Rapid Determination of Escherichia coli O157:H7 Lineage Types and Molecular Subtypes by Using Comparative Genomic Fingerprinting▿

In this study, variably absent or present (VAP) regions discovered through comparative genomics experiments were targeted for the development of a rapid, PCR-based method to subtype and fingerprint Escherichia coli O157:H7. Forty-four VAP loci were analyzed for discriminatory power among 79 E. coli O157:H7 strains of 13 phage types (PT). Twenty-three loci were found to maximize resolution among strains, generating 54 separate fingerprints, each of which contained strains of unique PT. Strains from the three previously identified major E. coli O157:H7 lineages, LSPA6-LI, LSPA6-LI/II, and LSPA6-LII, formed distinct branches on a dendrogram obtained by hierarchical clustering of comparative genomic fingerprinting (CGF) data. By contrast, pulsed-field gel electrophoresis (PFGE) typing generated 52 XbaI digestion profiles that were not unique to PT and did not cluster according to O157:H7 lineage. Our analysis identified a subpopulation comprised of 25 strains from a closed herd of cattle, all of which were of PT87 and formed a cluster distinct from all other E. coli O157:H7 strains examined. CGF found five related but unique fingerprints among the highly clonal herd strains, with two dominant subtypes characterized by a shift from the presence of locus fprn33 to its absence. CGF had equal resolution to PFGE typing but with greater specificity, generating fingerprints that were unique among phenotypically related E. coli O157:H7 lineages and PT. As a comparative genomics typing method that is amenable for use in high-throughput platforms, CGF may be a valuable tool in outbreak investigations and strain characterization

Can sugar maple establish into the boreal forest? Insights from seedlings under various canopies in southern Quebec

Understanding tree recruitment dynamics in various growth environments is essential for a better assessment of tree species’ adaptive capacity to climate change. We investigated the microsite factors influencing survival, growth, and foliar nutrition of natural and planted sugar maple seedlings (Acer saccharum) along a gradient of tree species that reflect the change in composition from temperate hardwoods to boreal forests of eastern Canada. We specifically tested whether the increasing abundance of conifers in the forest and its modifications on soil properties negatively affects foliar nutrition of natural seedlings as well as the survival and growth of seedlings planted directly in the natural soil and in pots filled with enriched soil. Results of natural seedlings indicate that under conifer-dominated stands, lower soil pH, accelerated dissolution of some minerals, lower temperature and moisture, and higher levels of phenolic compounds have created microsites that are less suitable for sugar maple foliar nutrition and regeneration. These conditions were omnipresent under hemlock. The growth of seedlings planted in the natural soil was negatively impacted by the overall low soil quality under all forest types (as compared to seedlings planted in pots with enriched soil). However, survival and growth of the seedlings were not negatively affected by conifers, regardless of planting type, likely because of stored nutrients from the nursery. Also, lower survival was found under maple–birch stands for seedlings planted both in the natural soil and in pots with enriched soil due to higher shading. This study has identified key microsite factors created by specific conifers that may impede or benefit the potential of sugar maple to maintain its current range or expand its range northward under climate change