Original research article

The authors used this protocol in:
PLOS Genetics
Mar 2018

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Quantification of Root Colonizing Bacteria   

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Here we describe a simple method to quantify the number of viable bacteria (e.g., Enterobacter sp. SA187) that colonize the root system of Arabidopsis thaliana.

Keywords: Arabidopsis thaliana, Colony forming unit, Endophytes


Colonization of roots by inoculated bacteria is an important step in the interaction between beneficial bacteria and the host plant. Enterobacter sp. SA187 is an endophytic bacterium that has been isolated from root nodules of the indigenous desert plant Indigofera argentea (Andrés-Barrao et al., 2017; Lafi et al., 2017). SA187 promotes the growth of the model plant Arabidopsis thaliana under diverse abiotic stresses such as salinity, drought or high temperature, demonstrating an important potential for application as Plant Growth Promoting Bacteria (PGPR) to improve abiotic resistance and yield of crops in arid lands. SA187 can colonize both roots and shoots of A. thaliana on ½ MS agar plates or in soil (de Zélicourt et al., 2018). To follow the fate of inoculant strain SA187 on the non-host plant A. thaliana, we applied a routinely cultivation-dependent method. This protocol has been successfully used to mounter the bacterial number colonized both root and shoot of the A. thaliana plant under different abiotic stresses (de Zélicourt et al., 2018).

Materials and Reagents

  1. Mechanical pipette tips
  2. 1.5, 2 ml Eppendorf tube
  3. Razor Blades (LabSupplyOutlaws, catalog number: 12-640 )
  4. NuncTM 96 Microtiter Plates (Thermo Fisher Scientific, Thermo FisherTM, catalog number: 262162 )
  5. Disposable Tissue Grinder Pestle (Corning, Axygen®, catalog number: PES-15-B-SI )
  6. TissueLyser II .Gentech Biosciences (GENTECH BIOSCIENCES, catalog number: 85300 )
  7. Lab Parafilm M (Labdirect, catalog number: PM992 )
  8. 100 mm Petri dish (Corning, Falcon®, catalog number: 351029 )
  9. Square Petri Dish with Grid (SIMPORT, catalog number: D210-16 )
  10. Stainless Steel Beads, 2.3 mm diameter (Bio Spec Products, catalog number: 11079123ss )
  11. Seeds of Arabidopsis (Arabidopsis thaliana)
  12. Murashige and Skoog Basal Salt Mixture (MS) (Sigma-Aldrich, catalog number: M5524 )
  13. LB Broth with agar (Lennox) (Sigma-Aldrich, catalog number: L2897 )
  14. Magnesium chloride anhydrous, ≥ 98% (Sigma-Aldrich, catalog number: M8266 )
  15. Sodium chloride BioXtra, ≥ 99.5% (Sigma-Aldrich, catalog number: S7653 )
  16. Potassium hydroxide (Sigma-Aldrich, catalog number: 484016 )
  17. Silwet® L-77 (PhytoTechnology Laboratories, catalog number: S7777 )


  1. Tweezers with Sharp Tip (Labdirect, catalog number: 560.002.115 )
  2. Top centrifuge (Eppendorf)
  3. Vortex (VWR digital Vortex Mixer)
  4. 28 °C shaker-incubator
  5. Growth chamber (Percival Scientific or similar types. Set the growth conditions to 22 °C, 16 h light/8 h dark cycles)
  6. TissueLyser II© (QIAGEN)
  7. Autoclave (TOMY SEIKO, model: LSX-500 or similar types)
  8. Mechanical pipettes (Gilson, catalog numbers: F123601 (P200) and F123602 (P1000)
  9. Analytical balance (0.1 mg resolution)


  1. Prepare the bacterial culture
    1. Revive the SA187 bacterial strains (or any other strain) on LB Agar media (or equivalent media) and incubate at 28 °C for 24 h.
    2. Inoculate 10 ml LB media with a single colony on a shaker incubator with 220 rpm at 28 °C for 16 h (overnight) (pre-culture).
    3. Take 100 µl of the O.N. culture to start a new fresh 2 ml culture and let the bacteria grow for 2-3 h.
    4. Prepare and autoclave ½ MS with 0.9% agar adjusted to pH 5.8 with 1 M KOH. Allow the medium to cool down to reach 37-40 °C before pouring the plates.

  2. Bacteralized vertical plate culture of Arabidopsis seedlings
    1. In a 50 ml Falcon tube mix 50 ml of warm ½ MS medium with 0.1 ml of a bacterial suspension (OD600 = 0.21) to obtain 107 bacteria, dispense the media in square Petri dishes (Figure 1) and let the agar solidify. For control plates (no bacteria) add 0.1 ml of liquid LB.

      Figure 1. Schematic illustration of different steps for preparing the bacteralized vertical plates of Arabidopsis seedlings

    2. Sterilize Arabidopsis seeds following a standard protocol (de Zélicourt et al., 2018) or similar methods described elsewhere and sow the sterilized seeds. Keep the plates and seeds at 4 °C in the dark for 2 days.
    3. Transfer the plates to a growth chamber and keep them vertically for 5 days in long day conditions: 16 h-light /8-h dark cycle at constant 22 °C.
    4. Transfer the colonized seedlings to ½ MS plates with or without 100 mM NaCl and incubate for 10 days or as desired.

  3. Bacterial Quantification: Colony Forming Units
    1. With forceps and razor blades, separate root and shoot and combine three roots and/or three shoots in one 1.5 ml tube, record the fresh weight.
    2. Physically grind using the plastic cone grinder first without MgCl2 and then add 500 μl 10 mM MgCl2 supplemented with 0.02% Silwet L-77 and vortex vigorously (Figure 2).

      Figure 2. Schematic illustration of different steps for the quantification of bacteria in Arabidopsis plants

    3. Use TissueLyserII with Stainless Steel Beads to homogenize the plant material.
    4. Proceed with serial dilutions by removing 10 μl and add to 90 μl of sterile distilled H2O in 96 microtiter plates.
    5. Spot 10-μl samples (3 replicates) from each dilution on LB agar plates. Allow spotted samples to dry, cover the plates, and wrap them with Parafilm.
    6. Incubate the plates at 28 °C for 24 h or until the colonies are clearly visible. Count colonies from each dilution, record the colony forming units (CFU), and calculate CFU/mg plant material.
      Note: All work shall be done under sterile conditions.

Data analysis

Calculate the number of bacteria (CFU) per milliliter or gram of sample by dividing the number of colonies by the dilution factor The number of colonies per ml reported should reflect the precision of the method and should not include more than two significant figures.
The CFU/ml can be calculated using the following formula:

CFU/ml = (number of colonies x dilution factor)/volume of culture plate

CFU value could also be divided by the root/shoot fresh weight to get CFU/mg plant material.


The authors would like to express their gratitude to all members of the Hirt lab and the technical support team. This publication is based upon work supported by the King Abdullah University of Science and Technology (KAUST), base fund (No. BAS/1/1062-01-01) for HH.
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


  1. Andrés-Barrao, C., Lafi, F. F., Alam, I., de Zelicourt, A., Eida, A. A., Bokhari, A., Alzubaidy, H., Bajic, V. B., Hirt, H. and Saad, M. M. (2017). Complete genome sequence analysis of Enterobacter sp. SA187, a plant multi-stress tolerance promoting endophytic bacterium. Front Microbiol 8: 2023.
  2. de Zélicourt, A., Synek, L., Saad, M. M., Alzubaidy, H., Jalal, R., Xie, Y., Andrés-Barrao, C., Rolli, E., Guerard, F., Mariappan, K. G., Daur, I., Colcombet, J., Benhamed, M., Depaepe, T., Van Der Straeten, D. and Hirt, H. (2018). Ethylene induced plant stress tolerance by Enterobacter sp. SA187 is mediated by 2-keto-4-methylthiobutyric acid production. PLoS Genet 14(3): e1007273.
  3. Lafi, F. F., Alam, I., Geurts, R., Bisseling, T., Bajic, V. B., Hirt, H. and Saad, M. M. (2017). Draft genome sequence of Enterobacter sp. Sa187, an endophytic bacterium isolated from the desert plant Indigofera argentea. Genome Announc 5(7): e01638-16.
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Copyright: © 2018 The Authors; exclusive licensee Bio-protocol LLC.
How to cite: Saad, M. M., de Zelicourt, A., Rolli, E., Synek, L. and Hirt, H. (2018). Quantification of Root Colonizing Bacteria. Bio-101: e2927. DOI: 10.21769/BioProtoc.2927.
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If you have any questions/comments about this protocol, you are highly recommended to post here. We will invite the authors of this protocol as well as some of its users to address your questions/comments. To make it easier for them to help you, you are encouraged to post your data including images for the troubleshooting.

If you have any questions/comments about this protocol, you are highly recommended to post here. We will invite the authors of this protocol as well as some of its users to address your questions/comments. To make it easier for them to help you, you are encouraged to post your data including images for the troubleshooting.

Muahammad Ahmad
Very helpful protocol
Just a short question: Is the 1/2 MS medium with sugar or without sugar? Thank you
3/16/2021 6:42:49 AM Reply
Axel de Zelicourt
Institut of Plant Sciences Paris-Saclay (IPS2), , UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, , France, France,

hello Muhammad

we used the MS medium basal salt and nothing else (no addition of vitamins or hormones) and of absolutely no sugar at all, as the bacteria would develop extremely rapidly and cover your plant :)

3/17/2021 1:12:27 AM Reply

Muahammad Ahmad

Thank you for the response.

Best Regards

3/31/2021 6:58:47 AM Reply

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