Predicting spatial patterns of soil bacteria under current and future environmental conditions

Soil bacteria are largely missing from future biodiversity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for example on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and diversity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.Peer reviewe

Soil protist function varies with elevation in the Swiss Alps

Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400-1000 m), this ratio increases to 12 at high elevation (2000-3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.Peer reviewe

Archaeorhizomycetes Spatial Distribution in Soils Along Wide Elevational and Environmental Gradients Reveal Co-abundance Patterns With Other Fungal Saprobes and Potential Weathering Capacities

Archaeorhizomycetes, a widespread fungal class with a dominant presence in many soil environments, contains cryptic filamentous species forming plant-root associations whose role in terrestrial ecosystems remains unclear. Here, we apply a correlative approach to identify the abiotic and biotic environmental variables shaping the distribution of this fungal group. We used a DNA sequencing dataset containing Archaeorhizomycetes sequences and environmental variables from 103 sites, obtained through a random-stratified sampling in the Western Swiss Alps along a wide elevation gradient (>2,500 m). We observed that the relative abundance of Archaeorhizomycetes follows a “humped-shaped” curve. Fitted linear and quadratic generalized linear models revealed that both climatic (minimum temperature, precipitation sum, growing degree-days) and edaphic (carbon, hydrogen, organic carbon, aluminum oxide, and phyllosilicates) factors contribute to explaining the variation in Archaeorhizomycetes abundance. Furthermore, a network inference topology described significant co-abundance patterns between Archaeorhizomycetes and other saprotrophic and ectomycorrhizal fungal taxa. Overall, our results provide strong support to the hypothesis that Archaeorhizomycetes in this area have clear ecological requirements along wide, elevation-driven abiotic and biotic gradients. Additionally, correlations to soil redox parameters, particularly with phyllosilicates minerals, suggest Archaeorhizomycetes might be implied in biological rock weathering. Such soil taxa-environment studies along wide gradients are thus a useful complement to latitudinal field observations and culture-based approaches to uncover the ecological roles of cryptic soil organisms

Above- and belowground biogeography : Spatial modelling of a hidden system

Global change affects ecosystems in complex and diverse ways. Interdisciplinary and systemic approaches are required in order to understand the multiple changes we are facing. In this regard, species distribution models (SDMs), which relate species observations to the environmental conditions where they occur, are widely use to tackle this issue. SDMs allow for the spatial prédiction of plant species, as well as potential future distributions under différent scénarios of climate warming. However, the realized environmental niche concept behind the development of SDMs implies that many environmental factors must be simultaneously accounted for in order to predict plant species distributions. Climatic and topographie factors are often included, whereas soil factors are frequently neglected even though soil properties have been widely shown to influence plant growth and distribution. The paucity of soil information available spatially and the lack of comparative study on this subject are the main causes of this neglect. It is important to emphasise that this gap not only impacts the quality of plant SDMs, but also our compréhension of the soil-vegetation relationship, especially in light of recent global change. Therefore, a deeper understanding of the spatial and temporal variation of soil, végétation and the link between them is essential to optimally conserve and manage the pedosphere-atmosphere interface. In this thesis I aim to identify, the most crucial soil factors for explaining alpine plant distributions and, among those identified, which ones further improve the prédictive power of plant SDMs. In addition, I investigate the appropriate spatial modelling techniques to map key soil properties. Finally, I explore the spatial and temporal variation in the soil, the végétation and the link between them over more than 40 years with a re¬visitation study taking place in the Swiss Western Alps. During this thesis I showed that geochemical variables (e.g., CaO, pH or inorganic carbon content), water- related variables (i,e„ bulk soil water content or soil water holding capacity) and finally a variable that could reflect biotic habitat [i.e., <S13CSOM] improved the prédictive capacity of the models for the large majority of plant species inhabiting the Swiss Western Alps. Moreover, I assessed the utility of prédictive approaches for digital soil mapping. In particular, I applied a technique called "weighted ensemble of small models", to overcome the challenge of creating maps for difficult-to-measure soil variables when only a small number of field sites can be measured. Finally, I identified a lack of temporal relationship between plant and soil system évolution. More specifically, I observed that soi! and végétation respond to différent climate change drivers, which could lead to a partial decoupling of these two ecosystem components. Overall, this thesis reveals that the soil system is important for capturing a species' niche and that even simple soil measurements can increase our ability to model plant species distributions. Moreover, this thesis highlighted that the soil-vegetation interface is a critical and complex system from which we typically have a partial snapshot if sampled only at a given time. A global understanding of ail compartments of the soil- vegetation interface is required to truly understand the future évolution of ecosystem and to be able to establish useful and integrated conservation programs. Above- and belowground biogeography : Spatial modelling of a hidden system Aline Buri, Institute of Earth Surface Dynamics, FGSE --- La complexité des effets des changements globaux sur les écosystèmes requière une approche interdisciplinaire et systémique indispensable à l'appréhension des multiples changements auxquels nous sommes confrontés. À cet égard, les modèles prédictifs de distribution (MPD) des espèces végétales, servant à établir des liens entre les observations des individus et les conditions environnementales, constituent un instrument performant. Ils permettent de prévoir la distribution spatiale des espèces végétales et d'estimer l'évolution de cette distribution en fonction de différents scénarios de changement climatique. Cependant, le développement des MPD repose sur le concept de niche environnementale qui implique une prise en compte simultanée de nombreux facteurs environnementaux pour assurer la prédiction de la répartition des espèces végétales. Les facteurs climatiques et topographiques sont régulièrement intégrés dans ce type de modélisation, alors que les facteurs liés au sol sont souvent négligés, malgré les nombreuses recherches démonlrant l'influence des propriétés du sol sur la croissance et la distribution des plantes. La faible prise en compte du sol et de ses caractéristiques dans les MDPs, est principalement liée à un manque d'informations spatiales disponibles sur les sols, ainsi que l'absence d'études comparatives. Ceci n'a pas seulement pour effet d'affaiblir la qualité des MDP des plantes, mais se répercute plus largement sur notre compréhension du lien entre le sol et la végétation et de son évolution dans le contexte des changements globaux auxquels nous faisons face. Il est donc essentiel d'améliorer notre compréhension des variations spatiales et temporelles des propriétés du sol et de la végétation ainsi que du lien qui existe entre eux, pour pouvoir assurer un maintien et une gestion optimale de l'interface pédosphère-atmosphère. Cette thèse vise à identifier, dans les préalpes vaudoises, les facteurs de sol cruciaux pour la distribution des plantes alpines, et à déterminer lesquels contribuent à une amélioration du pouvoir prédictif des MDP des espèces végétales. Différentes techniques de modélisation spatiale ont été expérimentées dans l'objectif de sélectionner les plus performantes dans la cartographie des propriétés clés des sols. Les variations spatiales et temporelles du sol, de la végétation et de leur interrelation ont pu être analysées, en réétudiant des données récoltées il y a plus de 40 ans dans la région d'étude. Les travaux réalisés ont permis de démontrés que des variables géochimiques (p. ex., CaO, pH ou teneur en carbone inorganique], des variables liées à l'eau (c.-à-d., la teneur en eau du sol ou la capacité de rétention en eau du sol] et enfin une variable pouvant refléter l'habitat biotique (c.-à-d„ £13CSOM) améliorent les capacités prévisionnelles des modèles de la grande majorité des espèces végétales habitant les Préalpes Suisse. De plus, l'efficacité des approches prédictives pour la cartographie numérique des sols a pu être évaluée. La méthode des « ensembles pondérés de petits modèles » a notamment permis de surmonter le défi de la réalisation de cartes pour des variables de sol difficiles à mesurer. Finalement, une absence de relation temporelle entre l'évolution des systèmes végétaux et pédologiques a pu être établie. En effet, les recherches menées ont permis d'observer des réactions variables du sol et de la végétation aux différents facteurs du changement climatique, mettant ainsi en lumière un découplage partiel potentiel entre ces deux composantes de l'écosystème. De manière générale, cette thèse a révélé que le système pédologique est important pour capturer la niche d'une espèce et que des mesures de sol relativement basiques peuvent contribuer à améliorer les modélisations de la distribution des espèces végétales. De plus, ce travail a également permis d'illustrer dans quelle mesure l'interface sol-végétation est un système particulièrement critique et complexe dont l'aperçu n'est que partiel si l'échantillonnage n'est réalisé qu'à un moment précis. Pour conclure, ce travail souligne les enjeux d'une compréhension globale de toutes les caractéristiques de l'interface sol- végétation pour cerner efficacement l'évolution future des écosystèmes et être en mesure d'établir des programmes de conservation efficaces

Differential allocation and deployment of direct and indirect defences by Vicia sepium along elevation gradients

Dissecting drivers of plant defence investment remains central for understanding the assemblage of communities across different habitats. There is increasing evidence that direct defence strategies against herbivores, including secondary metabolites production, differ along ecological gradients in response to variation in biotic and abiotic conditions. In contrast, intraspecific variation in indirect defences remains unexplored.Here, we investigated variation in herbivory rate, resistance to herbivores and indirect defences in ant-attracting Vicia species along the elevation gradient of the Alps. Specifically, we compared volatile organic compounds (VOCs) and ant attraction in high- and low-elevation ecotypes.Consistent with adaptation to the lower herbivory conditions that we detected at higher elevations in the field, high-elevation plants were visited by fewer ants and were more susceptible to herbivore attack. In parallel, constitutive volatile organic compound production and subsequent ant attraction were lower in the high-elevation ecotypes.We observed an elevation-driven trade-off between constitutive and inducible production of VOCs and ant attraction along the environmental cline. At higher elevations, inducible defences increased, while constitutive defence decreased, suggesting that the high-elevation ecotypes compensate for lower indirect constitutive defences only after herbivore attack.Synthesis. Overall, direct and indirect defences of plants vary along elevation gradients. Our findings show that plant allocation to defences are subject to trade-offs depending on local conditions, and point to a feedback mechanism linking local herbivore pressure, predator abundance and the defence investment of plants

Greater topoclimatic control of above- versus below-ground communities

Assessing the degree to which climate explains the spatial distributions of different taxonomic and functional groups is essential for anticipating the effects of climate change on ecosystems. Most effort so far has focused on above-ground organisms, which offer only a partial view on the response of biodiversity to environmental gradients. Here including both above- and below-ground organisms, we quantified the degree of topoclimatic control on the occurrence patterns of >1,500 taxa and phylotypes along a c. 3,000 m elevation gradient, by fitting species distribution models. Higher model performances for animals and plants than for soil microbes (fungi, bacteria and protists) suggest that the direct influence of topoclimate is stronger on above-ground species than on below-ground microorganisms. Accordingly, direct climate change effects are predicted to be stronger for above-ground than for below-ground taxa, whereas factors expressing local soil microclimate and geochemistry are likely more important to explain and forecast the occurrence patterns of soil microbiota. Detailed mapping and future scenarios of soil microclimate and microhabitats, together with comparative studies of interacting and ecologically dependent above- and below-ground biota, are thus needed to understand and realistically forecast the future distribution of ecosystems.Peer reviewe

Greater topoclimatic control of above‐ versus below‐ground communities

Assessing the degree to which climate explains the spatial distributions of different taxonomic and functional groups is essential for anticipating the effects of climate change on ecosystems. Most effort so far has focused on above‐ground organisms, which offer only a partial view on the response of biodiversity to environmental gradients. Here including both above‐ and below‐ground organisms, we quantified the degree of topoclimatic control on the occurrence patterns of >1,500 taxa and phylotypes along a c. 3,000 m elevation gradient, by fitting species distribution models. Higher model performances for animals and plants than for soil microbes (fungi, bacteria and protists) suggest that the direct influence of topoclimate is stronger on above‐ground species than on below‐ground microorganisms. Accordingly, direct climate change effects are predicted to be stronger for above‐ground than for below‐ground taxa, whereas factors expressing local soil microclimate and geochemistry are likely more important to explain and forecast the occurrence patterns of soil microbiota. Detailed mapping and future scenarios of soil microclimate and microhabitats, together with comparative studies of interacting and ecologically dependent above‐ and below‐ground biota, are thus needed to understand and realistically forecast the future distribution of ecosystems

Long-term neurological symptoms after acute COVID-19 illness requiring hospitalization in adult patients: insights from the ISARIC-COVID-19 follow-up study

in this study we aimed to characterize the type and prevalence of neurological symptoms related to neurological long-COVID-19 from a large international multicenter cohort of adults after discharge from hospital for acute COVID-19