The tomato rhizosphere, an environment rich in nitrogen-fixing Burkholderia species with capabilities of interest for agriculture and bioremediation.

It is well known that hundreds of thousands of bacterial species remain to be discovered and cultured, representing a substantial reservoir of genetic diversity and great potential for biotechnological applications. Although most of the bacteria inhabiting common environments (e.g., agricultural soils and plants) have not yet been grown in culture, many of them could be cultivated using standard methods. However, for many environments, research on microbial taxonomy and ecology is lacking. Unfortunately, novel bacterial species are often described based on the analysis of a very limited set of isolates (59), commonly one to three. This is true for many bacterial species, including several belonging to the genus Burkholderia. For example, the species B. kururiensis (80), B. sacchari (9), B. phenoliruptrix (16), B. terrae (79), B. tuberum, and B. phymatum (73) were recently described on the basis of a single isolate analyzed, and consequently, their environmental distribution and ecological role are unknown. B. kururiensis and B. sacchari were described as species with abilities to degrade trichloroethylene and to biotechnologically produce polyhydroxyalkanoic acids, respectively, but new studies related to their ecologies or applications are largely lacking. The nitrogen-fixing species B. xenovorans was described on the basis of three isolates (32); strain LB400T was isolated from polychlorinated biphenyl (PCB)-contaminated soil in Moreau, NY, strain CAC-124 was isolated from the rhizosphere of a coffee plant cultivated in Veracruz, Mexico, and strain CCUG 28445 was recovered from a blood culture in Sweden. Although strain LB400T is the best-studied PCB degrader, and its pathways for degradation of these compounds have been extensively characterized at the genetic and molecular levels (25, 35), strains CAC-124 and CCUG 28445 have been only partially analyzed and do not share the biphenyl-biodegrading capacities of strain LB400T (32). Recently, one B. xenovorans isolate was recovered from the rhizosphere of maize cultivated in The Netherlands (62). Although the complete genome of B. xenovorans LB400T was recently sequenced (12), it is noteworthy that the four extant B. xenovorans strains described in diverse studies have been randomly recovered from different environments and widely distant geographical regions, and there are no studies on the distribution of this PCB-degrading, nitrogen-fixing species or its association with plants. Emphasis has been given to studies of the isolation, taxonomy, and distribution of Burkholderia species related to human opportunistic pathogens, especially the B. cepacia complex species found in cystic fibrosis patients (33, 45, 52; for reviews, see references 15 and 42). In contrast, few studies have been performed on the overall diversity of the genus Burkholderia (61, 63), even though nonpathogenic Burkholderia species are frequently recovered from different environments (6, 40, 70), and despite their biotechnological potential in bioremediation and other applications (34, 70; for a review, see reference 48). Knowledge of novel diazotrophic Burkholderia species (11, 32, 50, 54), including legume nodule symbionts (14, 73), phylogenetically greatly distant from the B. cepacia complex species, has come very recently, but their environmental distribution and relevant features for agronomic and environmental applications are little known (13, 27, 32, 49). Bacteria are involved in degradation processes of many aromatic compounds released into the environment by the decay of plant material or by anthropogenic activity. Phenolic compounds and polymers containing benzene rings (e.g., lignins) are natural aromatic compounds (21, 29). However, phenol is a man-made aromatic compound and along with its derivatives is considered a major hazardous compound in industrial wastewater. Similarly, aromatic hydrocarbons like benzene and toluene are common pollutants of soil and groundwater (78). Soil microorganisms are capable of using aromatic compounds as sole carbon sources, owing to aerobic biodegradation catalyzed by mono- or dioxygenases (3, 78). In the last few years, rhizoremediation (microbial degradation of hazardous compounds in the rhizosphere) and phytoremediation (the use of plants to extract and degrade harmful substances) have been considered alternatives for decontamination of soils. In addition, bacteria are able to exert positive effects on plants through various mechanisms. For instance, nitrogen fixation (the natural transformation of atmospheric N2 to ammonia) contributes organic nitrogen for plant growth (28), while the bacterial enzyme 1-amino-cyclopropane-1-carboxylate (ACC) deaminase hydrolyzes ACC (the immediate precursor of ethylene) and lowers the levels of ethylene produced in developing or stressed plants, promoting root elongation (30). Some bacteria solubilize insoluble minerals through the production of acids, increasing the availability of phosphorus and other nutrients to plants in deficient soils (55). Several bacteria improve plant growth through suppression of pathogens by competing for nutrients, by antibiosis, or by synthesizing siderophores, which can solubilize and chelate iron from the soil and inhibit the growth of phytopathogenic microorganisms (23). This work was aimed at revealing the occurrence of nitrogen-fixing Burkholderia species associated with tomato (Lycopersicon esculentum) plants cultivated in different locations in Mexico. We found that the rhizosphere of tomato is a reservoir of different known and unknown diazotrophic Burkholderia species that are able to exhibit in vitro some activities involved in bioremediation, plant growth promotion, and biological control.