Microbial Diversity and Keystone Taxa in the Stratified Forest Floors of Beech Forests

In forest ecosystems, the forest floor acts as a boundary between the mineral soil and the atmosphere, serving as a hub for microbial nutrient turnover and transport. The forest floor is stratified and comprises several distinct layers characterized by successional changes in properties like nutrient quality, oxygen content or rate of disturbance. How microbial community development follows changes in chemical forest floor properties is not studied so far. This study aims to characterize the microbiome and identify key-stone taxa of the forest floor at a fine vertical resolution across temperate, beech-dominated forests.

Forest floor samples were collected from three German beech-dominated forests differing in climate and soil phosphorus content, spanning eight distinct layers of the forest floor and topsoil profile (OL0, OL1, OLF, OHF, OH, A (0-5 cm), A (5-10 cm), A (10-20 cm)). Prokaryotic community composition was analysed using 16S rRNA gene amplicon sequencing. Layer-specific keystone taxa were identified by finding taxa shared across the sites and evaluating their impact on SpiecEasi based cooccurrence networks. Community assembly processes of each layer were assessed through b-NTI analyses. Additionally, total elemental concentrations were measured by ICP-OES.

A clear stratification of the forest floor microbiome was observed. Proteobacteria and Bacteroidota dominated the litter layers but declined with depth, whereas Acidobacteria and Chloroflexi became more abundant with depth in the forest soil profile. Redundancy analysis revealed that layer-specific physicochemical parameters, such as total carbon, nitrogen, and pH, had a strong influence on microbiome composition, with sulfur, calcium, potassium, iron, and aluminum also significantly impacting microbial community composition. Generally, the impact increased with depth. We found a set of key-stone taxa specific for each forest floor layer and present at every site, each with a combined contribution between 10 and 20% of the total layer microbial abundance. Differences between the microbiomes of the three forest sites based on bray-curtis distances were most evident in the fresh litter layer and the mineral horizons, while the microbiome in the fragmented and humic layers was more uniform. This is further confirmed by community assembly analysis, which showed that homogenizing selection became more pronounced with progressing litter decomposition.

The vertical stratification of the forest floor is mirrored closely by microbial community composition and assembly. Each layer comprises different niches, which are formed by changes in substrate quality, and support distinct key-stone taxa. Compositional differences between forest sites are likely based on climatic conditions and bedrock type, whose influence is biggest at boundary layers like fresh litter and mineral soil, respectively. Similar successional trends of the microbiomes and high abundance of shared taxa were found between the sites, suggesting that litter type could be the primary driver of the forest floor microbiome composition. These findings enhance our understanding of how vertical stratification and substrate quality influence the forest floor microbiome.