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\section{Introduction}  Soil bacteria that associate with plants may confer neutral, beneficial, or inhibitory effects on their host. Plant growth promotion involves different bacterial relationships and these include symbiosis, colonization of plant intercellular tissues and the activities of cyanobacteria (Glick, 2012). Bacteria plant growth promotion could be either direct or indirect. Directly, they help in the acquisition of resources and regulate plant growth hormone levels. Indirectly, they promote plant growth and development by protecting the plant from harmful agents (Glick, 2012). The use of beneficial microorganisms in Agriculture has gained prominence recently and this is due to concerns over the harmful effects chemicals used on food produce may pose (Whips, 2001).  Stenotrophomonas play an important role in nature, particularly in biogeochemical cycling, and in recent times, they have also been used in applied microbiology and biotechnology (Ikemoto et al., 1980). The biotechnological interest in S. maltophilia stems from their potential plant growth promoting properties, their use in biological control of plant fungal pathogens, their capability to degrade xenobiotic compounds and their potential to decontaminate the soil (Suckstorff and Berg 2003, Hayward et al. 2009).   The ability of Stenotrophomonas isolates to control fungal infections in plants has been widely documented (Dunne et al., 1997, Suckstorff and Berg 2003, Hayward et al. 2009, Zhang and Yuen, 2000). For example, S. maltophilia strain W81, isolated from the rhizosphere of field-grown sugar beet, produced the extracellular enzymes chitinase and protease and inhibited the growth of the phytopathogenic fungus Pythium ultimum in vitro, resulting in reduction of damping-off of soil-grown sugar beet (Dunne et al., 1997). Zhang and Yuen (2000) also reported S. maltophilia isolate C3 to be a biological control agent, active in part through chitinase activity. This bacteria strain was effective in inhibiting germination of conidia of Bipolaris sorokiniana (Sacc.), a cereal pathogen. In the Nile Delta of Egypt, some strains of S. maltophilia (PD3532, PD3533, PD3534) have been demonstrated to have the potential to control brown rot of potato caused by the bacterium Ralstonia solanacearum (Messiha et al., 2007). Suckstorff and Berg (2003) found that three strains of S. maltophilia could enhance plant growth in in strawberry seedlings.   On the other hand, some S. maltophilia isolates cause disease in humans, including pneumonia, bacteremia, urinary tract infections, wound infections, bronchitis, endocarditis, meningitis, eye infections and catheter-associated infections (Schaumann et al., 2001; Brooke et al., 2007; Brooke, 2012). This pathogen has been shown to be an opportunistic bacterium usually associated with respiratory infections in immunocompromised individuals (Brooke, 2012) and has become a microbe of concern in hospitals in recent years. S. maltophilia is the third most common nosocomial non-fermenting Gram-negative bacilli after Pseudomonas aeruginosa and Acenitobacter species in patients in intensive care units. In addition, there are many multi-drug resistant strains of S. maltophilia that affect humans. More cases of drug-resistant S. maltophilia infections have been reported in the last decade, and high case/fatality ratios in susceptible populations have characterized these cases (Sader and Jones, 2005). Although S. maltophilia is naturally an environmental bacterium, its transition into an important nosocomial pathogen has likely been driven by natural selection and adaptation.   Extensive studies have been conducted on S. maltophilia-plant interactions but only a few of them have focused on using phenotypic data to compare clinical and environmental isolates. The overarching goal of this study was therefore to determine if environmental isolates of S. maltophilia are phenotypically distinct from clinical isolates. One of the ways to achieve this goal was to determine if the clinical isolates retain or lose their plant growth promotion properties once they leave the hospital environment. In addition, variability among S. maltophilia isolates in their ability to protect canola seedlings against the harmful effects of the blackleg fungus, Leptosphaeria maculans and the plant pathogenic bacterium Burkholderia cenocepacia (K56-2) was investigated. In order to generate information on genetic relatedness of the isolates used in this study, phylogenetic analysis was conducted.