Phyllosphere microbial associations improve plant reproductive success

The above-ground (phyllosphere) plant microbiome is increasingly recognized as an important component of plant health. We hypothesized that phyllosphere bacterial recruitment may be disrupted in a greenhouse setting, and that adding a bacterial amendment would therefore benefit the health and growth of host plants. Using a newly developed synthetic phyllosphere bacterial microbiome for tomato (Solanum lycopersicum), we tested this hypothesis across multiple trials by manipulating microbial inoculation of leaves and measuring subsequent plant growth and reproductive success, comparing results from plants grown in both greenhouse and field settings. We confirmed that greenhouse-grown plants have a relatively depauperate phyllosphere bacterial microbiome, which both makes them an ideal system for testing the impact of phyllosphere communities on plant health and important targets for microbial amendments as we move towards increased agricultural sustainability. We find that the addition of..., For 16s Sequencing related data, paired-end reads were filtered and trimmed to 230(F) and 160(R) base pairs (bps), using DADA2 with default parameters (Callahan et al., 2016). Following denoising, merging reads and removing chimeras, DADA2 was used to infer amplicon sequence variants (ASVs), which are analogous to operational taxonomic units (OTUs), and taxonomy was assigned using the DADA2-trained SILVA database. Using DNA extraction and PCR negative controls from 16S sequencing, the decontam package was implemented using default settings to identify and remove potential contamination from the samples (Davis et al., 2018). The assigned ASVs, read count data, and sample metadata were combined in a phyloseq object (McMurdie & Holmes, 2013) for downstream analyses. The phyloseq package was used to calculate beta diversity (using Bray-Curtis distance), and a permutational analysis (PERMANOVA) was performed on data rarified to 400 reads (Weiss et al., 2017) (to account for extraordinari..., All data is provided as either `.csv` files, or as `.rds` files, which can be opened and processed in R., # Phyllosphere microbial associations improve plant reproductive success

These data represent the processed sequencing data (mostly in the form of phyloseq objects) and the greenhouse and field tomato plant harvest results associated with the study. Data includes sequencing results, with both bacterial absolute and relative abundance, as well as tomato number, and tomato weight, either as weight per tomato or weight harvested per plant.

## Description of the data and file structure

Data is presented as one of two file types, either a `.csv` or a `.rds`. Most sequencing related data is presented as `.rds` files, which must be loaded into R in order to be utilized. Further, these data are formatted as `phyloseq` objects, and require the package `phyloseq` in order to be processed. Some sequencing related data (ie. absolute, `Trial_1_Greenhouse_Bacterial_Abundance.csv`, and relative abundance, `Trial_3_Greenhouse_and_Field_Bacterial_Abundance.csv`) are `.csv` files.

All of the greenhou...