Materials and Reagents

Millex^®-GP 33 mm syringe filter with a polyethersulfone membrane and 0.22 µm pore size (EMD Millipore, catalog number: SLGP033RB )
Polypropylene microcentrifuge tubes of 2.0 ml Eppendorf^® Safe-Lock (Eppendorf, catalog number: 0030120094 )
Paper towel
Aluminum foil
Pipette tips
15-ml conical polypropylene Greiner centrifuge tubes (Greiner Bio One International, catalog number: 188271 )
50-ml conical polypropylene Greiner centrifuge tubes (Greiner Bio One International, catalog number: 227261 )
Bridges for microcentrifuge tube (Milian, catalog number: 045427 )
Gloves
R. solanacearum strain GMI1000 (Salanoubat et al., 2002). This strain can be retrieved from the CIRM Biological Resource Center (http://www6.inra.fr/cirm_eng/CFBP-Plant-Associated-Bacteria) in the CIRM-BP collection (code CFBP6924)
Acetone > 99.8% AnalaR NORMAPUR^®(VWR, catalog number: 20066.296 )
Milli-Q water obtained at a resistivity of 18.2 MOhm cm at 25 °C
Acetyl acetone > 99% AnalaR NORMAPUR^®(VWR, catalog number: 20092.23 0)
Ethanol, 99.8% (Sigma-Aldrich, catalog number: 02851 )
4-(dimethylamino)benzaldehyde, 98% (Erlich’s reagent) (Sigma-Aldrich, catalog number: 109762 )
Sodium L-glutamic acid monohydrate (Sigma-Aldrich, catalog number: 49621 )
Iron(II) sulfate heptahydrate (FeSO₄·7H₂O) (Sigma-Aldrich, catalog number: F8263 )
Ammonium sulfate, (NH₄)₂SO₄ (Sigma-Aldrich, catalog number: A4418 )
Magnesium sulfate heptahydrate (MgSO₄·7H₂O) (Sigma-Aldrich, catalog number: M5921 )
Potassium phosphate monobasic (KH₂PO₄) (Sigma-Aldrich, catalog number: P5655 )
Potassium hydroxide (KOH) (Sigma-Aldrich, catalog number: 60377 )
Sodium chloride (NaCl) > 99.5% AnalaR NORMAPUR^® (VWR, catalog number: 27810.295 )
N-acetylgalactosamine, 98% (Sigma-Aldrich, catalog number: A2795 )
Hydrochloric acid (HCl), 37%, AnalaR NORMAPUR^® (VWR, catalog number: 20252.29 0)
Sodium carbonate (Na₂CO₃) > 99.9 AnalaR NOR MAPUR^® (VWR, catalog number: 27771.29 0)
Minimal medium (see Recipes)
5 M NaCl solution (see Recipes)
Standard samples of N-acetyl galactosamine (see Recipes)
N-acetylgalactosamine standard stock solution (see Recipes)
2% acetyl acetone, 1.5 M Na₂CO₃ solution (see Recipes)
Erlich’s reagent (see Recipes)

Equipment

Dry bath heater with dual block Corning^®(Corning, model: Corning^® LSE^TM Digital Dry Bath Heater, catalog number: 6786-DB )
Fume hood
Eppendorf^® microcentrifuge 5415 R (Eppendorf, model: 5415 R )
Mini microcentrifuges Corning^® (Corning, model: Corning^®LSE^TM Mini Microcentrifuge, catalog number: 6766 )
Vortex for microcentrifuge tubes
Ultrospec^TM 2100 pro UV/Visible spectrophotometer (GE Healthcare, model: Ultrospec^TM 2100 pro UV/Visible Spectrophotometer , catalog number: 80211221)
10 ml volumetric flask

Software

Appropriate software (SciDavis, Excel, etc.)

Procedure

Culture and sample preparation
1. Run a liquid R. solanacearum culture. Culture is performed in an Erlenmeyer containing 100 ml liquid minimal medium inoculated at 0.01 optical density at 600 nm, agitated at 180 rpm at a temperature of 28 °C.
2. Collect 1 ml culture broth in the exponential or stationary phase. The cell culture must be at least above an optical density of 0.1 (ideally around 0.6) at 600 nm or 5 x 10⁸ cell ml^-1to ensure passing the quorum sensing threshold and thus production of exopolysaccharide.
3. Filter the cell broth with a 0.22 µm filter and collect the supernatant in a 2.0 ml microcentrifuge tube.
4. Store the sample at -20 °C or run the extraction right away.
Exopolysaccharides extraction
1. To precipitate exopolysaccharide, mix 0.2 ml supernatant + 0.004 ml 5 M NaCl solution + 0.8 ml acetone in a 2.0 ml microcentrifuge tube. Mix well with a vortex for 10 sec and place the sample at 4 °C overnight (around 12 h).
2. Centrifuge the sample for 10 min at 16,000 x g (13,000 rpm) and at 4 °C and then discard the supernatant. Invert the tube on a paper towel to drain the pellet well during 15 min. Then, add 0.2 ml Milli-Q water to dissolve the pellet.
3. The sample can be stored at 4 °C for few days (optional) until quantification.
4. On the same day that the assay is to be performed, heat samples at 65 °C on dry bath heater for 10 min. Vortex well and then spin for 5 min at 16,000 x g (13,000 rpm), 4 °C. Collect the supernatant and place it in a new 2.0 ml microcentrifuge tube. The preparation is now referred to as the EPS (exopolysaccharide) sample.
Exopolysaccharide quantification
1. Turn on the dry bath heater positioned in a fume hood. Temperature needs to be at 115 °C before adding the samples.
2. Use the 200 μl of the EPS sample or you can gather EPS samples up to 450 ml. The chosen volume of the sample i is referred to be V_i in the data treatment step, see below.
3. Add 0.15 ml concentrated HCl (37%) to i) the EPS sample or gathered EPS sample up to 0.45 ml, ii) the standard samples, see Table 1. Add enough Milli-Q water to make 0.6 ml total. Mix with a vortex and close the tubes tightly by adding bridges.
  
  Table 1. Preparation of N-acetylgalactosamine standard samples. We recommend performing a standard curve at each run of the experiment, or at least running the 10 µg standard sample and the blank, see Table 1. The optical density at 530 nm in the 10 µg standard sample should be around 0.2.
4. Transfer the tubes to the dry bath heater. Maintain temperatures in the dry bath heater at 115 °C for 30 min. Cover the tubes and the dry bath heater with an aluminum foil if necessary.
5. Transfer the tubes to a rack and cool to room temperature. Then centrifuge for 5 sec the tubes at 2,000 x g (6,000 rpm) using a mini microcentrifuge so the liquid on the top falls back.
6. SLOWLY add, drop by drop using a pipette, 0.4 ml of 2 M Na₂CO₃ solution to each tube. Addition of this solution to the sample tubes will cause a very bubbly reaction. Mix gently but completely.
7. Add 0.5 ml of a freshly made solution containing 2% acetyl acetone in 1.5 M Na₂CO₃. Vortex each tube, then open them to remove last CO₂ released before heat in order to avoid opening of the tubes. Well close the tubes by adding bridges. Heat at 100 °C in a dry bath heater for 20 min.
8. Transfer the tubes to a rack and cool to room temperature. Then centrifuge the tubes quickly so the liquid on the top falls back.
9. Transfer liquid into a 15 ml tube and then add 1.0 ml 99.8% ethanol. Mix well.
10. SLOWLY add 0.5 ml Erlich’s reagent solution. Addition of this solution to the sample tubes will cause a very bubbly reaction, like champagne. Once bubbles slow down, first mix gently and then vortex well.
11. Let the tubes stand for about 30 min in the dark or with aluminum fold around. Then, read optical density of the solution at 530 nm. Use the water sample of the standard samples as blank, see Table 1.

Data analysis

Plot the measured OD at 530 nm (OD₅₃₀) by N-acetylgalactosamine mass (m_Ngal in µg) in the standard samples using appropriate software (SciDavis, Excel, etc.)
Determine the regression equation with the following equation and the value of the correlation factor, α:
Determine the concentration of [Ngal] in mM in the sample i using the following equation:

where,
ω is the mass weight of N-acetylgalactosamine, 221.2090 g mol^-1,
V_i is the volume of the sample supernatant i, usually from 0.2 ml to 0.450 ml depending on the step C2.

Notes

We recommend extreme carefulness during this essay since i) the protocol requires usage of concentrated HCl, ii) the acidic solutions are heated over 100 °C and the Eppendorf tube may open, iii) mixing the Na₂CO₃ and acidic solutions leads to a strong bubbling, and thus liquid may overflow out of the tubes. Hence, working under a fume hood and using gloves is required. Hence, we recommend usage of microcentrifuge tube bridges to avoid opening of the tubes during heat bath.
Using two dry bath heaters with 2 heat blocks each is convenient to avoid temperature adjustment between the different protocol steps and also for running the standard samples plus the replicates.

Recipes

Minimal medium
20 mM sodium L-glutamic acid monohydrate (carbon and energy source)
Salt composition:
1.25 x 10^-4g/L FeSO₄·7H₂O,
0.5 g/L (NH₄)₂SO₄
0.05 g/L MgSO₄·7H₂O
3.4 g/L KH₂PO₄
The pH is adjusted to 7 with 10 N KOH
Note: Sodium L-glutamic acid monohydrate is the sole source of carbon and energy in Minimal medium (Plener et al., 2010).
5 M NaCl solution (10 ml)
2.92 g NaCl
Milli-Q water
Dissolve 2.92 g NaCl in Milli-Q water using a 10 ml volumetric flask
N-acetylgalactosamine standard stock solution at 500 µg ml^-1 concentration (100 ml)
50 mg N-acetylgalactosamine
100 ml Milli-Q water
Dissolve 50 mg N-acetylgalactosamine in Milli-Q water using a 100 ml volumetric flask. Prepare 1 ml aliquots in 2.0 ml microcentrifuge tubes and store at -20 °C until use
Standard samples of N-acetyl galactosamine (10 samples with different concentration)
N-acetyl galactosamine standard stock solution at 500 µg ml^-1 concentration
Milli-Q water
Prepare the standards samples by diluting various quantity of the N-acetylgalactosamine standard stock solution at 500 µg ml^-1concentration with Milli-Q water to reach 0.450 ml final volume, see Table 1
2% acetyl acetone, 1.5 M Na₂CO₃ solution (20 ml)
3.18 g of Na₂CO₃
19.6 ml Milli-Q water
0.4 ml acetyl acetone
Dissolve 3.18 g of Na₂CO₃ in 19.6 ml Milli-Q water in a 50 ml Falcon tube. Then, add 0.4 ml acetyl acetone
Erlich’s reagent (12 ml, for 24 samples)
0.4 g 4-(dimethylamino)benzaldehyde (Erlich’s reagent)
6.0 ml 99.8% ethanol
6.0 ml HCl (37%)
Under a fume hood, dissolve the 4-(dimethylamino)benzaldehyde into 6 ml ethanol 99.8%. Then, carefully, add 6.0 ml of 37% HCl. Make fresh, just before use and protect from the light

Acknowledgments

This work was supported by EMBO (Long-Term Fellowship ALTF 1627-2011), Marie Curie Actions (EMBOCOFUND2010, GA-2010-267146), the Institut National de la Recherche Agronomique (Plant Health Division grant AAP SPE 2012) and the French Laboratory of Excellence project TULIP (ANR-10-LABX-41; ANR-11-IDEX-0002-02).

References

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