Figure S1 Plot Layout

Plot layout of a field experiment conducted from June through August 2011 (Corvallis, OR, USA) to test the effects of Bacillus thuringiensis (Bt) and non-Bt maize on the colonization ability and community diversity of arbuscular mycorrhizal fungi (AMF) in roots. Each plot measured 1 m by 1.2 m in size and there was a 1 m unplanted border around all plots. Each plot contained 20 plants (14 different cultivars B1-B9 and P1-P5) and each Bt cultivar was sown next to its non-Bt parental (P) isoline. Corresponding Bt/P pairs are indicated in the plot map as follows: B1/P1 = pink; B2/P2 = yellow; B3/P3 = purple; B4/P4 = gray; B5/P3 = brown; B6/P2 = green; B7/P5 = red; B8/P5 = blue; and B9/P5 = orange. Plant IDs followed by a "T" (in white) were used to trap spores for later experiments and are thus not included in the present study. Plant growth responses and percent AMF colonization in roots were recorded for all plants in the experiment (360 plants). Root samples collected from a subset of plots (2, 8, 10, 14, and 16; outlined in black) were used for molecular analysis of AMF communities using 454 pyrosequencing (90 plants)

Data from: Spatial soil heterogeneity has a greater effect on symbiotic arbuscular mycorrhizal fungal communities and plant growth than genetic modification with Bacillus thuringiensis toxin genes

Maize, genetically modified with the insect toxin genes of Bacillus thuringiensis (Bt), is widely cultivated, yet its impacts on soil organisms are poorly understood. Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots and may be uniquely sensitive to genetic changes within a plant host. In this field study, the effects of nine different lines of Bt maize and their corresponding non-Bt parental isolines were evaluated on AMF colonization and community diversity in plant roots. Plants were harvested 60 days after sowing, and data were collected on plant growth and per cent AMF colonization of roots. AMF community composition in roots was assessed using 454 pyrosequencing of the 28S rRNA genes, and spatial variation in mycorrhizal communities within replicated experimental field plots was examined. Growth responses, per cent AMF colonization of roots and AMF community diversity in roots did not differ between Bt and non-Bt maize, but root and shoot biomass and per cent colonization by arbuscules varied by maize cultivar. Plot identity had the most significant effect on plant growth, AMF colonization and AMF community composition in roots, indicating spatial heterogeneity in the field. Mycorrhizal fungal communities in maize roots were autocorrelated within approximately 1 m, but at greater distances, AMF community composition of roots differed between plants. Our findings indicate that spatial variation and heterogeneity in the field has a greater effect on the structure of AMF communities than host plant cultivar or modification by Bt toxin genes

Table S2 MaarjAM OTU IDs

Arbuscular mycorrhizal fungi (Family, Genus, Species) in roots of Bacillus thuringiensis (Bt) and non-Bt maize cultivated in a field experiment (Corvallis, Oregon, USA). Closest matching (97% nucleotide sequence identity) accession numbers were obtained via BLAST searches in the MaarjAM reference sequence database(http://maarjam.botany.ut.ee/). The accession numbers are linked to the National Center for Biotechnology Information (NCBI)

Table S1 Soil data

Percent organic matter (OM), pH, and soil nitrogen (N) and phosphorus (P) data collected from field plots (Corvallis, OR, USA). One composite sample was collected per plot and air-dried soils were analyzed for nutrients and soil properties at Indiana University

Figure S2 Alpha Rarefaction Plots

Rarefaction analysis of AMF communities in Bacillus thuringiensis (Bt) and non-Bt maize roots from a field experiment (Corvallis, OR, USA). Plots were generated by Qiime and use the Chao1 metric to measure alpha diversity in each sample at multiple levels of rarefaction

Table S4 Growth AMF and OTU data_molecular plots

Data file of growth responses, percent root colonization by arbuscular mycorrhizal fungi (AMF), and operational taxonomic units (OTU) obtained by 454 pyrosequencing for Bacillus thuringiensis (Bt) maize and non-Bt parental isolines harvested from a subset of five plots in a field experiment 60 days after sowing (Corvallis, OR, USA). The X,Y coordinates (cm) for each plant were used in the analysis of spatial variability of AMF communities (Mantel Correlogram; Fig. 4). The Legend, which provides information pertaining to each column heading, is located on the second sheet of the Excel file

OTU Consensus Sequences

FASTA file containing the consensus DNA sequences for the 143 operational taxonomic units (OTU) generated by AbundantOTU with a 97% sequence identity cutoff. Taxonomic information for each sequence is available in Table S2 and the read count for each OTU per sample is available in Table S4

Effect of permafrost thaw on plant and soil fungal community in a boreal forest: Does fungal community change mediate plant productivity response?

Permafrost thaw is leading to rapid shifts in boreal ecosystem function. Permafrost thaw affects soil carbon turnover through changes in soil hydrology; however, the biotic mechanisms regulating plant community response remain elusive. Here, we measured the response of fungal community composition and soil nutrient content in an intact permafrost plateau forest soil and an adjacent thermokarst bog and evaluated their potential to mediate shifts in plant composition. We used barcoded amplicon targeting ITS2 and 28S rRNA genes to determine fungal community composition. Next, we used the soils from the permafrost plateau and the thermokarst bog as soil inoculum in a greenhouse experiment to measure whether shifts in fungal community and soil water level regulate plant productivity and composition. Overall, we found that fungal community composition differed significantly between the thawed and intact permafrost sites, but soil nutrient content did not. Relative abundance of mycorrhizal fungal taxa decreased while relative abundance of putative fungal pathogens increased with permafrost thaw. In the greenhouse, we found that ecto‐ and arbuscular‐associated host plants had higher productivity in permafrost‐intact soils relative to thawed soils. However, productivity of non‐mycorrhizal tussock grass was more affected by soil water levels than soil communities. Synthesis. Our results suggest that fungal communities are crucial in mediating plant community response to permafrost thaws inducing hydrology changes