Root secretions: from genes and molecules to microbial associations.

As the field of root biology continues to gain momentum, researchers have begun to recognize the importance of root secretions in innumerable plant–plant and plant–microbe interactions hidden beneath the ground. It is well documented that diverse plant species form both beneficial and harmful associations with soil bacterial communities. Understanding all of the factors involved in these rhizosphere communications is the daunting task that has been laid before root biologists. However, Micallef et al. (2009) have made progress in this field by describing the influence of genetic background on root secretions in Arabidopsis thaliana and the implications of the unique root secretion patterns on associated bacterial communities. In the past, root secretion patterns of rice, wheat, and barley have been analysed and compared, revealing variations between species (Mazzola et al., 2004). In addition, root secretion profiles of the model plant A. thaliana (Columbia-0) have been analysed after treatment with biological elicitors and signalling molecules to reveal 289 possible different secondary metabolites present in the secretions (Walker et al., 2003; Narasimhan et al. 2003). These studies point to the countless combinations of secondary metabolites that may be present in the rhizosphere at any given time. Micallef et al. (2009) took the current research one step further and were interested in determining whether genetic influences within a species can produce unique root secretion cocktails. In their recent paper, they compared the differences between root secretion profiles, through HPLC, of eight different A. thaliana accessions (ecotypes) and determined that root secretion profiles did indeed differ in the compounds present and in the relative abundance of many of these compounds (Micallef et al., 2009). As all of the plants from different accessions were grown under the same conditions, natural genetic variation is attributed to cause differences in the secreted compounds. These data support the research of Clark et al. (2007) where it was demonstrated that when 20 A. thaliana accessions were compared, approximately 4% of the genome differed or were deleted with reference to the control (Columbia-0). As the eight different accessions tested by Micallef et al. (2009) were originally collected from a wide geographical range, it supports the suggestion that allelic variations between these plants may confer a selective advantage in certain environments, as has been demonstrated for traits such as flowering time and plant growth (Koornneef et al., 2004). Along these lines, Micallef et al. (2009) further investigated as to whether these unique secretion cocktails resulted in variations in bacterial community associations. Previous research by Broeckling et al. (2008) demonstrated that, in both model species, Medicago truncatula and A. thaliana, plants were able to maintain resident soil fungal populations but were not able to maintain non-resident populations, demonstrating that root exudates are able to regulate some soil microbe populations. Micallef et al. (2009) continued this line of research and demonstrated that bacterial populations are also influenced by root secretion compounds as they found that each of the eight accessions tested has distinct and reproducible bacterial community associations. These bacterial community associations differed in the species present and in the abundance of the species associated with the A. thaliana roots. Although a direct link was not examined, strong evidence has been presented to support that differences in bacterial community assemblages is a result, in part, of root secretions compounds. Other root traits that differ between accessions, such as root architecture are likely to play a role as well. It has long been known that microbial communities in the soil contribute valuable nutrients to plants (e.g. rhizobia and Azolla-associated cyanobacteria provide nitrogen to legumes and to rice, respectively). In addition, beneficial microbes can also protect plants from disease, as shown by the recognized ‘suppressive soil’’ effect (Schroth and Hancock, 1982). Yet relatively little is known about the diversity of microbes that associate with plants, i.e. the microbiome, and their combinatorial interactions and effects on performance and plant yields. Root-derived microbial colonization initiation and development is complex and not well understood due to the dynamic nature of plant root surfaces and microbial diversity. However, it remains unclear whether specific plant derived compounds influence colonization structures and if microbial colonization patterns affect the plant genomic and metabolic responses.