Highly diverse root endophyte bacterial community is driven by growth substrate and is plant genotype-independent in common bean (Phaseolus vulgaris L.).

Juan Carlos Vizuet-De-Rueda,Raúl Alvarez-Venegas,Aarón Barraza

doi:10.7717/peerj.9423

Abstract

The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet with an essential role in sustainable agriculture mostly based on the symbiotic relationship established between this legume and rhizobia, a group of bacteria capable of fixing atmospheric nitrogen in the roots nodules. Moreover, root-associated bacteria play an important role in crop growth, yield, and quality of crop products. This is particularly true for legume crops forming symbiotic relationships with rhizobia, for fixation of atmospheric N2. The main objective of this work is to assess the substrate and genotype effect in the common bean (Phaseolus vulgaris L.) root bacterial community structure. To achieve this goal, we applied next-generation sequencing coupled with bacterial diversity analysis. The analysis of the bacterial community structures between common bean roots showed marked differences between substrate types regardless of the genotype. Also, we were able to find several phyla conforming to the bacterial community structure of the common bean roots, mainly composed by Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes. Therefore, we determined that the substrate type was the main factor that influenced the bacterial community structure of the common bean roots, regardless of the genotype, following a substrate-dependent pattern. These guide us to develop efficient and sustainable strategies for crop field management based on the soil characteristics and the bacterial community that it harbors.

Highlights

Plants have evolved with an overabundance of microorganisms having important functions supporting plant growth and health
The resulting operational taxonomic units (OTUs) abundance of this study revealed an unexpectedly high diversity of bacteria that assemble the bacterial communities inside the roots of the common bean for all genotypes
We found that 50% to 60% of the common bean roots OTUs were shared between common bean roots WT and each common bean root transgenic genotype grown in soil (Fig. 4B), and 32% to 40% of the common bean roots OTUs were shared between common bean roots WT and each common bean root transgenic genotype grown in vermiculite (Fig. 4C)

Summary

Introduction

Plants have evolved with an overabundance of microorganisms having important functions supporting plant growth and health. Diverse root endophyte bacterial community is driven by growth substrate and is plant genotype-independent in common bean (Phaseolus vulgaris L.). Land plants host abundant and diverse microbial communities in the rhizosphere, the area surrounding the plant roots (McNear, 2013). The plants and microbes may have commensalistic, mutualistic, or even pathogenic relationships, and some rhizobacteria enter the root and live as endophytes (Buée et al, 2009). Rhizobacteria have been linked to soil-borne diseases, resistance to abiotic stresses, the facility of nutrient acquisition, and they are considered a crucial aspect of the plant’s performance, growth, survival, and are directly influenced by plant root exudates (rhizodeposition), mucilage, and cellular debris that influences the chemical and physical composition of the rhizosphere and provides signaling molecules and organic substrates for microbial growth (Wu et al, 2015; Bulgarelli, 2018)

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