La dominance mycorhizienne en tant que facteur local déterminant des processus écologiques forestiers

L'association mycorhizienne implique nombre de plantes et de champignons, étant sans doute la symbiose mutualiste la plus importante et la plus répandue au sein des écosystèmes terrestres. Étant donné que la plupart des arbres forment des mycorhizes arbusculaires ou des ectomycorhizes qui se distinguent par leur écophysiologie, il est judicieux de caractériser les forêts en fonction de leur dominance mycorhizienne afin d'en mesurer les impacts sur les processus écologiques. Ainsi, l'objectif de cette thèse est de quantifier les influences de la dominance mycorhizienne en forêt sur les propriétés abiotiques et biotiques du sol ayant un impact à l'échelle locale sur deux processus associés : la décomposition de la matière organique et la régulation de la diversité végétale. Les forêts étudiées, de dominance mycorhizienne très contrastée, présentent des propriétés physico-chimiques et des communautés microbiennes distinctes au niveau du sol, mais des patrons de distribution verticale des microorganismes du sol d'une similarité inattendue. Dans ces forêts nordiques décidues, la décomposition de la matière organique est favorisée dans les couches supérieures du sol, notamment grâce à la présence du réseau fongique et d'autant plus lorsque les ectomycorhizes prédominent, ce qui prouve l'aspect déterminant du contexte local. L'établissement d'arbres mycorhiziens arbusculaires peut être limité par la combinaison des conditions abiotiques et biotiques édaphiques de la forêt boréale, qui est dominée par les ectomycorhizes, contrairement aux forêts à dominance partagée entre mycorhize arbusculaire et ectomycorhize, où la diversité est favorisée à l'échelle de la communauté. Cette thèse démontre le rôle déterminant, au niveau local, exercé par la dominance mycorhizienne sur les processus écologiques, et soulève l'importance de l'hétérogénéité biotique et abiotique du sol pour mieux saisir le fonctionnement des écosystèmes terrestres.Mycorrhizas, which involve plants and fungi, are probably the most important and widespread mutual symbioses in terrestrial ecosystems. Since most trees form arbuscular mycorrhizas or ectomycorrhizas that are ecophysiologically distinct from each other, it is useful to characterize forests according to their mycorrhizal dominance in order to measure their respective impacts on ecological processes. The objective of this thesis is to quantify the impacts of forest mycorrhizal dominance on the abiotic and biotic properties of the soil, which influence at the local scale two associated processes: the decomposition of organic matter and the maintenance of plant diversity. The forests studied have opposite mycorrhizal dominance exhibit distinct soil physico-chemical properties and microbial communities, but more similar vertical distribution patterns of microorganisms than expected. Decomposition is favored by organic matter in the upper soil layers, but also by the presence of the fungal network, especially when ectomycorrhizas predominate, illustrating the importance of the local environmental context. Establishment of arbuscular mycorrhizal tree may be limited by the combination of abiotic and biotic edaphic factors of the boreal forest, which is ectomycorrhizal-dominated, in contrast to forests with shared dominance between arbuscular mycorrhizas and ectomycorrhizas, where tree species diversity is favored at the community level. This thesis demonstrates the decisive role, at the local scale, played by mycorrhizal dominance on ecological processes, and raises the importance of soil biotic and abiotic heterogeneity to better understand the functioning of terrestrial ecosystems

Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands

Ice-free areas are expanding worldwide due to dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. It has been proposed that the colonization dynamics of deglaciated terrains is different between surface and deep soils but that the heterogeneity between communities inhabiting surface and deep soils decreases through time. Nevertheless, tests of this hypothesis remain scarce, and it is unclear whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to test whether community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, and Oligochaeta) differ between the surface (0–5 cm) and deeper (7.5–20 cm) soil at different stages of development and across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution. The pattern was consistent across groups and soil depths. For Eukaryota and Mycota, alpha-diversity was highest at the surface. Time since glacier retreat explained more variation of community composition than depth. Beta-diversity between surface and deep layers decreased with time since glacier retreat, supporting the hypothesis that the first 20 cm of soil tends to homogenize through time. Several molecular operational taxonomic units of bacteria and fungi were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes

Foliar spectra and traits of bog plants across nitrogen deposition gradients

Bogs, as nutrient-poor ecosystems, are particularly sensitive to atmospheric nitrogen (N) deposition. Nitrogen deposition alters bog plant community composition and can limit their ability to sequester carbon (C). Spectroscopy is a promising approach for studying how N deposition affects bogs because of its ability to remotely determine changes in plant species composition in the long term as well as shorter-term changes in foliar chemistry. However, there is limited knowledge on the extent to which bog plants differ in their foliar spectral properties, how N deposition might affect those properties, and whether subtle inter- or intraspecific changes in foliar traits can be spectrally detected. The objective of the study was to assess the effect of N deposition on foliar traits and spectra. Usinganintegratingspherefittedtoafieldspectrometer,wemeasuredspectralpropertiesof leavesfromthefourmostcommonvascularplantspecies(Chamaedaphnecalyculata,Kalmiaangustifolia, RhododendrongroenlandicumandEriophorumvaginatum)inthreebogsinsouthernQuébecandOntario, Canada, exposed to different atmospheric N deposition levels, including one subjected to a 18-year N fertilization experiment. We also measured chemical and morphological properties of those leaves. We found detectable intraspecific changes in leaf structural traits and chemistry (namely chlorophyll b and N concentrations) with increasing N deposition and identified spectral regions that helped distinguish the site-specific populations within each species. Most of the variation in leaf spectral, chemical, and morphological properties was among species. As such, species had distinct spectral foliar signatures, allowing us to identify them with high accuracy with partial least squares discriminant analyses (PLSDA). Predictions of foliar traits from spectra using partial least squares regression (PLSR) were generally accurate, particularly for the concentrations of N and C, soluble C, leafwater,anddrymattercontent(<10%RMSEP).However,thesemulti-speciesPLSRmodelswerenot accuratewithinspecies,wheretherangeofvalueswasnarrow. Toimprovethedetectionofshort-term intraspecific changes in functional traits, models should be trained with more species-specific data. Our field study showing clear differences in foliar spectra and traits among species, and some within-speciesdifferencesduetoNdeposition,suggestthatspectroscopyisapromisingapproachfor assessing long-term vegetation changes in bogs subject to atmospheric pollution

Foliar Spectra and Traits of Bog Plants across Nitrogen Deposition Gradients

Bogs, as nutrient-poor ecosystems, are particularly sensitive to atmospheric nitrogen (N) deposition. Nitrogen deposition alters bog plant community composition and can limit their ability to sequester carbon (C). Spectroscopy is a promising approach for studying how N deposition affects bogs because of its ability to remotely determine changes in plant species composition in the long term as well as shorter-term changes in foliar chemistry. However, there is limited knowledge on the extent to which bog plants differ in their foliar spectral properties, how N deposition might affect those properties, and whether subtle inter- or intraspecific changes in foliar traits can be spectrally detected. The objective of the study was to assess the effect of N deposition on foliar traits and spectra. Using an integrating sphere fitted to a field spectrometer, we measured spectral properties of leaves from the four most common vascular plant species (Chamaedaphne calyculata, Kalmia angustifolia, Rhododendron groenlandicum and Eriophorum vaginatum) in three bogs in southern Qu&eacute;bec and Ontario, Canada, exposed to different atmospheric N deposition levels, including one subjected to a 18-year N fertilization experiment. We also measured chemical and morphological properties of those leaves. We found detectable intraspecific changes in leaf structural traits and chemistry (namely chlorophyll b and N concentrations) with increasing N deposition and identified spectral regions that helped distinguish the site-specific populations within each species. Most of the variation in leaf spectral, chemical, and morphological properties was among species. As such, species had distinct spectral foliar signatures, allowing us to identify them with high accuracy with partial least squares discriminant analyses (PLSDA). Predictions of foliar traits from spectra using partial least squares regression (PLSR) were generally accurate, particularly for the concentrations of N and C, soluble C, leaf water, and dry matter content (&lt;10% RMSEP). However, these multi-species PLSR models were not accurate within species, where the range of values was narrow. To improve the detection of short-term intraspecific changes in functional traits, models should be trained with more species-specific data. Our field study showing clear differences in foliar spectra and traits among species, and some within-species differences due to N deposition, suggest that spectroscopy is a promising approach for assessing long-term vegetation changes in bogs subject to atmospheric pollution

Urbanization impacts the taxonomic and functional structure of aquatic macroinvertebrate communities in a small Neotropical city

International audienceDue to habitat fragmentation, resource disruption and pollution, urbanization is one of the most destructive forms of anthropization affecting ecosystems worldwide. Generally, human-mediated perturbations dramatically alter species diversity in urban sites compared to the surroundings, thus influencing the functioning of the entire ecosystem. We investigated the taxonomic and functional diversity patterns of the aquatic macroinvertebrate communities in tank bromeliads by comparing those found in a small Neotropical city with those from an adjacent rural site. Changes in the quality of detrital inputs in relation to lower tree diversity and the presence of synanthropic species are likely important driving forces behind the observed structural changes in the urban site. Leaf-litter processors (i.e., shredders, scrapers) were positively affected in the urban site, while filter-feeders that process smaller particles produced by the activity of the shredders were negatively affected. Because we cannot ascertain whether the decline in filter-feeders is related to food web-mediated effects or to competitive exclusion (Aedes aegypti mosquitoes were present in urban bromeliads only), further studies are necessary to account for the effects of intra-guild competition or inter-guild facilitation

Toward a common set of functional traits for soil protists

International audienceProtists are major actors of soil communities and play key roles in shaping food webs, community assembly, and ecosystem processes, yet their functional diversity is understudied. High-throughput sequencing data have revealed their ubiquity and diversity, but lack of standardized traits has hampered the integration of functional information, limiting our understanding of soil ecosystems. Here, we propose a functional framework for soil protists, identify a set of common traits to characterize their functional diversity, and apply the framework on a broad-scale, real-world dataset. We reviewed studies on soil protists to identify the traits used in the literature, and define a framework based on 10 key traits that satisfy two criteria: availability of information, and applicability to most taxa. The framework was tested on a dataset of environmental DNA metabarcoding data from 1123 soil samples collected in 48 glacier forelands worldwide. Traits were assigned to the 570 Molecular Operational Taxonomic Units (MOTUs) detected in our dataset, leading to the production of a global trait-based dataset from glacier forelands. We estimated the functional space of protist communities and evaluated if the selected traits were effective in describing protist diversity. The functional space of protist communities showed that the MOTUs are clustered in three regions, mainly reflecting different nutritional and habitat preferences. The proposed framework is appropriate for multiple applications, including estimation of functional diversity and food web analyses, and provides a basis for ecological studies on soil protists, enabling the functional characterization of this essential but often neglected component of soil biodiversity

Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands

Ice-free areas are increasing worldwide due to the dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. Soils have a complex vertical structure. However, we know little about how microbial and animal communities differ across soil depths and development stages during the colonization of deglaciated terrains, how these differences evolve through time, and whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to describe how community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, Oligochaeta) differ between surface (0-5 cm) and relatively deep (7.5-20 cm) soils at different stages of development across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution; the pattern was consistent across different groups and soil depths. For Eukaryota, and particularly Mycota, alpha-diversity was generally the highest in soils close to the surface. Time since glacier retreat was a more important driver of community composition compared to soil depth; for nearly all the taxa, differences in community composition between surface and deep soils decreased with time since glacier retreat, suggesting that the development of soil and/or of vegetation tends to homogenize the first 20 cm of soil through time. Within both Bacteria and Mycota, several molecular operational taxonomic units were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes.Sequence data have been processed using the OBITools software suit (version 1.2.9) then filtered and analyzed in R (version 4.0). All scripts to reproduce data processing are provided here and described in the "Methods" section of the manuscript. See "Data Accessibility" section of the manuscript to access raw sequence data. Funding provided by: Horizon 2020 Framework ProgrammeCrossref Funder Registry ID: http://dx.doi.org/10.13039/100010661Award Number: Grant Agreement no. 772284 (IceCommunities)Funding provided by: H2020 European Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/100010663Award Number: 772284Libraries were prepared following the MetaFast protocol (Taberlet et al., 2018) and sequenced using the MiSeq (Bact02 and Fung02) or HiSeq 2500 (Arth02, Coll01, Euka02, Inse01, Olig01, Sper01) Illumina platforms (Illumina, San Diego, CA, USA) with a paired-end approach (2 × 250 bp for Bact02 and Fung02, and 2 × 150 bp for the others markers) at Fasteris (SA, Geneva, Switzerland). For each marker, the sequence depth corresponded to 10,000 reads per sample

Dynamics and drivers of mycorrhizal fungi after glacier retreat

International audienceSummary The development of terrestrial ecosystems depends greatly on plant mutualists such as mycorrhizal fungi. The global retreat of glaciers exposes nutrient‐poor substrates in extreme environments and provides a unique opportunity to study early successions of mycorrhizal fungi by assessing their dynamics and drivers. We combined environmental DNA metabarcoding and measurements of local conditions to assess the succession of mycorrhizal communities during soil development in 46 glacier forelands around the globe, testing whether dynamics and drivers differ between mycorrhizal types. Mycorrhizal fungi colonized deglaciated areas very quickly (< 10 yr), with arbuscular mycorrhizal fungi tending to become more diverse through time compared to ectomycorrhizal fungi. Both alpha‐ and beta‐diversity of arbuscular mycorrhizal fungi were significantly related to time since glacier retreat and plant communities, while microclimate and primary productivity were more important for ectomycorrhizal fungi. The richness and composition of mycorrhizal communities were also significantly explained by soil chemistry, highlighting the importance of microhabitat for community dynamics. The acceleration of ice melt and the modifications of microclimate forecasted by climate change scenarios are expected to impact the diversity of mycorrhizal partners. These changes could alter the interactions underlying biotic colonization and belowground–aboveground linkages, with multifaceted impacts on soil development and associated ecological processes

The importance of species addition ‘versus’ replacement varies over succession in plant communities after glacier retreat

International audienceThe mechanisms underlying plant succession remain highly debated. Due to the local scope of most studies, we lack a global quantification of the relative importance of species addition 'versus' replacement. We assessed the role of these processes in the variation (β-diversity) of plant communities colonizing the forelands of 46 retreating glaciers worldwide, using both environmental DNA and traditional surveys. Our findings indicate that addition and replacement concur in determining community changes in deglaciated sites, but their relative importance varied over time. Taxa addition dominated immediately after glacier retreat, as expected in harsh environments, while replacement became more important for late-successional communities. These changes were aligned with total β-diversity changes, which were more pronounced between early-successional communities than between late-successional communities (>50 yr since glacier retreat). Despite the complexity of community assembly during plant succession, the observed global pattern suggests a generalized shift from the dominance of facilitation and/or stochastic processes in early-successional communities to a predominance of competition later on