Methodology details
Preparation of the phosphate-buffer minimal salts mediumGrowth media composed of K2HPO4 (4.4 g/L), KH2PO4 (1.7 g/L) and yeast extract (50 mg/L) was sterilized by autoclaving (121 o C, 20 min.) after which it was supplemented with 10% salts medium. Filter sterilized (0.20 μm) 100x salts stock contained MgSO4x7H2O (19.5 g/L), MnSO4x4H20 (6.6 g/L), FeSO4x7H20 (1 g/L), CaCl2x6H20 (0.447 g/L) and several drops of concentrated H2SO4 to prevent precipitation of basic salts. Depending of the experiment organic carbon source in the form of glucose and nitrogen source, in the form of NH4Cl, were filter sterilized and added to the growth medium.
DNA extraction procedure, PCR amplifications and analysis detailsCultures were centrifuged (10 000 g, 10 min) and pellets were resuspended in the elution buffer.DNA was extracted from the harvested cells by combining chemical (addition of Lysis buffer and Proteinase K) and mechanical lysis steps (agitation for 12 min at max. speed, Vortex-Genie (MoBio). After centrifugation (11 000 g, 30 s) supernatant containing DNA was collected and transferred onto the Nucleospin Microbial DNA Column. DNA was purified by washing silica membrane with 2 different buffers following centrifugation steps (11 000 g, 30 s). DNA was eluted from the column after the addition of the elution buffer, incubation at room temperature (1 min) and subsequent centrifugation step (11 000 g, 30 s). Quality and quantity of the extracted DNA was assessed by NanoDrop spectrophotometer (BioSpec-nano, Shimadzu). PCR program used for amplification of the V4 16S rRNA region with primers 515/806 included: 94°C (for 3 min), 30 cycles (5 cycle used on PCR products) of 94°C (for 30 s), 53°C (for 40 s) and 72°C (for 1 min), after which a final elongation step at 72°C (5 min) was performed. After amplification,