Growing roots: Plant cues invite helpful bacteria to move in

Research Areas:

Gene regulation, Bacterial biofilms, Biofertilizer, B. subtilis

Imaging Needs:

Good sensitivity for yellow and cyan fluorescence

Imaging System:
  • Nikon Eclipse TE2000-U microscope
  • 20× Plan Apo objective and 60× Plan Apo oil objective
  • CFP/YFP dual-band filter set
  • Hamamatsu ORCA-ER CCD camera
  • MetaMorph and Adobe Photoshop software
Imaging Bacteria

Hamamatsu's ORCA-ER camera provided Beauregard et al. with the resolution and sensitivity needed to localize fluorescently labeled bacteria on plant roots. Find out how the enhanced low-light capability and precise localization of Hamamatsu’s ImageEM camera help Ashley Cadby and colleagues to zoom in on bacterial cell walls. Read now.


How does the beneficial bacterium Bacillus subtilis colonize plant roots?

The Gram-positive bacterium Bacillus subtilis lives in soil, often associated with the roots of a variety of plant species, including crops such as tomatoes. The bacterium can improve plant growth and protect against pathogens. For example, it secretes hormones that aid homeostasis and salt balance in some plants, as well as antimicrobials that can prevent infection. For its beneficial effects, B. subtilis is often used as a biofertilizer.


A great deal is known about how B. subtilis forms biofilms—multicellular communities protected by an extracellular matrix of proteins and polysaccharides—in cell culture. However, the mechanisms by which the bacterium colonizes plant roots and the importance of biofilms in the process are not well understood.


Bacillus subtilis biofilm induction by plant polysaccharides
Pascale B. Beauregard, Yunrong Chai, Hera Vlamakis, Richard Losick, and Roberto Kolter
PNAS. 2013 Apr 110(17): E1621–E1630. PMCID: PMC3637697.

Beauregard, et al,1 demonstrated that biofilm formation is essential to root colonization. Using a Hamamatsu ORCA-ER CCD camera and B. subtilis strains expressing genes for yellow or cyan fluorescent proteins, the researchers localized and co-localized bacteria with specific gene expression profiles on the surface of young plant roots. The results showed that genes important in biofilm formation in vitro also become active during root colonization.

Specific polysaccharides common to the surface of plant roots induced the bacteria to form biofilms. The polysaccharides also provided a source of sugars for the biofilm matrix. The authors conclude that plant root polysaccharides act as both a cue and a fuel to encourage bacterial colonization and biofilm formation.


Beauregard, et al, used the Hamamatsu ORCA-ER camera to co-localize bacterial cells with differing gene profiles on the surfaces of plant roots. Find out how other microbiologists are tracking individual cells down to 35–42 nanometers—read Exciting Insights into Cell Growth.


  1. Beauregard, et al. Bacillus subtilis biofilm induction by plant polysaccharides. PNAS. 2013 Apr 110(17): E1621–E1630. PMCID: PMC3637697.
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