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

Frank B Dazzo,Ashley Jones,Abdelgawad Y Elsadany,Youssef G Yanni

doi:10.3934/bioeng.2015.4.469

Abstract

Colonization of the rhizoplane habitat is an important activity that enables certain microorganisms to promote plant growth. Here we describe various types of computer-assisted microscopy that reveal important ecological insights of early microbial colonization behavior within biofilms on plant root surfaces grown in soil. Examples of the primary data are obtained by analysis of processed images of rhizoplane biofilm landscapes analyzed at single-cell resolution using the emerging technology of CMEIAS bioimage informatics software. Included are various quantitative analyses of the in situ biofilm landscape ecology of microbes during their pioneer colonization of white clover roots, and of a rhizobial biofertilizer strain colonized on rice roots where it significantly enhances the productivity of this important crop plant. The results show that spatial patterns of immature biofilms developed on rhizoplanes that interface rhizosphere soil are highly structured (rather than distributed randomly) when analyzed at the appropriate spatial scale, indicating that regionalized microbial cell-cell interactions and the local environment can significantly affect their cooperative and competitive colonization behaviors.

Highlights

In contrast to the predominantly oligotrophic status of bulk soil, the rhizosphere soil surrounding roots and their rhizoplane epidermal surfaces are nutritionally enriched habitats supported by exudation of plant photosynthates, resulting in biofilm colonization by zymogenous microorganisms that in turn, can significantly influence plant nutrition, health and disease, and are important for sustainability of natural terrestrial ecosystems and agriculture [1].Microscopy is the most direct way to examine microbial colonization of rhizoplane surfaces, but most often, that approach is only addressed qualitatively by presentation of “representative” micrographs of that landscape domain
Included are various quantitative analyses of the in situ biofilm landscape ecology of microbes during their pioneer colonization of white clover roots, and of a rhizobial biofertilizer strain colonized on rice roots where it significantly enhances the productivity of this important crop plant
We describe various applications of computer-assisted microscopy using Center for Microbial Ecology Image Analysis System (CMEIAS) bioimage informatics software to reveal important ecological insights of early microbial colonization behavior within biofilms developed on root surfaces grown in soil

Summary

Introduction

In contrast to the predominantly oligotrophic status of bulk soil, the rhizosphere soil surrounding roots and their rhizoplane epidermal surfaces are nutritionally enriched habitats supported by exudation of plant photosynthates, resulting in biofilm colonization by zymogenous microorganisms that in turn, can significantly influence plant nutrition, health and disease, and are important for sustainability of natural terrestrial ecosystems and agriculture [1].Microscopy is the most direct way to examine microbial colonization of rhizoplane surfaces, but most often, that approach is only addressed qualitatively by presentation of “representative” micrographs of that landscape domain. We have been developing a comprehensive suite of scientific software named Center for Microbial Ecology Image Analysis System (CMEIAS) to strengthen microscopy-based approaches that support microbial ecology research Advancement of this emerging technology of bioimage informatics is driven by the need to fill major gaps using quantitative computational techniques to analyze microbes at spatial scales directly relevant to their ecophysiology, and obtain useful knowledge of their ecology in situ without cultivation. We describe examples of bioimage informatics obtained by CMEIAS computer-assisted microscopy and digital image analysis of processed rhizoplane landscapes after their short-term growth in soil These data reveal important insights of the in situ abundance and intensity of cell-cell interactions of microorganisms during their pioneer colonization of white clover seedling roots, and of a rhizobial biofertilizer strain on rice roots that significantly enhances the productivity of this major cereal crop

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Results

Conclusion