Rhizosphere Biology Research in Bais Lab

Root Exudation: A novel rhizospheric interface to study biological interactions.

Focus

The rhizosphere encompasses the millimeters of soil surrounding a plant root where complex biological and ecological processes occur. Our lab efforts involve the elucidation of the role of root exudates in interactions between plant roots and other plants, microbes, and nematodes present in the rhizosphere. Evidence indicating that root exudates may take part in the signaling events that initiate the execution of these interactions has guided our lab’s research interests to identify root secreted factors that define such interactions. For instance, a variety of positive and negative plant-plant and plant-microbe interactions are yet to be defined at the molecular and the ecosystem scale. Furthermore, the methodologies and hypothesis developed in our lab would address these interactions under laboratory conditions.

Projects

Involvement of root exudates in defining positive root-microbe interactions. 

To address this hypothesis we will use Bacillus subtilis as a model system. Previous literature shows that B. subtilis acts as a bio-control agent and is used for most of the agricultural crops, though the mechanism involved in biocontrol activity of B subtillis is still unknown. We will elucidate the mechanism involved in the biocontrol activity of B. subtilis. Our studies show that B. subtilis forms a protective biofilm on root surfaces, which wards-off pathogenic bacteria by creating a space competition on the root surface. We will further check and identify the root secreted component involved in triggering B. subtilis biofilm formation. We will carefully analyze the involvement of two-step root communication by checking the effect of root volatiles and secretions on bacterial motility and  attachment responses. We will also evaluate the participation of rhizospheric nematodes as possible vectors in delivering B. subtilis to roots.

Participation of root exudates in heavy metal speciation and mobilization

Toxic heavy metal phytoremediation utilizing metal hyperaccumulator plants offer a unique source for decontamination of soil. The plant Alyssum murale is known for its ability to hyperaccumulate the heavy metal nickel (Ni2+), however the reasons for hyperaccumulation remain unproven. Little is known about the role of root exudates in heavy metal hyperaccumulation in plants. Our lab, in collaboration with Dr. Donald Sparks, will utilize A. murale, to define the role of root exudation in Ni2+-speciation and translocation. We will also decipher the root exudation component involved in Ni2+-hyperaccumulation in A. murale. Briefly, we will dissect the A. murale‘s exudation metabolome in the presence and absence of Ni2+. We will then examine the involvement of organic acid exudation in Ni2+-speciation, and compare the exudation metabolome in both hyper and non-hyperaccumulating Alyssum species. The results of this work will help to define the role of root exudation in the important agronomical and environmental processes of heavy metal phyto- remediation.

Natural Killers

Our lab is interested in understanding the mechanism involved in plant invasion of US coast lines. Phragmites australis, or common reed, is a wetland plant species found in every U.S. state. The species is invasive particularly in the eastern states along the Atlantic Coast and increasingly across much of the Midwest and in parts of the Pacific Northwest. The basic biology behind the invasiveness of P. australis still remains unknown. Our lab, in collaboration with Dr. John Gallagher, will elucidate the involvement of allelopathy in P. australis invasion and other noxious marine plants. We will also identify the molecular targets of the produced toxin in P. australis using the model plant system Arabidopsis. The identification of a resistance gene against P. australis toxins would lead to the engineering of native plants to defend against P. australis invasion.

Identification of Type-III secretion and biofilm inhibitors from root exudates against opportunistic Gram-negative bacteria

The mechanisms of infections of the opportunistic plant pathogens involve production of toxins via the type-III secretion system and pathogenic biofilm formation. Our lab is interested in exudate mining to identify potential biofilm and type-III secretion inhibitors. To this end, we will use Pseudomonas aeruginosa model system. P. aeruginosa causes infections in cystic fibrosis patients. Our studies will involve testing of different plant root exudates for a possible type-III and biofilm inhibition activity. Identification of novel plant-based inhibitors would lead to elucidation of new molecular targets in P. aeruginosa. We will also screen chemical library (~50K) compounds to look for potential biofilm and type-III secretion inhibitors.

Chemical-genomics approach

Screening root exudates of native plant species along with  chemical library of ~50K small chemical compounds to study the genome wide response in the model plant Arabidopsis and worm Caenorhabtidis elegans for a possible herbicidal and nemeticidal activity. We will also make efforts to correct single gene defects in both plant and nematode models using a chemical library screen. To this end, we will use obvious defective phenotypes in both plant and nematode models. Arabidopsis produces fine root hairs, but loss of function of one gene (rhd- root hair defective) results in either complete loss or  defective root hair formation. We will exploit a chemical genetic forward screen to correct this defect using rhd mutants. On the similar note, we will use a C. elegans  mutant unc-1 (uncoordinated), which is unable to perform typical serpentine movements because of single gene defect. We will try to correct this genetic defect by using the approach as described above for the plants. The implication of this research has both basic as well as applied values in terms of finding molecular targets in both plant and invertebrate models.