Additional file 1 of A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization

Additional file 1. Overview of the 144 bacteria isolated from hyphal samples. This file contains Unique ID, taxonomy, FASTA sequence of the hyphal bacterial isolates. Fig. S1. Effects of field management practices on soil microbial communities in Experiment I. Fig. S2. Photo of root colonization in COMP3 of a representative mesocosm at the end of Experiment II. Fig. S3. Effects of field management practices on soil microbial communities in Experiment I. Fig. S4. Bacterial ASVs with significantly different abundance between hyphal and soil samples in Experiments I (A) and II (B). Fig. S5. Isolation of AM-associated microbes using two strategies. Fig. S6. Pearson’s correlation between AM fungi root colonization (%) and plant P accumulation. Fig. S7. Schematic representation of the wet sieving protocol used to sample hyphae from COMP 5 as described in the Methods section. Fig. S8. Stereo microspore images of AM hyphae. Table S1. Effect of sample type on fungal and bacterial communities of experiment I. Table S2. Effect of preceding soil management practices in the FAST experiment on microbial communities of root, hyphal and soils samples at the end of experiment I. Table S3. Effect of the presence of plant on soil microbial communities. Table S4. Effect of sample type on fungal and bacterial communities of experiment II. Table S5. Hoagland solution ingredients. Table S6. Overview of microbial genes involved in N metabolism for which orthologs were putatively found in the genome of Devosia sp. ZB163. Table S7. Primers used for amplification of microbial ITS and 16S. Table S8. Two step PCR cycling conditions for amplifying ITS, 16S. Table S9. AM-associated bacteria isolation media. Table S10. PCR cycling conditions for amplifying 16S. Table S11. Modified Strullu and Romand (MSR) medium supplemented with 1% sucrose

Ecosystem respiration

To asses the effect of vascular plant removal in aforementioned experiment, one year after the start of the experiment, we measured carbon dioxide respiration rates on 10 cm diameter collars using an automated soil CO2 flux system (LI-8100, LI-COR Biosciences, USA). We compare the fluxes from the vascular plant removal plots with respiration rates from comparable areas in the control plots with little or no vascular plant cover, and assessed the relationship with the amount of removed biomass

Potential methane oxidation, production, organic matter compositon, gene copies, and environmental data

In early June 2011, 48 experimental plots (50 × 50 cm) were established in lawn (n = 24) and hummock microhabitats (n = 24) in a Sphagnum-dominated ombrotrophic peatland in the Store Mosse National Park, Sweden (57°17’54 N, 14°00’39 E). In both microhabitats, the vascular plant functional type (PFT) composition was manipulated by removing (clipping) ericoids (–Eric), graminoids (–Gram), or both. A set of control plots remained intact. One year later, peat samples (c. 20 g. f. wt) were collected from all plots (n =48) at the aerobic/anaerobic boundary (10 – 30 cm below the peat surface, microhabitat dependent). These samples were used to measure potential methane production, potential methane oxidation, organic matter chemistry, pmoA gene copies, and environmental data