CMEIAS bioimage informatics that define the landscape ecology of immature microbial biofilms developed on plant rhizoplane surfaces

Dazzo, Frank B.; Yanni, Y. G.; Jones, Ashley; Elsadany, Abdelgawad Y.

doi:10.3934/bioeng.2015.4.469

Cited by 8 publications

(20 citation statements)

References 10 publications

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“…The mission of our CMEIAS project is to develop, document and release a comprehensive suite of bioimage informatics analysis software applications designed to strengthen quantitative, microscopy-based approaches for understanding microbial ecology, at spatial scales directly relevant to microbes and their ecological niches without the need for cultivation [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16]. The wealth of information gained by CMEIAS analysis of digital images can bridge with other modern genotypic and phenotypic technologies to fill knowledge gaps revealing additional insights of in situ phenotypic characteristics of ecological importance to microbial cells, populations, communities and microbiomes.…”

Section: Cmeias Software Developmentmentioning

confidence: 99%

“…The wealth of information gained by CMEIAS analysis of digital images can bridge with other modern genotypic and phenotypic technologies to fill knowledge gaps revealing additional insights of in situ phenotypic characteristics of ecological importance to microbial cells, populations, communities and microbiomes. Examples include their biodiversity, productivity (conversion of available nutrient resources into biomass and metabolic energy), food-web dynamics, landscape ecology, strategies of successful colonization behavior, adaptations and resilience to environmental stresses, and intensities of interaction with each other within biofilms [2][3][4][5][6][7][8][9][10][11][12][13][14][15]. When finalized, the copyrighted CMEIAS software tools and their comprehensive documentations are released as free downloads at our project website [1].…”

Section: Cmeias Software Developmentmentioning

confidence: 99%

“…Algorithms featured in CMEIAS JFrad software [15] were used to compute the fractal dimensions of microcolony biofilm coastlines and fractal patterns of individual cell distributions by 11 methods, including corner perimeter, cumulative intersection, corner count, parallel lines, fast, fast hybrid, box counting, dilation, Euclidian distance map, mass radius (long) and mass radius (short). Other metrics (biovolume, biomass carbon, 1st and 2nd nearest neighbor distances, empirical distribution function of the 1st nearest neighbor distance, and cluster index [1st nearest neighbor distance −1 ]) used here have also been previously described [5,7,[10][11][12][13]16,20,[45][46][47][48], including a comprehensive ground truth analysis of accuracy for the shape-adaptable biovolume formula [10]. New metrics used here and planned for incorporation into CMEIAS include:…”

Section: Data Acquisition and Analysismentioning

confidence: 99%

“…These architectural differences between the two communities of microcolony biofilms prompted us to explore the fractal geometry component of their landscape architecture. We anticipated that the more productive microstructured biofilm of community B would exhibit a greater fractal dimension on the polystyrene substratum, reflecting its more intense colonization behavior of successful positioning to maximize nutrient resource acquisition and allocation within the hierarchical fractal-like nature of resource distribution networks within landscape microenvironments [5,7,15,[25][26][27][30][31][32]34]. The fractal dimensions of microcolony biofilm coastlines in the inverted grayscale images were analyzed using optimized segmentation settings (Table 1), an 85% brightness threshold, and all 11 methods of fractal analysis using the automated batch process available in CMEIAS JFrad software [15].…”

Section: Landscape Ecology Of River Microbial Biofilms At Microcolonymentioning

confidence: 99%

“…The dependence of spatially structured heterogeneity on ecosystem function provides the impetus to include analyses of spatial ecology in studies of microbial biofilm communities [5][6][7]9,11,12,15,25,27,[30][31][32]38,45,62,[69][70][71][72][73][74]. Analysis of the in situ spatial patterns of microbes within biofilms reveals statistically defendable data that support ecological theories of biogeography indicating that their colonization behavior involves a spatially explicit process rather than occurs independent of their location in this microenvironment [5][6][7]25,31,38,[69][70][71][72][73][74]. Spatial dependence is considered positive when neighboring organisms aggregate due to cooperative interactions that promote their localized productive growth, and is considered negative when conflicting/inhibitory interactions result in their uniform, self-avoiding colonization behavior [5][6][7]9,27,30,38,61,[69][70]…”

Section: Spatial Ecology Of River Microbial Biofilm Communities Analymentioning

confidence: 99%

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Influence of Substratum Hydrophobicity on the Geomicrobiology of River Biofilm Architecture and Ecology Analyzed by CMEIAS Bioimage Informatics

et al. 2017

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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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Section: Cmeias Software Developmentmentioning

confidence: 99%

Section: Cmeias Software Developmentmentioning

confidence: 99%

Section: Data Acquisition and Analysismentioning

confidence: 99%

Section: Landscape Ecology Of River Microbial Biofilms At Microcolonymentioning

confidence: 99%

Section: Spatial Ecology Of River Microbial Biofilm Communities Analymentioning

confidence: 99%

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Influence of Substratum Hydrophobicity on the Geomicrobiology of River Biofilm Architecture and Ecology Analyzed by CMEIAS Bioimage Informatics

et al. 2017

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Rhizosphere Plant–Microbe Interactions Under Abiotic Stress

Sharma

Chandra

Sharma

2020

Rhizosphere Biology

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Rhizobia promote the growth of rice shoots by targeting cell signaling, division and expansion

Peng

Yang

et al. 2018

Plant Mol Biol

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The growth-promotion of rice seedling following inoculation with Sinorhizobium meliloti 1021 was a cumulative outcome of elevated expression of genes that function in accelerating cell division and enhancing cell expansion. Various endophytic rhizobacteria promote the growth of cereal crops. To achieve a better understanding of the cellular and molecular bases of beneficial cereal-rhizobia interactions, we performed computer-assisted microscopy and transcriptomic analyses of rice seedling shoots (Oryza sativa) during early stages of endophytic colonization by the plant growth-promoting Sinorhizobium meliloti 1021. Phenotypic analyses revealed that plants inoculated with live rhizobia had increased shoot height and dry weight compared to control plants inoculated with heat-killed cells of the same microbe. At 6 days after inoculation (DAI) with live cells, the fourth-leaf sheaths showed significant cytological differences including their enlargement of parenchyma cells and reduction in shape complexity. Transcriptomic analysis of shoots identified 2,414 differentially-expressed genes (DEGs) at 1, 2, 5 and 8 DAI: 195, 1390, 1025 and 533, respectively. Among these, 46 DEGs encoding cell-cycle functions were up-regulated at least 3 days before the rhizobia ascended from the roots to the shoots, suggesting that rhizobia are engaged in long-distance signaling events during early stages of this plant-microbe interaction. DEGs involved in phytohormone production, photosynthetic efficiency, carbohydrate metabolism, cell division and wall expansion were significantly elevated at 5 and 8 DAI, consistent with the observed phenotypic changes in rice cell morphology and shoot growth-promotion. Correlation analysis identified 104 height-related DEGs and 120 dry-weight-related DEGs that represent known quantitative-trait loci for seedling vigor and increased plant height. These findings provide multiple evidences of plant-microbe interplay that give insight into the growth-promotion processes associated with this rhizobia-rice beneficial association.

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CMEIAS bioimage informatics that define the landscape ecology of immature microbial biofilms developed on plant rhizoplane surfaces

Cited by 8 publications

References 10 publications

Influence of Substratum Hydrophobicity on the Geomicrobiology of River Biofilm Architecture and Ecology Analyzed by CMEIAS Bioimage Informatics

Influence of Substratum Hydrophobicity on the Geomicrobiology of River Biofilm Architecture and Ecology Analyzed by CMEIAS Bioimage Informatics

Rhizosphere Plant–Microbe Interactions Under Abiotic Stress

Rhizobia promote the growth of rice shoots by targeting cell signaling, division and expansion

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