Erwinia amylovora, causative agent of fire blight disease of apple and pear trees, has evolved to use small RNAs for post-transcriptional regulation of virulence traits important for disease development. The sRNA ArcZ regulates several virulence traits, and to better understand its roles, we conducted a transcriptomic comparison of wild-type and ΔarcZ mutant E. amylovora. We found that ArcZ regulates multiple cellular processes including genes encoding enzymes involved in mitigating the threat of reactive oxygen species (katA, tpx, osmC), and that the ΔarcZ mutant has reduced catalase activity and is more susceptible to exogenous hydrogen peroxide. We quantified hydrogen peroxide production by apple leaves inoculated with E. amylovora and found that the while wild-type E. amylovora cells produce enough catalase to cope with defense peroxide, the ΔarcZ mutant is likely limited in virulence because of inability to cope with peroxide levels in host leaves. We further found that the ArcZ regulon overlaps significantly with the regulons of transcription factors involved in oxidative sensing including Fnr and ArcA. In addition, we show that ArcZ regulates arcA at the post-transcriptional level suggesting a role for this system in mediating adaptations to oxidative state, especially during disease development.
Microbial biogeography in terrestrial and freshwater ecosystems is mainly dominated by community biofilm lifestyles. Here, we describe applications of computer-assisted microscopy using CMEIAS (Center for Microbial Ecology Image Analysis System) bioimage informatics software for a comprehensive analysis of river biofilm architectures and ecology. Natural biofilms were developed for four summer days on microscope slides of plain borosilicate glass and transparent polystyrene submerged in the Red Cedar River that flows through the Michigan State University campus. Images of the biofilm communities were acquired using brightfield and phase-contrast microscopy at spatial resolutions revealing details of microcolonies and individual cells, then digitally segmented to the foreground objects of interest. Phenotypic features of their size, abundance, surface texture, contour morphology, fractal geometry, ecophysiology, and landscape/spatial ecology were digitally extracted and evaluated by many discriminating statistical tests. The results indicate that river biofilm architecture exhibits significant geospatial structure in situ, providing many insights on the strong influence that substratum hydrophobicity-wettability exert on biofilm development and ecology, including their productivity and colonization intensity, morphological diversity/dominance/conditional rarity, nutrient apportionment/uptake efficiency/utilization, allometry/metabolic activity, responses to starvation and bacteriovory stresses, spatial patterns of distribution/dispersion/connectivity, and interpolated autocorrelations of cooperative/conflicting cell-cell interactions at real-world spatial scales directly relevant to their ecological niches. The significant impact of substratum physicochemistry was revealed for biofilms during their early immature stage of development in the river ecosystem. Bioimage informatics can fill major gaps in understanding the geomicrobiology and microbial ecology of biofilms in situ when examined at spatial scales suitable for phenotypic analysis at microcolony and single-cell resolutions.
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