Biology subjects

Bibinger, S.

Publications and source records attributed to Bibinger, S..

3 recordsLinked to original sources

bioRxiv2026

Vertical stratification drives additive prokaryotic diversity in beech forest floors, while site conditions shape boundary layers

The forest floor is a key interface regulating carbon and nutrient processing and transfer to the mineral soil, yet it is threatened by climate-change-driven reductions in organic layer mass. How its prokaryotic microbiome is structured across the fine-scale vertical gradient from fresh litter to mineral topsoil remains poorly resolved. We characterised prokaryotic communities across eight sequential layers spanning fresh litter, organic layers at different stages of decomposition, and mineral topsoil in three temperate beech forests using 16S rRNA gene amplicon sequencing. The decomposition stage was the dominant driver of community assembly, resulting in a strongly vertically stratified prokaryotic microbiome. While alpha diversity peaked within the fragmented litter layers, the overall high diversity of the forest floor was primarily an additive effect of vertical stratification. Site-specific effects were pronounced in the litter layer and the mineral topsoil, but diminished in the intermediate organic layers, where high local heterogeneity masked between-site differences. Redundancy analysis further showed that the environmental drivers of community structure shifted with depth, from litter quality in the upper horizons to mineral-associated properties in the mineral topsoil. At the same time, predicted 16S rRNA gene copy numbers indicate that the humified layers harbour the highest abundance of oligotrophic life strategists in the profile. By resolving the fine-scale vertical structure of the forest floor prokaryotic microbiome, our results provide a baseline for predicting how climate-change induced loss of organic layer mass threatens layer-specific communities, particularly the oligotrophic taxa in the humified layers, with consequences for the carbon turnover, tree nutrition, and nutrient cycling functions they mediate.

microbiology↗

bioRxiv2025

Provenance Legacies Override Species Effects in Shaping Oak Rhizosphere Microbiomes and Metabolomes

As climate change drives more frequent and intense drought-heat extremes, selecting drought-tolerant trees is crucial for future forest resilience. However, the role of tree-microbial associations for this key trait remains largely unclear. In this study, we investigated how geographic origin, species identity, and intrinsic water-use efficiency (iWUE) shape the rhizosphere microbiome and root-rhizosphere metabolome of pedunculate (Quercus robur) and sessile (Q. petraea) oaks. In a six-year common garden experiment, we analyzed trees from both species, each grown from seeds from two distinct geographic origins, the upper Rhine basin (URB) and the north-east German lowlands (NGL), differing in water availability, using 16S and ITS rRNA gene based metabarcoding and untargeted metabolomics. We found a consistent legacy effect of seed origin on the composition of the prokaryotic rhizosphere microbiome and the metabolome, whereas tree species had no significant impact. The bacterial family Pseudonocardiaceae was enriched at trees from the drier origin NGL, while Blastocatellaceae and Micromonosporaceae were positively associated with iWUE across samples. Higher iWUE was furthermore significantly correlated with lower prokaryotic diversity and shifts in {beta}-diversity, thereby linking a drought-adaptive host trait to the assembly of the belowground environment. Ellagic acid, a plant derived polyphenol associated with drought tolerance, was enriched in the drier origin NGL and linked to several prokaryotic taxa in correlation networks. The rhizosphere fungal community, however, was largely unaffected by origin or species. Solely fungal community evenness declined with increasing iWUE. Together, our findings suggest that ecotypic adaptation linked to origin can outweigh the effect of species-level traits in shaping the oak rhizosphere microbiome and metabolome. These findings emphasize that provenance-driven ecotypic adaptation can strongly influence plant-microbe interactions and underscore the need for provenance-aware selection and microbiome-informed assisted migration as strategies to strengthen forest drought resilience under global climate change.

ecology↗

bioRxiv2025

Mrx6 binds the Lon protease Pim1 N-terminal domain to confer selective substrate specificity and regulate mtDNA copy number

Mitochondrial DNA (mtDNA) copy number regulation remains incompletely understood, despite its importance in cellular function. In Saccharomyces cerevisiae, Mrx6 belongs to the Pet20-domain-containing protein family, consisting of Mrx6, Pet20, and Sue1. Notably, absence of Mrx6 leads to increased mtDNA copy number. Here, we identify the C-terminus of Mrx6 as essential for its stability and interaction with the mitochondrial matrix protein Mam33. Deletion of Mam33 mimics the effect of Mrx6 loss, resulting in elevated mtDNA copy number. Bioinformatics, mutational analyses, and immunoprecipitation studies reveal that a subcomplex of Mam33 and Mrx6 trimers interacts with the substrate recognition domain of the conserved mitochondrial Lon protease Pim1 through a bipartite motif in the Pet20 domain of Mrx6. Loss of Mrx6, its paralog Pet20, Mam33, or mutations disrupting the interaction between Mrx6 and Pim1 stabilize key proteins required for mtDNA maintenance, the RNA polymerase Rpo41 and the HMG-box-containing protein Cim1. We propose that Mrx6, alongside Pet20 and Mam33, regulates mtDNA copy number by modulating substrate degradation through Pim1. Additionally, Mrx6 loss alters Cim1s function, preventing the detrimental effect on mtDNA maintenance observed upon Cim1 overexpression. The presence of three Pet20-domain proteins in yeast implies broader roles of Lon protease substrate recognition beyond mtDNA regulation.

cell biology↗