Supporting Information Figs S1 & S2, Tables S1–S5 and Methods S1
Methods S1 Data analyses
Phylogenetic trees were inferred by Bayesian analysis in MrBayes version 3.2 (Ronquist et al.,
2005; http://mrbayes.scs.fsu.edu/index.php), using the General Time Reversible sequence
evolutionary model. Branch support values correspond to the posterior probabilities of two Markov
chain Monte Carlo samplings over 2-6 million generations and a tree sampling every 100
generations after discarding the initial 10%. The phylograms were drawn in FigTree version 1.3.1
(http://tree.bio.ed.ac.uk/software/figtree/) and edited in Adobe Illustrator CS4.
Trees inferred from the multiple alignment of the entire partial ribosomal DNA cistron
(SSU-ITS2-LSU) sequences were rooted with the concatenated sequence accessions FR717169,
FR717187, and FR717205 of isolate BEG75 of Rhizophagus irregularis (N. C. Schenck & G. S.
Sm.) C. Walker & A. Schüßler (new classification by Schüßler & Walker, 2010; formerly known as
Glomus irregulare. The tree inferred from the partial SSU sequences was rooted with Geosiphon
pyriformis (sequence accession X86686) as an outgroup.
The adequacy of community and population sampling by the clone library RFLP
fingerprinting and recombinant plasmid sequencing was verified, using individual-based rarefaction
curves (Gotelli & Colwell, 2001) with sequences and clones considered as units of replication,
calculated in EstimateS version 8.2 (Colwell, 2009; http://purl.oclc.org/estimates).
References
Colwell RK. 2009. EstimateS, Version 8.2: Statistical estimation of species richness and shared
species from samples (Software and user’s guide). Freeware for Windows and Mac OS.
http://viceroy.eeb.uconn.edu/EstimateS.
Gotelli N, Colwell RK. 2001. Quantifying biodiversity: Procedures and pitfalls in the
measurement and comparison of species richness. Ecology Letters 4: 379-391.
Ronquist F, Huelsenbeck JP, van der Mark P. 2005. MrBayes 3.1.
http://mrbayes.csit.fsu.edu/index.php.
1
2
3
4
5
6
Fig. S1 (a) Schematic representation of the nuclear ribosomal DNA cistron showing the binding
sites of the employed PCR primers targeted to the 5′ ends of the small and large subunit (SSU,
LSU) ribosomal RNA genes. The universal eukaryote forward primer NS31 (Simon et al., 1992) is
shown above and the Glomeromycota-specific reverse primer LSUGlom1 (Renker et al., 2003)
below the gene. The total amplicon is approximately 2200 bp long. For reference, the forward and
reverse PCR primers SSUmAf/Cf and LSUmBr/Ar (Krüger et al., 2009) are shown above and
below the gene boxes with the amplicon length covered by these primers indicated as being
approximately 1.8 kb. (b) Nucleotide variation in the partial sequence of the SSU gene (≈ 1280 bp),
the internal transcribed spacer 1 (ITS1 ≈ 110 bp), the 5.8S gene (≈ 160 bp), the ITS2 (≈ 230 bp) and
the partial sequence of the LSU gene (≈ 380 bp) of arbuscular mycorrhizal (AM) fungi. Average pdistances were calculated as the mean of all pairs of sequences from the 44 AM fungal sequences,
displayed in Fig. 1 of the main text.
7
Fig. S2 Sampling effort curves based: (a) on all generated sequences of Funneliformis mosseae of
the two isolates AZ225C and IMA1/BEG12, and on all analysed F. mosseae sequences native to the
inoculation field trial; (b) on the total number of analysed recombinant plasmids with inserts of
arbuscular mycorrhizal (AM) fungi from environmental PCR amplicons. The environmental root
samples were from Medicago sativa plants collected three months after inoculation with the two
non-native F. mosseae isolates, AZ225C and IMA1, and a mock inoculum (control). Thousand
simulated datasets, using resampling with replacement were used to calculate the curves.
8