Abstract:In this review, we describe computational features of computer-assisted microscopy that are unique to the Center for Microbial Ecology Image Analysis System (CMEIAS) software, and examples illustrating how they can be used to gain ecophysiological insights into microbial adaptations occurring at micrometer spatial scales directly relevant to individual cells occupying their ecological niches in situ. These features include algorithms that accurately measure (1) microbial cell length relevant to avoidance of protozoan bacteriovory; (2) microbial biovolume body mass relevant to allometric scaling and local apportionment of growth-supporting nutrient resources; (3) pattern recognition rules for morphotype classification of diverse microbial communities relevant to their enhanced fitness for success in the particular habitat; (4) spatial patterns of coaggregation that reveal the local intensity of cooperative vs. competitive adaptations in colonization behavior relevant to microbial biofilm ecology; and (5) object segmentation of complex color images to differentiate target microbes reporting successful cell-cell communication. These unique computational features contribute to the CMEIAS mission of developing accurate and freely accessible tools of image bioinformatics that strengthen microscopy-based approaches for understanding microbial ecology at single-cell resolution. OPEN ACCESSComputation 2015, 3 73

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.