Supporting Information Table S1 and Methods S1

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1 Supporting Information Table S1 and Methods S1 Methods S1 Power analysis for multivariate data. Recent developments in computational biology have made it possible to conduct power analyses on multivariate datasets (La Rosa et al., 2012, 2013). Specifically the R-package HMP (La Rosa et al., 2015) was used to examine changes in experimental power with changes in the number of samples per treatment and sequences per sample. We used two published arbuscular mycorrhizal fungi (AMF) community datasets Denmark (Lekberg et al., 2012) and Montana (Lekberg et al., 2013) for which data consisted of multiple samples per site, and samples were in the form of sequence abundance. Data frames were set up such that each row was a single sample and each column a single taxon, with the final column labelled rare taxa in which all taxa with an experiment-wide sequence abundance <1% of the total number of sequences were combined (La Rosa et al., 2012). All subsequent analyses were performed with raw count data using the DM.MoM function to fit the recommended Dirichlet-multinomial (DM) model. For an experimental significance level of α = 0.05 we calculated the experimental power for varying numbers of sequences and varying numbers of samples using the function mc.xmcupo for each of the two datasets (see Table 1). Additionally the effect size function Xmcupo.effectsize and Generalized Wald-type test function Xmcupo.sevsample were applied to the Denmark and Montana datasets examine whether the original conclusions about community differences were supported using the HMP approach. In each case analysis with HMP supported the original conclusions.

2 Table S1 Published most frequently used for arbuscular mycorrhizal fungi (AMF) studies Reference Primer set Target region White et al. (1990) NS1, NS2, NS4, NS5, NS8 SSU ITS1, ITS4 ITS Notes Universal eukaryote used as first PCR and followed by a nested specific PCR, or in combination with specific Simon et al. (1992) NS31 SSU Universal eukaryote primer vantuinen et al. (1998) LR1, NDL22 LSU Universal eukaryote Helgason et al. (1998) AM1 SSU Paired with universal forward primer, can amplify other groups of fungi, limited coverage of Paraglomeraceae Trouvelot et al. (1999) FLR2 LSU Paired with LR1 for fungi only Kjøller & Rosendahl (2000) LSURK4f, LSURK7r LSU Glomus group primer, nested within LR1-NDL22 Redecker et al. (2000) ARCH1311, LETC1670, GLOM1310, ACAU1660, GLOM5.8R, GIGA5.8R GeoA1, GeoA2, Geo10, Geo11, GeoNS1, ART4 SSU & ITS Taxon group specific Schwarzott & Schüssler (2001) SSU AMF specific Renker et al. (2003) SSUGlom1, LSUGlom1 ITS Primary PCR with restriction digest prior to secondary amplification using universal ITS Gollotte et al. (2004) FLR3, FLR4 LSU AMF specific, nested within LR1-FLR2 Saito et al. (2004) AMV4.5F, AMV4.5R, SSU AMF specific

3 AMV4.5NF, AMV4.5NR Sato et al. (2005) AMDGR SSU AMF specific reverse primer with improved coverage for basal lineages Wubet et al. (2006) GlomerWT0, GlomerWT1, GlomerWT2,GlomerWT3, GlomerWT4, Glomer1536 SSU General AMF specific and group specific Santos-Gonzalez et al. (2007) AM2, AM3 SSU Variants of AM1 that increase taxon coverage Lee et al. (2008) AML1, AML2 SSU Longer fragment than NS31-AM1, improved AMF taxon coverage, amplifies some plants Krüger et al. (2009) SSUmAf, SSUmCf, LSUmBr, LSUmAr SSU- ITS-LSU Composite primer mixtures for high taxon coverage Lekberg et al. (2012) Glo454 LSU Combined with NDL22 for 454 sequencing References where original primer sequence was published are cited, with notes on coverage and typical primer combinations. SSU, small subunit; ITS, internal transcribed spacer; LSU, large subunit.

4 References Gollotte A, Van Tuinen D, Atkinson D Diversity of arbuscular mycorrhizal fungi colonising roots of the grass species Agrostis capillaris and Lolium perenne in a field experiment. Mycorrhiza 14: Helgason T, Daniell TJ, Husband R, Fitter AH, Young JPW Ploughing up the wood-wide web? Nature 394: 431. Kjøller R, Rosendahl S Detection of arbuscular mycorrhizal fungi (Glomales) in roots by nested PCR and SSCP (single stranded conformation polymorphism). Plant and Soil 226: Krüger M, Stockinger H, Krüger C, Schüßler A DNA-based species level detection of Glomeromycota : one PCR primer set for all arbuscular mycorrhizal fungi. New Phytologist 183: La Rosa PS, Brooks JP, Deych E, Boone EL, Edwards DJ, Wang Q, Sodergren E, Weinstock G, Shannon WD Hypothesis testing and power calculations for taxonomic-based human microbe data. PLoS ONE 7: e La Rosa PS, Deych E, Shands B, Shannon WD HMP: hypothesis testing and power calculations for comparing metagenomic samples from HMP. R package version URL: La Rosa PS, Zhou Y, Sodergren E, Weinstock G, Shannon WD Hypothesis testing of metagenomic data. In: Izard J, Rivera M, eds. Metagenomics for microbiology. London, UK: Academic Press, Lee J, Lee S, Young JPW Improved PCR for the detection and identification of arbuscular mycorrhizal fungi. FEMS Microbiology Ecology 65: Lekberg Y, Schnoor T, Kjøller R, Gibbons SM, Hansen LH, Al-Soud W A, Sørensen SJ, Rosendahl S sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities. Journal of Ecology 100: Lekberg Y, Gibbons SM, Rosendahl S. Ramsay PW Severe plant invasions can increase mycorrhizal fungal abundance and diversity. ISME Journal 7: Redecker D Specific PCR to identify arbuscular mycorrhizal fungi within colonized roots. Mycorrhiza 10: Renker C, Heinrichs J, Kaldorf M, Buscot F Combining nested PCR and restriction digest of the internal transcribed spacer region to characterize arbuscular mycorrhizal fungi on roots from the field. Mycorrhiza 13: Saito K, Suyama Y, Sato S, Sugawara K Defoliation effects on the community structure of arbuscular mycorrhizal fungi based on 18S rdna sequences. Mycorrhiza 14: Santos-González JC, Finlay RD, Tehler A Seasonal dynamics of arbuscular mycorrhizal fungal communities in roots in a seminatural grassland. Applied and Environmental Microbiology 73:

5 Schwarzott D, Schüßler A A simple and reliable method for SSU rrna gene DNA extraction, amplification, and cloning from single AM fungal spores. Mycorrhiza 10: Simon L, Lalonde M, Bruns TD Specific amplification of 18S fungal ribosomal genes from vesicular-arbuscular endomycorrhizal fungi colonizing roots. Applied and Environmental Microbiology 58: Trouvelot S, van Tuinen D, Hijri M, Gianinazzi-Pearson V Visualization of ribosomal DNA loci in spore interphasic nuclei of glomalean fungi by fluorescence in situ hybridization. Mycorrhiza 8: Van Tuinen D, Jacquot E, Zhao B, Gollotte A, Gianinazzi-Pearson V Characterization of root colonization profiles by a microcosm community of arbuscular mycorrhizal fungi using 25S rdna-targeted nested PCR. Molecular Ecology 7: White TJ, Bruns T, Lee S, Taylor J Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols: a guide to methods and applications. New York, NY, USA: Academic Press, Wubet T, Weiss M, Kottke I, Teketay D, Oberwinkler F Phylogenetic analysis of nuclear small subunit rdna sequences suggests that the endangered African Pencil Cedar, Juniperus procera, is associated with distinct members of Glomeraceae. Mycological Research 110: