Fig. 1

A flow chart displaying the analysis workflow (black arrows) for inferring the influence of ecological processes (box labels) on the kiwifruit vine microbiome, and a summary of the putative assembly processes. The vine signifies the regional microbial species pool or metacommunity. Two environments with different conditions are represented by a grey leaf (environment 1) and a white leaf (environment 2), respectively. For each pair of local communities (run separately for each substrate and time point, n = 60), the observed level of phylogenetic turnover, or beta mean nearest taxon distance, was determined (βMNTDobs). A null distribution of phylogenetic turnover values (βMNTDnull) was computed by randomly shuffling species names and abundances across the tips of the phylogeny. β-nearest taxon index values (βNTI) represent the difference between the βMNTDobs and the mean of the βMNTDnull. A βNTI value of < − 2 or >  + 2 indicates that the community composition was significantly consistent with selection as the assembly process. A βNTI value of < − 2 indicates that homogeneous selection was the principal assembly process. A βNTI value of >  + 2 indicates that heterogeneous selection was the principal assembly process. Further separation of the data was done for samples for which pairwise comparisons were not dominated by either homogeneous or heterogeneous selection (BNTI <|2|). We compared the observed pairwise Bray–Curtis dissimilarity (BCobs) between samples to values obtained from a null distribution of Bray–Curtis values (BCnull). Raup-Crick, based on Bray Curtis dissimilarity (RCBray), uses the deviation between BCobs and BCnull to disentangle variation in community dissimilarity from variation in α-diversity and ranges between − 1 and + 1. An RCBray value of < − 0.95 or >  + 0.95 specifies lower or higher turnover than expected if the sole mechanism shaping the community composition were due to ecological drift. An RCBray value of < − 0.95 indicates that homogenising dispersal was the dominant assembly process. An RCBray value of >  + 0.95 indicates that dispersal limitation was the dominant assembly process. The portion of insignificant RCBray values for each pairwise comparison ( <|0.95|) are those where drift is estimated to dominate community assembly