DOI: 10.25829/bexis.31497-13
title: Fragaria vesca microbiome experiment 2021 - Main dataset including single plant and plant community scans and associated bacterial and fungal ASVs and taxonomy

description: Land-use intensity affects the diversity and composition of communities, ecosystem functioning, and plant phenotypes. Furthermore, direct effects of land-use on the diversity of plant-associated bacteria have been demonstrated, which, in turn, may affect the plant phenotype. Previous correlational findings suggest that plant-associated bacteria may mediate the relationship between plant species diversity and ecosystem functions.<br>Using the framework of the common garden at the University of Marburg with plant communities from all three Exploratories, Fragaria vesca plants were grown for 3 months, serving as phytometers to test whether microbes mediate land use effects on plant phenotypes and performance as well as ecosystem functions.To test for a mediation of land-use effects on the phenotype via the microbiome, we assessed bacterial and fungal communities on the F. vesca plants (next-generation 16SrRNA gene amplicon sequencing of leaf and root samples) and captured the phenotype of the plants through single-plant phenotyping with a customized plant phenotyping system. Furthermore, a subsequent lab experiment where we inoculated seed-sterilized Fragaria vesca plants that have grown in a sterile environment with the ‘treatment-specific’ microbiome of the field Fragaria vesca plants was supposed to validate any correlative findings on the relationship of microbiome and plant phenotype through direct experimental results. These lab Fragaria vesca plants were also scanned with the digital phenotyping system after 3 months of growth after the inoculation.<br>This dataset contains 13 morphological and physiological parameters from digital phenotyping of plant communities, field Fragaria vesca plants and lab Fragaria vesca plants as well as manually measured performance proxies (herbivory, fruit set, vegetative reproduction) of the field Fragaria vesca plants.<br>Files in the attachment section of this dataset contain the counts and taxonomy of bacterial and fungal ASVs from leaf and root samples of Fragaria vesca plants.<br>Bacterial_ASVs.csv: Bacterial ASV counts from leaf and root samples.<br>Bacterial_ASVs_taxonomy.csv: Taxonomy of bacterial ASVs.<br>Fungal_ASVs.csv: Fungal ASV counts from leaf and root samples.<br>Fungal_ASVs_taxonomy.csv: Taxonomy of fungal ASVs.<br>The data collection and analysis was part of the project EXClAvE within the framework of the DFG-funded joint project Biodiversity Exploratories (https://www.biodiversity-exploratories.de).
description: Study design: The common garden contains 168 grass sods (taken from 13 plots per Exploratory; plus 12 subplots with sterilized soil) that were selected to best represent a land-use gradient from all three regions. The sods were then split into four parts and each part was subsequently randomly assigned to one of four experimental land-use treatments. Treatments differed in mowing frequency and application of fertilizer in a full factorial design: ‘Control’ (= mowing once per year), ‘Mowing’ (= mowing twice per year), ‘Fertilizer’ (= mowing once per year and fertilizing once per year) and ‘Mowing and Fertilizer’ (= mowing twice per year and fertilizing once per year) and the Fragaria vesca plants received the same treatment shortly after having been planted in the middle of the plant communities.<br>We planted one individual of F. vesca (including pot and former soil) into each plant community of the common garden in the middle of May 2021. After a one-week acclimatization period, Fragaria vesca plants concurrently received the same land-use treatment as the surrounding plant community. For the mowing treatment, plants were cut at ~2cm above ground and the fertilizer quantity was adjusted accordingly to match the fertilizer treatment of the plant communities in the common garden that are fertilized every year (99 kg Nitrogen per ha per year).<br>Attached files:<br>ASVs of leaf and root samples of Fragaria vesca plants that have been growing in plant communities in the common garden for 3 months, including taxonomy. |Sampling design: After the plants have been growing in the common garden for three months, we recorded herbivory (% of leaf damage), fruit set (number of fruits and flowers) and vegetative reproduction (number of stolons and offshoots) as proxies for performance.<br>The field Fragaria vesca plants were scanned from two opposing sides of the pot using an automated digital phenotyping system (see Zieschank et al. 2023). To eliminate any possible remaining variation between individual Fragaria vesca plants, we calculated the difference for each parameter from digital phenotyping (parfieldFragaria = parafter - parbefore). Additionally, one leaf and root sample was taken from each plant for next generation sequencing (attached files).<br>Plant communities were scanned as well.<br>In a subsequent lab experiment we inoculated seed-sterilized Fragaria vesca plants with the whole-plant microbiome extracted from the field Fragaria vesca plants that have been growing in the common garden for three months and have been subjected to different land-use treatments (see above). Lab Fragaria vesca plants grew for three months in a climate chamber at 20°C and identical daylight lighting conditions produced by fluorescent tubes with a 15h/9h light/dark cycle and were finally scanned with the same digital phenotyping system for an optimal comparability of morphology and physiology of communities and single plants from both experiments. |Sample preparation: For data of attached filerd: Microbial DNA was extracted using the ZymoBIOMICS DNA Miniprep Kit following the manufacturers’ instructions. |Sample analysis: Digital automated phenotyping of plant communities in a common garden, Fragaria vesca plants that were growing within these communities for three months, and seed-sterilized Fragaria vesca plants that were inoculated with the microbiome of the Fragaria vesca plants from the common garden. Additional one-time measuring of performance proxies from the field Fragaria vesca plants.<br>For data of attached files:<br>We analyzed the microbiome samples by next-generation sequencing. Microbiome profiling of isolated DNA was performed on the Qiita web platform, where bacterial ASVs were obtained using Deblur and fungal ASVs were obtained using DADA2. Raw sequences can be found on the ENA (see under repositories). |Equipment: Automated plant phenotyping system PlantEye F500 (Phenospex, Heerlen, The Netherlands) with a customized frame for mobile outdoor use.<br>Attached files:<br>Zymo-BIOMICS DNA Miniprep Kit, Zymo Research, Irvine, CA for sample preparation; samples were then sent to Eurofins for sequencing.