Integrating environmental DNA, niche modeling and trait-based ecology to explore the plant-soil-microbial continuum under climate and land-use change

This thesis investigates how the integration of trait-based ecology, environmental DNA metabarcoding, and species distribution modelling can improve ecological inference in plant-soil systems across spatial and organizational scales, and how plant distributions, functional strategies, and plant-associated microbial communities respond to climate and land-use change. The central premise is that ecological responses – particularly under rapidly changing and unstable global-change scenarios – cannot be robustly interpreted through any single axis of information, whether species distributions, functional traits, or microbial composition alone, as each captures only a partial representation of the processes shaping habitats, species performance, and spatial redistribution. The thesis therefore develops and applies an integrative framework grounded in the plant- soil-microbial continuum, explicitly linking above- and belowground compartments and combining correlative prediction (species distribution models) with functional interpretation (plant traits) and molecular characterization of soil and rootassociated microbial diversity (metabarcoding). This framework is applied to highly transitional ecological contexts shaped by climate change and anthropogenic land-use or management change. These include high-elevation and alpine landscapes experiencing upslope shifts in plant communities under recent climatic change; northern boreal regions often considered potential northern refugia in response to ongoing northward shifts in plant ranges; and agrosystems undergoing management transitions based on nature-based solutions. The four case studies were selected because they lie at the intersection of these paradigms and allow complex ecological dynamics to be examined through a deliberately multidisciplinary perspective. Across systems, the thesis is structured around four broad ecological questions which are intended as guiding principles that reflect current conceptual challenges in plant and microbial ecology under global change: (i) Do functional and trait-based approaches complement or provide greater ecological resolution than taxonomy-based methods in disentangling ecological processes along environmental gradients? How effectively do they capture transitional dynamics under climatic and land-use change? (ii) Is it still meaningful to address plant ecology and soil microbial ecology as separate research paradigms, or does the study of ecological responses under contemporary global change require their explicit integration within a plant-soil-microbial continuum framework? (iii) Can highly specific ecological contexts – such as high-elevation landscapes or managed agrosystems – reveal generalizable ecological patterns when approached multidisciplinarily, while retaining the ecological specificity that large-scale biogeographic or macroecological analyses cannot address? (iv) Does the integration of distributional modelling, molecular approaches, and functional trait analysis generate emergent ecological insights that cannot be obtained from these methods in isolation, particularly in detecting complex anthropogenic or climatic influences on ecological systems? The four case studies composing this thesis jointly address the core research questions outlined above, with each study contributing to multiple questions through complementary methodological perspectives rather than mapping one-to-one onto a single objective. Each case study is positioned at the intersection of at least two methodological domains (trait- based ecology, eDNA metabarcoding, species distribution modelling) and targets two or more of the core questions within a specific ecological context. Together, they provide a progressive test of how functional, molecular, and distributional modelling approaches can be combined to improve ecological inference across scales and degrees of complexity of each system