The translation of the genotype into phenotype, represented for example by the expression of genes encoding enzymes required for the biosynthesis of phytochemicals that are important for interaction of plants with the environment, is largely carried out by transcription factors (TFs) that recognize specific cis-regulatory elements in the genes that they control. TFs and their target genes are organized in gene regulatory networks (GRNs), and thus uncovering GRN architecture presents an important biological challenge necessary to explain gene regulation. Linking TFs to the genes they control, central to understanding GRNs, can be carried out using gene- or TF-centered approaches. In this study, we employed a gene-centered approach utilizing the yeast one-hybrid assay to generate a network of protein-DNA interactions that participate in the transcriptional control of genes involved in the biosynthesis of maize phenolic compounds including general phenylpropanoids, lignins, and flavonoids. We identified 1100 protein-DNA interactions involving 54 phenolic gene promoters and 568 TFs. A set of 11 TFs recognized 10 or more promoters, suggesting a role in coordinating pathway gene expression. The integration of the gene-centered network with information derived from TF-centered approaches provides a foundation for a phenolics GRN characterized by interlaced feed-forward loops that link developmental regulators with biosynthetic genes.

Soil fauna communities are major drivers of many forest ecosystem processes. Tree species diversity and composition shape soil fauna communities, but their relationships are poorly understood, notably whether or not soil fauna diversity depends on tree species diversity. Here, we characterized soil macrofauna communities from forests composed of either one or three tree species, located in four different climate zones and growing on different soil types. Using multivariate analysis and model averaging we investigated the relative importance of tree species richness, tree functional type (deciduous vs. evergreen), litter quality, microhabitat and microclimatic characteristics as drivers of soil macrofauna community composition and structure. We found that macrofauna communities in mixed forest stands were represented by a higher number of broad taxonomic groups that were more diverse and more evenly represented. We also observed a switch from earthworm-dominated to predator-dominated communities with increasing evergreen proportion in forest stands, which we interpreted as a result of a lower litter quality and a higher forest floor mass. Finally, canopy openness was positively related to detritivore abundance and biomass, leading to higher predator species richness and diversity probably through trophic cascade effects. Interestingly, considering different levels of taxonomic resolution in the analyses highlighted different facets of macrofauna response to tree species richness, likely a result of both different ecological niche range and methodological constraints. Overall, our study supports the positive effects of tree species richness on macrofauna diversity and abundance through multiple changes in resource quality and availability, microhabitat, and microclimate modifications. Keywords Community ecology • Forest ecosystems • Biodiversity-ecosystem functioning • Aboveground-belowground linkagesCommunicated by Stefan Scheu .

Depending on their tree species composition, forests recruit different soil microbial communities. Likewise, the vertical nutrient gradient along soil profiles impacts these communities and their activities. In forest soils, bacteria and fungi commonly compete, coexist, and interact, which is challenging for understanding the complex mechanisms behind microbial structuring. Using amplicon sequencing, we analyzed bacterial and fungal diversity in relation to forest composition and soil depth. Moreover, employing random forest models, we identified microbial indicator taxa of forest plots composed of either deciduous or evergreen trees, or their mixtures, as well as of three soil depths. We expected that forest composition and soil depth affect bacterial and fungal diversity and community structure differently. Indeed, relative abundances of microbial communities changed more across soil depths than in relation to forest composition. The microbial Shannon diversity was particularly affected by soil depth and by the proportion of evergreen trees. Our results also reflected that bacterial communities are primarily shaped by soil depth, while fungi were influenced by forest tree species composition. An increasing proportion of evergreen trees did not provoke differences in main bacterial metabolic functions, e.g., carbon fixation, degradation, or photosynthesis. However, significant responses related to specialized bacterial metabolisms were detected. Saprotrophic, arbuscular mycorrhizal, and plant pathogenic fungi were related to the proportion of evergreen trees, particularly in topsoil. Prominent microbial indicator taxa in the deciduous forests were characterized to be r-strategists, whereas K-strategists dominated evergreen plots. Considering simultaneously forest composition and soil depth to unravel differences in microbial communities, metabolic pathways and functional guilds have the potential to enlighten mechanisms that maintain forest soil functionality and provide resistance against disturbances.