Abstract
This paper describes the utility of CMEIAS (Center for Microbial Ecology Image Analysis System) computer-assisted microscopy to extract data from accurately segmented images that provide 63 different insights into the ecophysiology of microbial populations and communities within biofilms and other habitats. Topics include quantitative assessments of: (i) morphological diversity as an indicator of impacts that substratum physicochemistries have on biofilm community structure and dominance-rarity relationships among populations; (ii) morphotype-specific distributions of biovolume body size that relate microbial allometric scaling, metabolic activity and growth physiology; (iii) fractal geometry of optimal cellular positioning for efficient utilization of allocated nutrient resources; (iv) morphotype-specific stress responses to starvation, environmental disturbance and bacteriovory predation; (v) patterns of spatial distribution indicating positive and negative cell–cell interactions affecting their colonization behavior; and (vi) significant methodological improvements to increase the accuracy of color-discriminated ecophysiology, e.g., differentiation of cell viability based on cell membrane integrity, cellular respiratory activity, phylogenetically differentiated substrate utilization, and N-acyl homoserine lactone-mediated cell–cell communication by bacteria while colonizing plant roots. The intensity of these ecophysiological attributes commonly varies at the individual cell level, emphasizing the importance of analyzing them at single-cell resolution and the proper spatial scale at which they occur in situ.
Highlights
A major challenge in microbial ecology is to develop reliable methods of computer-assisted microscopy that can analyze complex digital images of microorganisms at single cell resolution and reveal insights about their ecology in situ without cultivation
These data set the stage for exploring the measurement attributes that CMEIAS can extract from these images to gain insight into the ecophysiological forces that structure these differences in microbial community ecology, thereby shedding light on ways that the environmental variable of hydrophobicity in substratum physicochemistry impacts on development and cell–cell interactions of sessile microbial communities and biofilm architecture in freshwater aquatic ecosystems
Image analysis software can strengthen microscopy-based approaches for understanding the ecophysiology of microorganisms at single-cell resolution and at the dimensions that they occur in situ
Summary
A major challenge in microbial ecology is to develop reliable methods of computer-assisted microscopy that can analyze complex digital images of microorganisms at single cell resolution and reveal insights about their ecology in situ without cultivation. This paper documents the use of computer-assisted microscopy to extract the wealth of ecologically relevant information present in accurately segmented images of microbial populations and communities, and various quantitative methods to analyze those attributes to reveal insights about microbial ecophysiology in situ. The intensity of these attributes commonly varies at the individual cell level, emphasizing the importance of analyzing them at single-cell resolution and the proper spatial scale at which they occur
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