Additional file 2. Supporting material on phylotype sequences related to Tables S1, S2, S4, and S5.

NanoSIMS measurement of 13C, 15N and 18O transfer from hyphae of Pythium ultimum to spores and vegetative cells of Bacillus subtilis.
NanoSIMS measurements:
- Measurements were carried out in negative extraction mode with a DC source of primary Cs+ ions.
- 2 pA beam focused into 70 nm spot
- energy of collision was set to 16 keV
- scanning: 512 x 512 px matrix with 5msec dwell time per pixel
before analysis, samples surface of 60 x 60 µm was treated with 10 nA of low-energy (50 eV) Cs+ beam for 10 min
- detected secondary ion species: ¹²C-, ¹³C-, ¹⁶O-, ¹⁸O-,¹²C¹⁴N-, ¹²C¹⁵N-, ¹³C¹⁴N-, ³²S-
- mass resolving power: between 8000 and 12000, exit slit: 40 µm, wide entrance slit: 40 µm, aperture slit: 200 µm, energy slit: cutting 30% of secondary ions in high energy tail
- Bacterial and fungal biomass was analysed on a conductive chromium-coated, round-shaped silicon wafer
- Experiments were performed in duplicate
- fields of either 20 x 20, 30 x 30 or 40 x 40 µm were analysed depending on the arrangement of hyphae and bacterial cells
- Data were analysed with the Look@NanoSIMS software

• qualitative analysis of sample composition and yields of secondary ion species
  - measurements with a ToF-SIMS.5 (ION-TOF GmbH, Münster)
  - measurement in imaging modeof ToF-SIMS.5 in combination with delayed extraction of negative secondary ions
  - Mass resolving power above 3000 and lateral resolution of about 130 nm
  - 30 keV NanoProbe, 0.02 pA of primary Bi3+ cluster ions in 100 ns pulses with 200 µm repetition period
  - analysis in 400 scans/plains with 5 shots of primary Bi3+ cluster ions per pixel -> distributed randomly in 512 x 512 raster over 56 x 56 µm area on silicon wafer
  Analysis:
  - stacking of scans after lateral drift correction
  - total stack was analysed for lateral distribution of ion yields using SurfaceLab 6.5 software (ION-TOF GmbH)
  
  
  

• qualitative analysis of sample composition and yields of secondary ion species
  - measurements with a ToF-SIMS.5 (ION-TOF GmbH, Münster)
  - measurement in imaging modeof ToF-SIMS.5 in combination with delayed extraction of negative secondary ions
  - Mass resolving power above 3000 and lateral resolution of about 130 nm
  - 30 keV NanoProbe, 0.02 pA of primary Bi3+ cluster ions in 100 ns pulses with 200 µm repetition period
  - analysis in 400 scans/plains with 5 shots of primary Bi3+ cluster ions per pixel -> distributed randomly in 512 x 512 raster over 56 x 56 µm area on silicon wafer
  Analysis:
  - stacking of scans after lateral drift correction
  - total stack was analysed for lateral distribution of ion yields using SurfaceLab 6.5 software (ION-TOF GmbH)
  
  
  

NanoSIMS measurement of 13C, 15N and 18O transfer from hyphae of Pythium ultimum to spores and vegetative cells of Bacillus subtilis.
NanoSIMS measurements:
- Measurements were carried out in negative extraction mode with a DC source of primary Cs+ ions.
- 2 pA beam focused into 70 nm spot
- energy of collision was set to 16 keV
- scanning: 512 x 512 px matrix with 5msec dwell time per pixel
before analysis, samples surface of 60 x 60 µm was treated with 10 nA of low-energy (50 eV) Cs+ beam for 10 min
- detected secondary ion species: ¹²C-, ¹³C-, ¹⁶O-, ¹⁸O-,¹²C¹⁴N-, ¹²C¹⁵N-, ¹³C¹⁴N-, ³²S-
- mass resolving power: between 8000 and 12000, exit slit: 40 µm, wide entrance slit: 40 µm, aperture slit: 200 µm, energy slit: cutting 30% of secondary ions in high energy tail
- Bacterial and fungal biomass was analysed on a conductive chromium-coated, round-shaped silicon wafer
- Experiments were performed in duplicate
- fields of either 20 x 20, 30 x 30 or 40 x 40 µm were analysed depending on the arrangement of hyphae and bacterial cells
- Data were analysed with the Look@NanoSIMS software

Additional file 2. Supporting material on phylotype sequences related to Tables S1, S2, S4, and S5.