Method S1. Samples, RNA isolation and quantitative reverse transcription-PCR

Mycorrhizal roots were ground in liquid nitrogen and total RNA was isolated using the RNeasy Plant Mini kit (Qiagen, Darmstadt, Germany). The DNA-free set (Ambion, Austin, USA) was used to digest remaining DNA after RNA purification. Full-length double-stranded cDNAs corresponding to mRNAs expressed in plant roots wereobtained using the SMART–PCR cDNA Synthesis Kit (Clontech, Palo Alto, CA, USA). Quantification of AMT transcripts was performed using a two-step quantitative RT-PCR (qRT-PCR) procedure. Total RNA was measured with a spectrophotometer (Nanodrop ND-1000, Witec, Switzerland) and then reverse-transcribed (100 ng per reaction) using the iScriptcDNA Synthesis kit (Bio-Rad, Paolo Alto, CA, USA). cDNAs were used as templates in real time quantitative PCR reactions with gene-specific primers designed with Primer 3 ( and amplify 3.1 ( (Table S3). The following criteria were used: product size between 100 and 400 bp, melting temperature 60°C and a GC percentage > 50%. Primers used as controls or for analysis had an efficiency ranging between 90% and 110%. Reactions of qPCR were run using the 7500 real-time PCR system (Applied Biosystems). The following cycling parameters were applied: 95°C for 3 min and then 40 cycles of 95°C for 30 s, 60°C for 1 min and 72°C for 30 s. A control with no cDNA was run for each primer pair. Primers used as controls, or for analysis, had efficiency ranged between 90% and 110%. Primers for sorghum AMTs were design by Koegel et al.(2013). All used primers are listed in Table S3.

All full-length cDNAs were sequenced by cDNA walking PCR: amplification of the full-length cDNAs, from the start to the stop codon, with primers designed using the nucleotide sequences of manually annotated gene models (Table S2), was performed on a T3 thermocycler (Biometra, Labgene Scientific SA, Switzerland) using the Advantage 2 Polymerase Mix (Clontech). PCR reactions resulted in single bands on a 1% agarose gel (Promega, Madison, WI, USA) in 0.5% TAE (Tris Acetate-EDTA) stained with Midori Green according to manufacturer’s instructions (Labgene, Chatel-St-Denis, Switzerland). Amplified products were purified with ExoSAP treatment (USB, Cleveland, Ohio, USA) and direct cDNA sequencing was performed on a 3500 Genetic Analyser (Applied Biosystems, Courtaboeuf, France).

Method S2. S. cerevisiae uptake studies

S. cerevisiae uptake studies were performed with yeast cells grown to logarithmic phase. Cells were harvested at an OD600 of 0.9, washed twice in water, and resuspended in buffer A (0.6 M sorbitol, 50 mM potassium phosphate, at the desired pH) to a final OD600 of 5. Prior to the uptake measurements, the cells were supplemented with 100 mM glucose and incubated for 5 min at 30°C. To start the reaction, 100 µl of this cell suspension was added to 100 µl of the same buffer containing at least 15.8 kBq [14C]-methylammonium, specific activity 7.66 GBq/mmol (Amersham) and unlabeled amino acid to the concentrations used in the experiments. Sample aliquots of 45 µl were removed after 15, 60, 120, and 240 s, transferred to 4 ml of ice-cold buffer A, filtered on glass fiber filters, and washed twice with 4 ml of buffer A. Carbon-14 uptake was determined by liquid scintillation counting. Transport measurements were repeated independently and represent the mean of at least three experiments.

Methods S3. Design of amiRNAs

Rice cDNA sequences of AMT3;1 and AMT4 were downloaded from the MSU Rice Genome Annotation Project ( Sequence homology of miRNA precursors to available rice cDNAs was determined by BLAST and multiple alignments were performed using Mega4 (Tamura et al. 2007). The possible amiRNA candidate sequences were generated using WMD3 (Schwab et al. 2006; Ossowskiet al. 2008). WMD3 ( supports different plant species including Oryza sativa (TIGR v5) and designs 21bp sequences directed against one or several genes. The program suggests suitable amiRNA candidates after a two‐step selection process based on empirically established criteria for efficiency and specificity while minimizing possible off‐target effects to other genes in the rice genome. The hybridization energy was chosen between ‐35 and ‐38 kCal.

Methods S4. amiRNA Constructs

For each miRNA construct, three modification PCRs were performed with primers G‐4368+II, I+IV and III+G‐4369 on pNW55 as template, yielding fragments of 256, 87 and 259 bp lengths, respectively. Primer I contains the amiRNA in sense orientation, primer II its reverse complement, primer III the amiRNA* sequence in sense and primer IV the amiRNA* sequence in antisense orientation. The primers G‐4368 and G‐4369 are vector primers and were the same for all amiRNA constructs. amiRNA primers were designed using the primer design function of WMD3. A list of all primers can be seen in Table S3. The three resulting fragments were gel-purified with Zymoclean Gel DNA Recovery Kit (Zymo Research) and then fused by one PCR with the two flanking primers G‐4368 and G‐4369 on a mixture of 1 μl from each previous PCR as template. All PCRs were performed with Phusion DNA Polymerase (Biolabs) in a volume of 50 μl according to the manufacturer’s recommendation. The fusion product of 554 bp was again gel purified (Zymo Research), and cloned using the BP clonase step from Gateway Cloning Technology (Invitrogen) in a pC5300overExp vector (from Emmanuel Guiderdoni, CIRAD, France). The sequence was verified by excising the insert with HindIII/Acc65I and sequencing. All five amiRNA plant expression vectors were transformed into Agrobacterium tumefaciens.

Methods S5. Plant growth performance and symbiotic interaction

After acid digestion of the sample material (Murphy and Riley 1962), plant 33P contents were measured using a Packard 2000 liquid scintillation counter (Hewlett-Packard). Plant samples were analysed for total N concentration and 15N/14N ratios using an elemental analyser (EA) coupled to aINTEGRA2 (Sercon Ltd., Crewe, UK) continuous-flow sotope-ratio mass spectrometer (EA-CF-IRMS).

References

Koegel S, AitLahmidi N, Arnould C et al.(2013)The family of ammonium transporters (AMT) in Sorghum bicolor: two AMT members are induced locally, but not systemically in roots colonized by arbuscularmycorrhizal fungi. New Phytol198: 853‐865.

Murphy J, Riley JP(1962)A modified single solution method for the determination of phosphate in natural waters. Anal ChimActa27: 31‐36.

Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D (2006)Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18: 1121‐1133.

Tamura K, Dudley J, Nei M, Kumar S (2007)MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. MolBiolEvol24: 1596‐1599.