The ‘phyllosphere meeting’ is a (typically) quinquennial event that brings together experts from around the world with a scientific interest in leaves (and other above-ground parts of plants and trees...

Fusarium graminearum (F. graminearum) pathogen induces wheat phyllosphere alkalinization, promoting the development of Fusarium head blight (FHB). Xu et al. show that host-acidifying Pseudomonas, sele...

Abstract. Microorganism-driven ecosystems on leaf surfaces play pivotal roles in regulating plant health and fitness. While individual leaves provide disti

Abstract. Plants can respond to pathogen attack by assembling disease-suppressive microbiomes. In Arabidopsis thaliana, infection by the obligate foliar do

Scientific Reports - Reproducing plant microbiome research reveals site and time as key drivers of apple tree phyllosphere bacterial communities

The phyllosphere - the aerial parts of plants - harbors a rich and diverse microbial community, including bacteria, filamentous fungi, yeasts and viruses. This environment is both harsh and dynamic, e...

Microbial transmission between hosts is known to have dramatic consequences for host-symbiont interactions. The question of whether this holds true for complex microbiomes remains largely unexplored. ...

The ‘phyllosphere meeting’ is a (typically) quinquennial event that brings together experts from around the world with a scientific interest in leaves (and other above-ground parts of plants and trees...

Understanding how plant-associated microbiomes interact with host genome variation to influence agronomic traits is essential for advancing microbiome⍰assisted crop improvement. In this study, we characterized the phyllosphere and rhizosphere microbiomes of 164 diverse Nicotiana tabacum accessions using 16S rRNA sequencing and integrated these data with host genomic variation and 22 agronomic traits. The two microbiomes exhibited distinct taxonomic structures, diversity patterns, and predicted metabolic functions. Microbiome genome⍰wide association studies identified extensive host genetic control over microbial abundance, including 49 shared genomic loci that explained nearly half of the heritable variation in both microbiomes. Microbiome⍰wide association studies revealed biologically meaningful associations between specific ASVs and agronomic traits. However, network analysis demonstrated that microbial sub⍰communities, rather than individual taxa, contributed substantially to phenotypic variation. Then, colocalization analysis further identified genetic variants jointly influencing microbial abundance and metabolite traits, highlighting potential host-microbe-trait causal links. Incorporating microbiome data into genomic selection models, we successfully improved prediction accuracy for several traits, especially plant architecture and flowering. Together, this work provides a comprehensive population⍰level framework linking host genetics, microbiome composition, and agronomic traits in tobacco, offering new insights for microbiome⍰informed breeding strategies.

The plant-associated microbiome is a key contributor to plant health, influencing nutrition, stress tolerance, and disease outcomes. Manipulating these microbiomes is a potentially powerful tool for p...