Mélody Rousseau

1. In forest ecosystems, soil microbial communities play an integral role by serving as mediators of biophysical and biochemical processes (Baldrian 2017; Lladó, López-Mondéjar, and Baldrian 2017; ...

Background and aims: Deadwood plays a vital role in forest ecosystems, influencing soil biodiversity through nutrient enrichment and niche partitioning. While the effects of specific attributes of deadwood logs on soil biodiversity are well studied, it remains unclear whether and how the volume of deadwood affects soil biodiversity at the scale of forest stands. Additionally, the effects on soil biodiversity may differ between gradually accumulated deadwood and large volumes resulting from sudden stand-level disturbance events. In this study, we aim to assess such effects on alpha and beta diversity of soil microbes and microfauna. Methods: Soil samples were gathered from forest plots following a gradient of deadwood volumes in European temperate forests in Germany and The Netherlands. Using extracellular DNA metabarcoding, we analysed the soil diversity of bacteria, fungi and microarthropods. For the Bavarian Forest National Park, we also compared the diversity patterns of these biotas between areas affected by bark beetle outbreaks and unaffected areas of Norway spruce forest. Results: Increased deadwood stock had a marginal effect on soil microbial and microarthropod community composition, with no impact on overall diversity. Bark beetle-affected areas had distinct soil communities, with a lower fungal and microarthropod diversity. Conclusion: Our study provides the first insights into soil diversity patterns associated with increased deadwood volume at the forest stand. While shifts in soil biodiversity composition were minimal, the retention of deadwood in European temperate forests can promote heterogeneity in soil communities. Furthermore, changes in soil biodiversity following bark beetle outbreaks may have long-term consequences on forest regeneration.

Fungi represent a significant portion of Earth's biological diversity and are essential for ecosystem functions like organic matter decomposition and nutrient cycling. While fungi associated with plant roots have been extensively studied, our understanding of fungi in the forest canopies remains limited. To investigate the landscape-scale variation in the canopy mycobiome of temperate beech and spruce forest stands in the Bavarian Forest National Park (Germany), we examined the influence of geophysical conditions and host traits. We found that elevation significantly influenced fungal diversity and composition, with distinct effects observed in both beech and spruce stands. Moreover, canopy water content, a key indicator of tree vitality, was also strongly associated with changes in the canopy fungi community, suggesting a potential link between forest water stress and the forest canopy mycobiome. Our differential abundance analysis further identified a total of 41 fungal families as potential bioindicators: 17 families in beech stands and 9 in spruce stands were significantly associated with elevation, while 9 families in beech stands and 6 in spruce stands were linked to variations in leaf water content. These findings enhance our understanding of the spatial patterns of forest canopy microbial biodiversity and species distributions.

Despite a decrease in industrial nitrogen and sulfur deposition over recent decades, soil acidification remains a persistent challenge to European forest health, especially in regions of intense agriculture and urbanisation. Using topsoil eDNA metabarcoding and functional annotations from a sample of 49 plots (each 30 × 30 m) located in The Netherlands and Germany, we investigated the effect of severe acidification on bacterial taxonomic diversity under different forest types and explored potential functional implications for nutrient cycling. Furthermore, we assessed which soil parameters known to influence soil bacterial communities affect these acidophilic communities. Here, we are the first to demonstrate under natural conditions that soil bacterial diversity in extremely acidic soils (pH <4.5) continues to decline similarly across forest types as pH further decreases under intensifying human activity. Our results confirmed pH as the key driver of soil bacterial communities, even in extremely acidic soils. Ongoing severe acidification continues to reduce bacterial communities, favouring taxa adapted to extreme acidity and primarily involved in recalcitrant carbon‐degradation compounds (e.g. cellulolysis potential = 0.78%–9.99%) while simultaneously diminishing taxa associated with nitrogen cycling (e.g. fixation potential = 6.72%–0.00%). Altogether, our findings indicate a further decline in bacterial diversity in already extremely acidic soils, likely disrupting nutrient cycling through changes in immobilisation and mineralisation processes. Our study highlights the continuous acidification of European temperate forests to extremely low pH levels, further disrupting forest ecosystem functioning. The significant reduction in bacterial diversity under such a severe acidification gradient, as demonstrated here, underscores the necessity to include severely acidified forests in conservation programmes and monitoring to prevent further degradation of European soils beyond repair.

Fallen deadwood is essential for biodiversity and nutrient cycling in forest ecosystems. In modern forest management, there is growing interest in developing accurate and efficient methods for field estimation of deadwood volume due to its many benefits (e.g. carbon storage, habitat creation, erosion control). The most common methods for deadwood inventories are fixed-area sampling (FAS) and line-intersect sampling (LIS) methods. While the estimations of deadwood volume by LIS generally show results comparable to FAS estimations, active management (e.g. production forestry clearcutting, logging, and thinning activities) can impair LIS accuracy by changing local deadwood patterns. Yet, the comparison of LIS and FAS methods has typically focused on production forests where deadwood is limited and deadwood volumes are comparably low. In this study, we assessed fallen deadwood volume in two large national parks—one being a more actively managed landscape (including, e.g., selective thinning for maintaining cultural–historical values and enhancing recreational opportunities) with overall lower levels of fallen deadwood, and the other having a strict non-intervention approach with higher levels of deadwood. No significant differences between average FAS and LIS estimations of deadwood volumes were detected. Additional experimentations using simulated data under varied stand conditions confirmed these results. Although line-intersect sampling showed a slight overestimation and some variability at the individual plot level, it remains an efficient, time-saving field sampling method providing comparable results to the more laborious fixed-area sampling. Line-intersect sampling may be especially suitable for rapid field inventories where relative changes in deadwood volume rather than absolute deadwood volumes are of large interest. Due to its practicality, flexibility, and relative accuracy, line-intersect sampling may gain wider use in natural resource management to inform national park managers, foresters, and ecologists.

Background: The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce). Results: We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families. Conclusions: While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.

Aims: The phyllosphere and soil are crucial and distinct microbial spheres in forests, connected through trees that interact with both. As part of the tree's holobiont, these communities are vital to the fitness and evolution of the host. Differences between the spheres may be particularly evident at the two extreme ends of tall and long-lived trees of natural temperate forest; the top-canopy and the soil. Here, we evaluated the connectivity between the top-canopy and soil microbial communities of European beech and Norway spruce trees to determine the significance of tree-sphere and host-species identity, and to assess the contribution of taxa inhabiting both spheres.Methods: Bacterial and fungal community composition was determined through metabarcoding analysis of linked top-canopy leaf and bulk soil samples collected from tall (old) trees in the natural forest of Bavarian Forest National Park.Results: This study shows sphere-specific communities in European temperate forests, characterized by low connectivity. Results highlight that spheres exert stronger influence than host identity. Only a few taxa inhabited both spheres, yet they accounted for the bulk of the (relative) abundance in each sphere.Conclusion: Analysing the divergence and shared characteristics of these interlinked communities redefines the tree holobiont concept and enhances our understanding of the evolution of plant-associated microbial communities in a sphere-specific manner. This study emphasizes the importance of examining multiple microbiome components for a thorough understanding of temperate forest ecology, while also highlighting the existence of a small group of overlapping taxa that may play a bigger role than previously anticipated.