Changes in the bacterial community of soybean rhizospheres during growth in the field.

Kazufumi Yazaki,Hisabumi Takase,Matthew W Fields,Takahiro Zushi,Yoshikatsu Ueda,Akifumi Sugiyama

doi:10.1371/journal.pone.0100709

Kazufumi Yazaki, Hisabumi Takase + Show 4 more

Open Access

https://doi.org/10.1371/journal.pone.0100709

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Journal: PloS one	Publication Date: Jun 23, 2014
Citations: 252	License type: CC BY 4.0

Affiliation: Kyoto University

Abstract

Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field.

Highlights

The rhizosphere is the small region around the roots, defined as ‘‘the zone of soil surrounding the root which is affected by it’’ [1,2], where plants and millions of microbes interact with each other [3]
The average well color development (AWCD) of rhizosphere soil was 1.5 to 3-fold higher than that of bulk soil throughout soybean growth when same amount of soil was used (Figure 2), indicating that tested metabolic capabilities of rhizosphere soil were higher than bulk soil and that the physiological profile of the two sets of soil samples differed significantly
When BioLog data were normalized with 16S ribosomal RNA (rRNA) gene, higher activities were observed in rhizosphere soil than bulk soils at vegetative and flowering stages, but not in mature stage

Summary

Introduction

The rhizosphere is the small region around the roots, defined as ‘‘the zone of soil surrounding the root which is affected by it’’ [1,2], where plants and millions of microbes interact with each other [3]. Mycorrhiza and rhizobia provide phosphorous and nitrogen, respectively, and microbes called plant-growth-promoting rhizobacteria (PGPR) exert both direct and indirect effects on plant growth, such as the prevention of colonization by pathogens and modulation of plant immunity [5,6,7]. These rhizosphere microbes are regarded as prominent components of sustainable agriculture that reduce the use of fertilizers and pesticides [8]. Microbial communities have been found to depend on the plant species grown in the same type of soil [13,14,15,16], demonstrating a tight interaction between plants and rhizosphere microbial communities [17]

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Conclusion