| Abstract: | Root exudates influence the surrounding soil microbial community, and recent evidence demonstrates the involvement of ATP-binding cassette (ABC) transporters in root secretion of phytochemicals. In this study, we examined effects of seven Arabidopsis (Arabidopsis thaliana) ABC transporter mutants on the microbial community in native soils. After two generations, only the Arabidopsis abcg30 (Atpdr2) mutant had significantly altered both the fungal and bacterial communities compared with the wild type using automated ribosomal intergenic spacer analysis. Similarly, root exudate profiles differed between the mutants; however, the largest variance from the wild type (Columbia-0) was observed in abcg30, which showed increased phenolics and decreased sugars. In support of this biochemical observation, whole-genome expression analyses of abcg30 roots revealed that some genes involved in biosynthesis and transport of secondary metabolites were up-regulated, while some sugar transporters were down-regulated compared with genome expression in wild-type roots. Microbial taxa associated with Columbia-0 and abcg30 cultured soils determined by pyrosequencing revealed that exudates from abcg30 cultivated a microbial community with a relatively greater abundance of potentially beneficial bacteria (i.e. plant-growth-promoting rhizobacteria and nitrogen fixers) and were specifically enriched in bacteria involved in heavy metal remediation. In summary, we report how a single gene mutation from a functional plant mutant influences the surrounding community of soil organisms, showing that genes are not only important for intrinsic plant physiology but also for the interactions with the surrounding community of organisms as well.The diversity of the microbial (bacterial and fungal) communities in soil is extraordinary; 1 g of soil contains more than 10 billion microorganisms belonging to thousands of different species (Roselló-Mora and Amann, 2001). Soil microbial populations are involved in a framework of interactions known to affect key environmental processes like biogeochemical cycling of nutrients, plant health, and soil quality (Pace, 1997; Barea et al., 2004; Giri et al., 2005). Most of the dynamic soil microbial interactions happen near the plant roots and root soil interface, an area called the rhizosphere (Lynch, 1990; Barea et al., 2002; Bais et al., 2006; Prithiviraj et al., 2007). Rhizosphere microbial communities differ between plant species (Priha et al., 1999; Innes et al., 2004; Batten et al., 2006), between ecotypes/chemotypes within species (Kowalchuk et al., 2006; Micallef et al., 2009), between different developmental stages of a given plant (Mougel et al., 2006; Weisskopf et al., 2006), and from those present in bulk soil (Broz et al., 2007). Different root types can also cultivate specific microbes (Lilijeroth et al., 1991; Yang and Crowley, 2000; Baudoin et al., 2002), a response that has generally been attributed to the microenvironments surrounding a root and the varying ability of specific root types to uptake nutrients from soils and secrete exudates. Recent evidence suggests that specific plant species support a highly coevolved soil fungal community, and this process is mediated by root-secreted compounds (Broeckling et al., 2008). Rhizosphere interactions are initiated by the release of compounds from different organisms, and it is believed that carbon compounds secreted by roots act as substrates for certain species of microbes in the rhizospshere (Morgan et al., 2005).Root exudates are released into the rhizosphere by three major pathways: diffusion, ion channel, and vesicle transport (Bertin et al., 2003). Recent evidence has implicated ATP-binding cassette (ABC) transporters in the secretion of phytochemicals present in the root exudates of Arabidopsis (Arabidopsis thaliana) and other plants (Loyola-Vargas et al., 2007; Sugiyama et al., 2007; Badri et al., 2008; Badri and Vivanco, 2009). ABC transporters are the largest family of membrane transport proteins found in all organisms from bacteria to humans (Higgins, 1992). These transmembrane proteins use the energy of ATP to pump a wide variety of substrates across the membranes, including peptides, carbohydrates, lipids, heavy metal chelates, inorganic acids, steroids, and xenobiotics (Goossens et al., 2003). ABC transporters are also involved in plant disease resistance at the leaf level (Kobae et al., 2006; Stein et al., 2006).There is accumulating evidence that root exudates play a role in establishing specific interactions with particular microbes in the rhizosphere (legume''s symbiotic interaction with rhizobia, interaction of plants with mycorrhizae, and plant-growth-promoting rhizobacteria [PGPR]; Nagahashi and Douds, 2000; Bais et al., 2006, 2008; Prithiviraj et al., 2007; Rudrappa et al., 2008). However, how root exudation processes that result in large-scale changes to the surrounding soil microbial community compared to individual microbes have not been determined, although some recent reviews have referred to it as a biological frontier (O''Connell et al., 1996; Kuiper et al., 2004; Ryan et al., 2009). In contrast, gene deletions and overexpression of specific genes in plants have been shown to attract or deter specific microbes (Widmer, 2007), herbivores, or their predators (Baldwin et al., 2006; Pandey and Baldwin, 2007; Mitra and Baldwin, 2008), and recently it has been shown that mutations in nonpigment floral chemistry genes affect flower visitation by native pollinators (Kessler et al., 2008). Thus, it is possible that gene expression manipulation leading to an altered spectrum of root exudates can influence the widespread community of soil organisms surrounding a plant. Using all available information described above, we present the most comprehensive study on the effect of a single gene mutation in an ABC transporter involved in root secretion of phytochemicals by Arabidopsis on the natural and coevolved soil microbial composition. We further determine the compounds that are likely to have an effect on moderating the microbial composition and characterized specific and natural microbes that interact with Arabidopsis in the soil by employing pyrosequencing technology. |
