Plant-associated Bacillus modulates the expression of auxin-responsive genes of rice and modifies the root architecture

Plant growth promoting rhizobacteria (PGPR) impact the root morphogenesis and subsequently modify the root system architecture of a plant. This study was conducted to assess the early modifications of rice root architecture by a PGPR strain, Bacillus altitudinis (strain FD48). Rice seedlings grown in culture tubes under gnotobiotic conditions were inoculated with FD48, and root architecture variables of growing roots were measured in a nondestructive manner using 2-dimensional imaging and processing at periodic intervals. Among the twenty root architecture variables pulled out from the image analysis, the variables such as maximum number of roots, number of lateral roots, root thickness, area, volume and bushiness were significantly increased with time course due to PGPR inoculation than uninoculated control. Specific root length, root depth and length distribution were negatively impacted by PGPR. FD48 inoculation regulated the indole-3-acetic acid accumulation in rice root as compared to uninoculated control. To validate the hormonal modulation leading the root phenotypic modification, the expression of auxin-responsive genes (AUX/IAA) of rice were assessed by reverse transcriptase quantitative PCR. The time course expression pattern of the genes responsible for shortening of primary roots (OsIAA1 and OsIAA4) and genes for lateral root formation (OsIAA11 and OsIAA13) were modulated by PGPR inoculation. These results demonstrate that PGPR play a major role in controlling endogenous IAA levels in rice roots by regulating the auxin-responsive genes and thereby cause changes in root architecture of rice.