposition, leading to higher FB, but no evidence of HFA effects was observed. Conversely, higher FB in natural forests and positive HFA in Eucalyptus plantations were observed at the late stage of decomposition, but only in coarse-mesh litterbags. This suggests that the decline in ecosystem functioning following forest conversion is linked to the loss of larger-sized macrofauna. Therefore, while Eucalyptus plantations caused less disturbance to microbial communities and early-stage decomposition processes than slash-and-burn fallows, they may not fully replace the multiple ecological roles of native forests, particularly for the functions requiring more specialised organisms and taxa.Read the free for this article on the Journal blog.

Soil biodiversity as a critical component of terrestrial ecosystems and their functioning varies across spatial scales and environmental conditions. However, it remains unclear whether and how biodiversity patterns co-vary among different soil taxa across ecosystems. In this study, we compared diversity patterns of plants, earthworms, nematodes, bacteria, and fungi, as five major groups of soil organisms, across six strongly contrasting ecosystems ranging from mountain peatland to crop fields, including within-ecosystem variation in soil moisture. We hypothesized co-variation in taxonomic richness (alpha diversity) and composition (beta diversity) of multiple groups of soil organisms across ecosystems, moisture conditions and spatial scales. In partial contrast to our initial hypothesis, co-variation in the taxonomic richness among these groups was limited, though significant positive associations were found among bacteria, fungi, and earthworms across all sites. Plant diversity showed distinct associations with soil organism diversity, particularly with earthworms and bacteria, highlighting above-belowground biodiversity linkages. Beta diversity showed substantial co-variation among all soil organism groups, reflecting a spatial coupling of their communities that was influenced by differences in soil moisture conditions. These patterns were more pronounced in near-natural and no-till agroecosystems compared to conventional agricultural systems. Our results highlight that ecosystem type shapes broad-scale taxonomic richness, while local soil moisture critically influences soil biodiversity and spatial community composition, emphasizing the multi-scale drivers of soil biodiversity.

Understanding how crop management influence soil biodiversity is crucial for maintaining soil functions and long-term ecosystem health. Nematodes are key bioindicators of soil quality due to their sensitivity to both soil management and water availability. In Mediterranean regions, where drought events are becoming more frequent and intense under climate change, it is essential to identity practices that can buffer their effects. Here, we assessed the combined effect of crop management and irrigation on soil nematode communities in maize crops in southern France. The experiment compared four treatments: conservation agriculture (CA) vs. conventional tillage (CT), each under irrigated and non-irrigated conditions. Soil samples were collected in March 2022 (0-10 cm depth), and soil nematodes were extracted, counted and identified with subsequent calculation of community and functional indices. Total nematode density was 70% higher under CA compared to CT. Irrigation increased total nematode density (+30%) under CA plots, whereas it had a negative effect under CT plots. Under no-irrigation, CA maintained high predator densities and reduced plant-parasitic nematodes compared to CT. Consistently, irrigation under CT favored opportunistic and plant parasite taxa. Overall, our exploratory insights underlined that CA supports a more stable and complex soil food-web, helping to mitigate the disturbing effects of irrigation on soil nematode communities. These findings highlight CA as a promising strategy to enhance soil resilience to drought in Mediterranean agroecosystems. Larger sample sizes and repeated seasonal sampling would be needed to confirm and generalize these patterns.

Plant-parasitic nematodes are known to impair plant development and can cause severe crop loss. Agroforestry is a promising land use management system for the preservation of soil fertility and biodiversity conservation, but very few studies have focused on the regulation of plant-parasitic nematodes with the inclusion of tree alleys in cropping systems. In this study, the capacity of the soil to suppress plant-parasitic nematodes was assessed in Southern France. Fresh and heated soils from different combinations of land use (monospecific crop, agroforestry or tree plantation) and plant cover (crop or tree) were tested for their capacity to suppress Meloidogyne javanica in a laboratory assay. In the samples taken under tree cover, the suppressive capacity of fresh soils was improved compared to that of the monospecific crop samples. As the suppressive capacity of the heated soils remained low, we considered that soil fauna was responsible for part of the soil suppressiveness. The characterization of nematode communities revealed no Meloidogyne spp. on the experimental site, but other plant-parasitic nematodes were found. The total density of Pratylenchus spp. was lower while the relative density of Helicotylenchus spp. was higher under tree cover, compared with the monospecific crop soils. In agroforestry, the relative density of herbivores was ca 200 % higher under tree cover compared to under crop cover but the parasitic pressure (assessed by the Plant-Parasitic Index/Maturity Index ratio) was ca 30 % lower. Moreover, the crop soils had the highest Enrichment Index while the tree row soils in agroforestry had the highest Structural Index. The suppressive capacity in agroforestry was associated with a specific nematofauna, including more predatory taxa than in the monospecific crop. This study showed that including trees in a cropping system in a Mediterranean area created a favorable niche for potential herbivore regulators among the soil fauna. Further investigations are required to validate the regulation of plant-parasitic nematodes, and to disentangle the complex interactions explaining it in agroforestry.

In tropical humid Africa, sandy soils under periodically burnt herbaceous savannas exhibit generally low carbon (C) content and nitrogen (N) availability. Savanna afforestation may overcome these limitations through changes in soil functioning, yet these processes still need to be explored. In this study, we investigated whether changes in the composition of soil micro-food web may explain soil C and N cycling increases following savanna afforestation. We conducted a 7-year experiment in Congo including Eucalyptus and N2-fixing Acacia monocultures and Eucalyptus-Acacia mixtures established on former herbaceous savannas. We assessed in each of these modalities the soil attributes: organic C and N, pHH2O, nitrate, ammonium, net C and N mineralization and nitrification rates, along with the abundances of bacteria, fungi, nematodes, ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the top 10 cm layer. Afforestation of savannas with Eucalyptus for timber production increased soil C by 1.7 times, soil net N mineralization rates by 1.9 times and soil inorganic nitrogen by 2.5 times. Mixed AcaciaEucalyptus and Acacia monoculture plantations further improved the rate of net nitrogen mineralization by a factor of 1.4 and soil inorganic N by a factor of 2.3 compared with Eucalyptus monocultures. These changes were associated with a gradual increase in AOA abundance from savanna to Eucalyptus monoculture, Eucalyptus-Acacia mixtures and finally Acacia monoculture. Savanna afforestation resulted in a significant increase in the absolute abundance of bacterial-feeding nematodes by 678 %, but to a decrease in the abundance of both fungal-feeders, and omnivores and predators. Increase in N cycling was positively associated with both AOA and nematode bacterial-feeder abundances, underlining the importance of monitoring micro-food web structure to understand better how land use changes affect soil biogeochemical cycling in the context of tropical afforestation.

Conservation agriculture systems leaning on living mulch show particular promise thanks to their benefits on soil biological activity, but weed pressure in these cropping systems strongly depends on the amount of mulch. To assess the ability of these cropping systems to sustain soil health considering pest regulation, we investigated the combined influence of tillage and crop management (conventional, CONV and no-tillage with living mulch, NTLM) and weeding regimes (weekly hand-weeding and none) on soil free-living and plant-parasitic nematodes. To do so, we leant on a split-plot field experiment in Madagascar highlands 7 years after crop establishment. Overall, the abundance of soil free-living nematodes was 3.9 times higher in NTLM than CONV, primarily due to a preferential increase in fungal-feeders (+585 %) and in omnivores and predators (+633 %). Conversely, plantparasitic nematodes had the same abundance in both systems, but not the same taxonomic composition, with a dominance of endoparasitic taxa in CONV, and of ectoparasitic taxa in NTLM. Weeding management affected only populations in NTLM, leading to increased abundance of fungal-feeders (+191 %) and lower abundance of semi-endoparasites (-89 %) in the unweeded systems, which were associated with changes in plant community diversity. In this context, conservation agriculture and no-weeding proved beneficial for promoting free-living nematode communities but also to decrease the overall plant parasitic pressure through plant diversification. As no weeding may nonetheless affect crop yield, a trade-off has therefore to be found to promote soil ecosystem services while maintaining crop production.

Cushion plants, which dominate nival ecosystems, are known to host a large diversity of plant, microbe, and animal life. However, a comprehensive assessment of this diversity is still lacking, particularly with regard to invertebrate soil fauna. In this study, we sampled soil beneath cushion plants in various climatic and geological conditions throughout the French Alps. Our results demonstrate that cushion plants host a remarkably high abundance and diversity of invertebrates, with some individual cushions hosting nearly 400 specimens belonging to 15 different families. Across all samples, 8845 specimens were found. The taxonomic diversity is particularly notable, with groups such as Collembola, Acari, and Nematoda, as well as Gastropoda, Diptera, Coleoptera, Hymenoptera, and Hemiptera. In total, 44 different families were identified. In particular, our findings show that cushion plants not only function as habitats for adult invertebrates, but also as site for the egg laying and larval development of several insect groups, including Diptera, Hemiptera, and Lepidoptera. In addition, different species of cushion plant tend to host distinct invertebrate communities, which makes them a key driver spatial variation in invertebrate populations. However, the factors determining the alpha diversity of invertebrates assemblages in nival environments remain unclear. Overall, our results emphasize the key role of cushion plants in maintaining biodiversity in the nival vegetation belt.

In Northern Vietnam, farmers are converting significant areas of their allocated rice paddy fields into organic tea plantations to increase and diversify their income. Our previous study indicated that as tea soil is strongly acidic, suitable solutions such as lime application can help to mitigate soil acidity. However, to date, the impact of these strategies on soil chemical properties, soil biodiversity and crop productivity in tea farming has not been thoroughly investigated. This study examined how liming affects soil chemical and biological indicators using amplicon Illumina sequencing analyses, and crop productivity in organic tea farming with different land use histories. Nine months after applying lime, soil pH increased by 0.4 units, soil organic matter content by 0.28 %, and P availability by 23.1 mg/100 g while soil exchangeable Al and Mn were reduced. The abundance and composition of macrofauna in soil and organic mulch were altered by lime addition but were not significantly correlated to land use history. Liming also enhanced tea root mycorrhization by native arbuscular mycorrhizal fungi (AMF) and tea yield, regardless of land use history. Despite this, the relative abundance and composition of soil bacteria, fungi, and AMF showed a significant response to land use history rather than liming. This study provides valuable insights into how soil liming and land use history affect tea soil food webs, plant growth, and tea organic yields, and suggests that liming could be an effective strategy to improve acidic soils, restore soil biodiversity in these soils, and sustain crop productivity in this tropical region.

Nematodes provide essential ecosystem functions, yet their specific contributions remain insufficiently quantified. Among them, bacterivorous nematodes (BN) are abundant and functionally diverse, but their ecological roles are often overlooked. Here, we combine a comprehensive literature review with a meta-analysis to assess the contribution of BN to terrestrial ecosystem functions from controlled experiments. Across 1131 effect sizes, our meta-analysis shows that BN significantly promote key soil processes: they increase microbial biomass by 20%, microbial respiration by 31%, and enhance nutrient cycling, raising soil-available N and P by 21% and 17%, respectively. They regulate bacterial community composition through selective feeding and dispersal, and can stimulate enzymatic activities compared to soil without BN. BN also improve shoot and total biomass by 19% and 13%, shoot N amount by 22%, and root N amount by 35%. In addition, BN influence root morphological traits (e.g., lengths, branching) and can modulate mutualistic interactions, particularly with mycorrhizae and rhizobia. Finally, BN can also contribute to the degradation of soil contaminants, the regulation of pathogens, and carbon sequestration. However, these effects are modulated by several factors; they vary widely with nematode species, life-history strategy, soil nutrient status (especially soil C:N ratio and P availability), and experiment duration. We discuss underlying mechanisms, including consumer-driven nutrient recycling and microbial stimulation, and identify major research gaps in the functional ecology of soil BN. Our synthesis highlights BN as pivotal players in soil functioning and calls for broader recognition of their roles in sustainable agroecosystem management.

Millet/cowpea intercropping is a promoted practice in Sub-Saharan agriculture. However, because cowpea is known as a host for plant-parasitic nematodes that may also infect millet, we examined whether intercropping may increase the risk of nematode-mediated millet damage, and if this risk may be controlled by organic amendments. In twelve Senegalese farmers’ fields which had been either non-manured or regularly manured over the past 10 years at least, we assessed the effects of intercropping millet and cowpea on the abundance of free-living and plant-parasitic nematodes, ecological indices, and land equivalent ratios (LER). Six fields were manured, and six non-manured. Each field included four plots: millet and cowpea as pure stands, and two plots with millet intercropped with cowpea sown at two densities. Soil nematofauna was evaluated before sowing and at cowpea flowering. Soil nematofauna was dominated by plant-parasitic nematodes. Before manure application and crop sowing, regularly manured fields had higher structure indices of nematofauna than non-manured ones, and Pratylenchus was almost absent. At crop flowering, abundance of Pratylenchus increased and was drastically higher in pure cowpea (149 individuals 100 g −1 dry soil) than in intercropping and pure millet (18 and 17 individuals 100 g −1 dry soil, respectively), regardless of the manuring regime. Manuring had significant positive effects on various bacterivorous families, on fungivorous and plant-parasitic trophic groups, but not on Pratylenchus . Millet and cowpea yields of manured fields were the highest, regardless of cropping pattern. LER averaged 1.7 and 1.5 in manured and non-manured intercropping, respectively. Regardless of the treatments, ecological indices indicated that the soil food web was undisturbed, with moderate enrichment, and suppressive against crop pests. Intercropping millet with cowpea, even in poorly manured fields and with high cowpea density, constitutes an appropriate way to improve productivity without increasing Pratylenchus pressure in nutrient-poor soils of central Senegal.

Summary The lack of affordable mineral fertilizers and scarcity of organic materials cause decline in soil fertility for smallholder farmers and producers in the highlands of Madagascar, challenging crop productivity. To fulfill plant growth and nutrition, we explored the effect of 132 combinations of 17 different fertilizing resources, both organic and mineral, on rice growth and nutrition using a greenhouse experiment. Two clustering approaches were used to evaluate the effects of fertilizing resources: elemental clustering and functional clustering. Elemental clustering grouped resources based on their elemental intrinsic composition, while functional clustering grouped resources based on their effect in improving plant growth and nutrition when combined in soil. We found that some resources closely grouped based on their elemental composition exhibited different effects on plant growth and nutrition when combined in soil. Zebu horn emerged as a particular organic resource in elemental clustering, and a key resource in functional clustering by promoting plant growth and nutrition when combined with other resources in soil. Its unique elemental composition played a significant role in driving positive interactions with other resources. We proposed to extend the concept of ‘assembly motif’ within soil fertilization strategy, suggesting that the combination of functional groups of resources determines better their fertilizing effect than their elemental composition. Resources inducing high interaction effects should be combined with those having high elemental composition to optimize crop productivity.

Forest management strategies can effectively mitigate the impacts of drought on tree species, but their effects on soil fauna remain largely unexplored. Among soil organisms, soil nematodes can serve as valuable bioindicators to assess the impact of forest management on soil biodiversity and soil functioning. Consequently, we investigated two related questions in a Mediterranean Pinus halepensis Mill. forest located in southeastern France. First, how do soil nematodes respond to forest management practices? Second, can forest management practices help modulate the effects of Mediterranean summer drought on these soil organisms? We conducted a field experiment in which we explored the influence of two forest management techniques-tree thinning (intense, moderate, or absent) and understory removal (shrubs present or absent)-on soil nematodes before and after the summer drought. We found that only total and bacterivorous nematode abundances were positively influenced by the forest management practices. The highest values were observed under conditions of intense thinning combined with shrub presence, with an average of 97,509 individuals per kg of dry soil. In contrast, the abundances of all nematodes, with the exception of predaceous nematodes, were lower after the summer drought with a reduction ranging from-55 % to-82 %. Total, bacterivorous, and fungivorous nematode abundances were less negatively affected by the summer drought under conditions of moderate thinning when shrubs were present versus absent. More generally, we discovered that bacterivorous and fungivorous nematodes were particularly sensitive to the forest management practices and the summer drought. It is thus apparent that habitat alterations induced by forest management can strongly affect nematode community structure and could therefore prompt shifts in ecosystem functioning. Finally, this study highlights that, in forests, understory vegetation can have significant positive impacts on soil nematode populations when severe dry periods occur.

Although involved in key functions of the terrestrial ecosystems, the activity and the diversity of soil microorganisms can be severely limited by energy and nutrients in weathered tropical soils. To optimize nutrient cycling for crop nutrition, assessing which nutrients limit the activity of the microbial food web is thus essential. This was our aim in this study carried out on a tropical ferrallitic soil from a natural grassland in Madagascar. For this purpose, we employed an innovative nutrient-omission approach in microcosms to test the distinct effects of omitting C, six nutrients (N, P, K, S, Ca, Mg) and a cocktail of micronutrients (B, Mn, Cu, Na and Mo) on the composition, biomass and activities of the microbial community and on the abundance and biomass of their nematode grazers. C and P were identified as primary limitations, but other nutrients (N, Mg and S) played significant roles as co-limiting factors. Some bacterial and fungal taxa were significantly associated to specific nutrient deficiencies and can act as biological indicators. Additionally, the abundance and biomass of microbial-feeding nematodes provided valuable insights into the responses of the soil microbial community to nutrient deficiencies. These findings contribute to our understanding of nutrient dynamics and microbial community growth in tropical grassland ecosystems and have implications for sustainable crop fertility management and ecosystem ecology in similar environments.

In the Highlands of Madagascar, providing organic amendments (OAs) is the main farmer fertilization practice in upland rainfed agrosystems dominated by nutrient-depleted Ferralsols. Therefore, enhancing the performance of OAs on plant functions is particularly important for improving both plant productivity and agrosystem sustainability. Earthworms are well-known ecosystem engineers involved in the decomposition of organic matter and play a critical role in nutrient turnover. Inoculating earthworms could be a promising approach to improve the fertilizer performance of OAs. However, there is limited knowledge regarding the interaction between earthworms and OAs of varying biochemical qualities on plant growth and nutrition. In this microcosm experiment, we assessed the effect of different types of OAs (i.e., unamended control, conventional farmyard manure, kraal manure, improved farmyard manure, compost, vermicompost, urban waste, taroka, poultry droppings, pig manure) and earthworm inoculation (with and without earthworms) on the growth and nutrition of rice. The endogeic species Pontoscolex corethrurus (Rhinodrilidae) was used in the experiment. After eight weeks of growth, the poultry droppings had the best fertilizer performance, followed by improved farmyard manure and pig manure in treatments without earthworms. The main driver of fertilizer performance appeared to be the quality of OAs. However, other mechanisms, such as an increase in soil pH, may also play a significant role. The inoculation of earthworms significantly enhanced the fertilizer performance of OAs but the magnitude of this enhancement depends on the OAs. Overall, OAs with low fertilizer performance showed a more pronounced response to earthworms. Additionally, earthworms improved the performance of high-quality OAs likely by enhancing the availability of P and Mg. Our findings emphasize the synergistic effects of earthworms and OAs of various qualities on plant growth and nutrition, offering valuable insights for improving fertilization practices in nutrient-poor Ferralsols of Madagascar.

Upland rainfed rice cropping in the highlands of Madagascar is strongly limited by poor Ferralsol mineral fertility. There is an urgent need to identify efficient and sustainable fertilization practices that improve soil fertility without inducing pest proliferation. For that purpose, using a field trial for 2 successive years, we tested the effect of 16 fertilization practices on the abundance and taxonomic diversity of soil active nematodes, which are known to be biological indicators of soil fertility. We tested both fertilization practices traditionally used by farmers and innovative ones based on the assemblage of organic, mineral and biological (earthworms and mycorrhiza) fertilizers. We identified eight types of practices: (1) no fertilization; (2) fertilization with NPK and urea; (3) low input rates (3 t dry matter ha−1) of organic fertilizers without NPK; (4) low input rates of organic fertilizers with NPK; (5) high input rates (6 t dry matter ha−1) of organic fertilizers; (6) high input rates of organic fertilizers with mineral fertilizers; (7) high input rates of a mixture of organic fertilizers and (8) high input rates of a mixture of organic fertilizer with mineral fertilizers. After 2 years, we identified 41 soil nematode taxa. The taxonomic composition of the nematode communities revealed that Ferralsols are a stressful environment for the soil biota. The low abundance of opportunistic bacterivores indicated that the different fertilization practices did not significantly and deeply increase the amount of plant-available nutrients, and thus soil fertility. However, organic fertilizers significantly increased the abundance of omni-predators, indicating a moderately mature food web. Some practices induced worrying increases in the endoparasitic Meloidogyne and Pratylenchus, which requires monitoring of root symptoms to avoid the establishment of their populations. Monitor soil nematode communities in upland rice growing on Ferralsols could be used as agronomic indicators to promote sustainable rice production systems in Madagascar.