Camille Martinez-Almoyna

Arthropods play a vital role in ecosystems; yet, their distributions remain poorly understood, particularly in mountainous regions. This study delves into the modelling of the distribution of 31 foliar arthropod genera in the French Alps, using a comprehensive approach encompassing multi‐trophic sampling, community DNA metabarcoding and random forest models. The results underscore the significant importance of vegetation structure, such as herbaceous vegetation density, and forest density and heterogeneity, along with climate, in shaping the distributions of most arthropods. These responses to environmental gradients are consistent across trophic groups, with the exception of nectarivores, whose distributions are more sensitive to landscape structure and water availability. By leveraging community DNA metabarcoding, this study sheds light on the understudied drivers of arthropod distributions, emphasizing the importance of modelling across diverse trophic groups to anticipate arthropod responses to global change.

Soil trophic networks are key to biogeochemical cycles, in particular decomposition. However, few studies have yet quantified how microbial decomposition activity along environmental gradients is jointly driven by bacteria, fungi, and their respective consumers. Here, we quantified these direct and indirect effects on decomposition and contrasted them between forests and open habitats using multiple elevational gradients in the French Alps. While environmental control on microbial decomposition activity was comparable in the two habitats, the pathways and strengths of biotic predictors strongly differed. The fungal channel composition played a moderate role in forests, while the bacterial channel composition was critical in open habitats. Importantly, we found trophic regulation by consumers to be a key modulator of the direct environmental effects on decomposition in open habitats. These results highlight the need to integrate trophic regulation when predicting future ecosystem functioning.

Our knowledge of the factors influencing the distribution of soil organisms is limited to specific taxonomic groups. Consequently, our understanding of the drivers shaping the entire soil food web is constrained. To address this gap, we conducted an extensive soil biodiversity monitoring program in the French Alps, using environmental DNA to obtain multi-taxon data from 418 soil samples. The spatial structure of resulting soil food webs varied significantly between and within habitats. From forests to grasslands, we observed a shift in the abundance of trophic groups from fungal to bacterial feeding channels, reflecting different ecosystem functioning. Furthermore, forest food webs were more strongly spatially structured which could only partly be explained by abiotic conditions. Grassland food webs were more strongly driven by plant community composition and soil characteristics. Our findings provide valuable insights into how climate and land use changes may differentially affect soil food webs in mountains.

Although soil ecology has benefited from recent advances in describing the functional and trophic traits of soil organisms, data reuse for large-scale soil food-web reconstructions still faces challenges. These obstacles include: (1) most data on the trophic interactions and feeding behaviour of soil organisms being scattered across disparate repositories, without well-established standard for describing and structuring trophic datasets; (2) the existence of various competing terms, rather than consensus, to delineate feeding-related concepts such as diets, trophic groups, feeding processes, resource types, leading to ambiguities that hinder meaningful data integration from different studies; (3) considerable divergence in the trophic classification of numerous soil organisms, or even the lack of such classifications, leading to discrepancies in the resolution of reconstructed food webs and complicating the reuse and comparison of food-web models within synthetic studies. To address these issues, we introduce the Soil Food Web Ontology, a novel formal conceptual framework designed to foster agreement on the trophic ecology of soil organisms. This ontology represents a collaborative and ongoing endeavour aimed at establishing consensus and formal definitions for the array of concepts relevant to soil trophic ecology. Its primary objective is to enhance the accessibility, interpretation, combination, reuse, and automated processing of trophic data. By harmonising the terminology and fundamental principles of soil trophic ecology, we anticipate that the Soil Food Web Ontology will improve knowledge management within the field. It will help soil ecologists to better harness existing information regarding the feeding behaviours of soil organisms, facilitate more robust trophic classifications, streamline the reconstruction of soil food webs, and ultimately render food-web research more inclusive, reusable and reproducible.

Experiments and observations have shown that plants and soil biotic and abiotic properties are linked by feedback loops at local scale, in particular because plant functional traits determine the decomposability of the organic matter, which in turn influences the availability of nutrients essential for plant growth. However, the influence of plant-soil linkages on plant distributions and ecosystem functions is understudied at large biogeographic scales.Here, I present results of studies along 18 elevational gradients in the French Alps. In a first study, I show how the distributions of 44 plant species does not only depend on climate but also on soil physico-chemical properties and microbial decomposition activity and that plant functional traits play an important role in these distributions. Using hierarchical effects and multi-species distribution models, we found that, in addition to climate, the combination of soil C/N, as a measure of organic matter quality, and exoenzymatic activity, as a measure of microbial decomposition activity, strongly improved predictions of plant distributions. In accordance with the ‘fast-slow’ plant economics spectrum, species with conservative traits performed better under limiting nutrient conditions but were outcompeted by exploitative plants in more favorable environments, resulting in a spatial segregation of plants with different ecological strategies. In a second study, we moved from species to community level to estimate the impact of these plant-soil linkages on ecosystem functions. Using an undirect partial correlation network revealed that the influence of plant traits on the quality of organic matter links aboveground and belowground ecosystem functions. Finally, I show how specific soil trophic groups, notably saprophytic fungi, play key roles in these linkages. This result highlights that decomposition and the organisms involved in this process are the corner stone of ecosystem multifunctionality in nutrient depleted ecosystems such as mountains. Together these results highlight the importance of considering plants and soil biodiversity along with abiotic predictors for better understanding and modelling ecosystem processes and functions in a world where both climatic and soil systems are undergoing profound and rapid transformations.

While soil ecosystems undergo important modifications due to global change, the effect of soil properties on plant distributions is still poorly understood. Plant growth is not only controlled by soil physico‐chemistry but also by microbial activities through the decomposition of organic matter and the recycling of nutrients essential for plants. A growing body of evidence also suggests that plant functional traits modulate species’ response to environmental gradients. However, no study has yet contrasted the importance of soil physico‐chemistry, microbial activities and climate on plant species distributions, while accounting for how plant functional traits can influence species‐specific responses. Using hierarchical effects in a multi‐species distribution model, we investigate how four functional traits related to resource acquisition (plant height, leaf carbon to nitrogen ratio, leaf dry matter content and specific leaf area) modulate the response of 44 plant species to climatic variables, soil physico‐chemical properties and microbial decomposition activity (i.e. exoenzymatic activities) in the French Alps. Our hierarchical trait‐based model allowed to predict well 41 species according to the TSS statistic. In addition to climate, the combination of soil C/N, as a measure of organic matter quality, and exoenzymatic activity, as a measure of microbial decomposition activity, strongly improved predictions of plant distributions. Plant traits played an important role. In particular, species with conservative traits performed better under limiting nutrient conditions but were outcompeted by exploitative plants in more favorable environments. We demonstrate tight associations between microbial decomposition activity, plant functional traits associated to different resource acquisition strategies and plant distributions. This highlights the importance of plant–soil linkages for mountain plant distributions. These results are crucial for biodiversity modelling in a world where both climatic and soil systems are undergoing profound and rapid transformations.

Much effort has been devoted to better understanding the effects of environment and biodiversity on ecosystem functioning. However, few studies have moved beyond measuring biodiversity as species richness of a single group and/or focusing on a single ecosystem function. While there is a growing recognition that along environmental gradients, the compositional turnover of multiple trophic groups influences not only productivity but multiple ecosystem functions, we do not know yet which components of multi‐trophic β‐diversity influence which ecosystem functions. Here, we captured the biodiversity found in soils using environmental DNA to study total soil multi‐trophic β‐diversity (between all taxa regardless of their trophic group association), horizontal β‐diversities (β‐diversities within trophic groups) and vertical β‐diversity (β‐diversity across trophic groups) along a 1,000 m elevational gradient in the French Alps. Using path analyses, we quantified how these β‐diversity components mediate the effects of environmental turnover on the turnover of multiple ecosystem functions (i.e. productivity, N‐cycling, N‐leaching) and overall multifunctionality. While we found a strong direct effect of soil properties on the turnover of multiple ecosystem functions, we also found an indirect effect of climate and soil properties through multi‐trophic β‐diversity. More specifically, only total multi‐trophic β‐diversity and the horizontal β‐diversity of saprophytic fungi were strongly related to the turnover of multifunctionality and, to a lower extent, the turnover of productivity and N‐cycling. Our results suggest that decomposition processes and resulting nutrient availability are key to understand how ecosystem functions change along soil properties and climatic gradients in alpine ecosystems. By demonstrating how saprophytic fungi and their associated trophic groups can offset the direct responses of multiple ecosystem functions to environmental change, our study highlights the paramount importance of multi‐trophic diversity for better understanding ecosystem multifunctionality in a changing world. A freePlain Language Summarycan be found within the Supporting Information of this article.