There are cores, indicators, and differences - a high-throughput and quantitative PCR study of the Ambrosia artemisiifolia L. leaf, root, and seed endophytic bacterial microbiomes within the European invasive range

Abstract

Ambrosia artemisiifolia L. is among the most harmful invasive plants in Europe, a major agricultural weed and a source of severe allergenic pollen. Endophytes may affect invasion, but this species' endophytic bacteria were profiled by high-throughput sequencing only in a single study from China. We aimed to characterize the leaf, root, and seed endobacteriome and test whether tissue type, habitat, or region shape its composition within the European invasive range. Plants were sampled from six sites in Poland and Slovakia across three habitat types. 16S rRNA gene amplicons from surface-sterilized tissues and soil were sequenced and bacterial load quantified by qPCR. Analyses included alpha and beta diversity, core microbiome, indicator analysis, differential abundance, and functional prediction. Tissue type, not region or habitat, structured communities. Gammaproteobacteria exceeded Alphaproteobacteria in most plant tissue samples, but in soil the reverse was true. Mean bacterial load in plant tissues ranged from 1.73-3.49 x 108 16S rRNA gene copies g dry weight-1. The pan-tissue core (80% prevalence) contained 13 genera, 9 of them absent from the soil core. Seeds had significantly lower alpha diversity, the smallest core and no seed-exclusive predicted functional indicators. Leaves and roots differed significantly in taxonomic composition but not in predicted functions. Tissues shared a core that overlapped only partly with the soil core. Seeds carried a reduced subset of the endobacteriome that, in this annual invader, may pass across generations. Further studies should compare these communities with native-range populations and test the enhanced mutualism and pathogen spillback hypotheses.