Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria

Abstract

BackgroundIn recent years, the number of human infections caused by opportunistic pathogens has increased dramatically. Plant rhizospheres are one of the most typical natural reservoirs for these pathogens but they also represent a great source for beneficial microbes with potential for biotechnological applications. However, understanding the natural variation and possible differences between pathogens and beneficials is the main challenge in furthering these possibilities. The genus Stenotrophomonas contains representatives found to be associated with human and plant host.ResultsWe used comparative genomics as well as transcriptomic and physiological approaches to detect significant borders between the Stenotrophomonas strains: the multi-drug resistant pathogenic S. maltophilia and the plant-associated strains S. maltophilia R551-3 and S. rhizophila DSM14405T (both are biocontrol agents). We found an overall high degree of sequence similarity between the genomes of all three strains. Despite the notable similarity in potential factors responsible for host invasion and antibiotic resistance, other factors including several crucial virulence factors and heat shock proteins were absent in the plant-associated DSM14405T. Instead, S. rhizophila DSM14405T possessed unique genes for the synthesis and transport of the plant-protective spermidine, plant cell-wall degrading enzymes, and high salinity tolerance. Moreover, the presence or absence of bacterial growth at 37°C was identified as a very simple method in differentiating between pathogenic and non-pathogenic isolates. DSM14405T is not able to grow at this human-relevant temperature, most likely in great part due to the absence of heat shock genes and perhaps also because of the up-regulation at increased temperatures of several genes involved in a suicide mechanism.ConclusionsWhile this study is important for understanding the mechanisms behind the emerging pattern of infectious diseases, it is, to our knowledge, the first of its kind to assess the risk of beneficial strains for biotechnological applications. We identified certain traits typical of pathogens such as growth at the human body temperature together with the production of heat shock proteins as opposed to a temperature-regulated suicide system that is harnessed by beneficials.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-482) contains supplementary material, which is available to authorized users.

Stenotrophomonas maltophilia Encodes a VirB/VirD4 Type IV Secretion System That Modulates Apoptosis in Human Cells and Promotes Competition against Heterologous Bacteria, Including Pseudomonas aeruginosa

“…Stenotrophomonas acidaminiphila, Stenotrophomonas nitritireducens, Stenotrophomonas panacihumi, Stenotrophomonas rhizophila, and Stenotrophomonas terrae lacked all of the VirB/D4 T4SS proteins, whereas S. humi only had a homolog of VirB11, which had 34% identity to the K279a counterpart (E value of 2.6EϪ44). An earlier study comparing S. maltophilia and S. rhizophila had also reported a lack of T4SS in S. rhizophila (33). Looking beyond the genus, we determined that this S. maltophilia T4SS is most related in terms of amino acid similarity to one encoded by the chromosome of Xanthomonas spp.…”

GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

“…It holds 9 strains of contrasting geographic and ecological provenances, ranging from Chinese soil and plantassociated bacteria like the rice-root endophyte RR10 (Zhu et al, 2012), the grassland-soil tetracycline degrading isolate DT1 (Naas et al, 2008), and strain B418, isolated from a barley rhizosphere and displaying plant-growth promotion properties , to clinical isolates (22_SMAL, 179_SMAL, 453_SMAL, 517_SMAL) collected and studied in the context of a large genome sequencing project carried out at the University of Washington Medical Center (Roach et al, 2015). Cluster Sm11 tightly groups the well-characterized poplar endophyte R551-3, which is a model plantgrowth-promoting bacterium (Alavi et al, 2014;Ryan et al, 2009;Taghavi et al, 2009) and SBo1, cultured from the gut of the olive fruit fly Bactrocera oleae (Blow et al, 2016). Cluster Sm 12 contains the environmental strain SKA14 (Adamek et al, 2014), along with the clinical isolates ISMMS3 (Pak et al, 2015) and 860_SMAL (Roach et al, 2015).…”

Characteristics of bacterial community in cloud water at Mt Tai: similarity and disparity under polluted and non-polluted cloud episodes

“…Two strains from Stenotrophomonas (S. rhizophila) and Phyllobacterium (P. myrsinacearum) are typical rhizospheric microorganisms, which were typically dispersed into the atmosphere from soil. As plant-associated strains, S. rhizophila fulfill plantprotective roles and have been safely applied in biotechnology (Alavi et al, 2013). P. myrsinacearum is a predominant rhizospheric bacterium, which has been utilized in plant growth promotion and biological control of soil-borne diseases due to its capability of azotification (Gonzalezbashan et al, 2000).…”