All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean (Phaseolus vulgaris) in Its Centre of Domestication

Abstract

Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing ‘at home’.

Microbiome of Nodules and Roots of Soybean and Common Bean: Searching for Differences Associated with Contrasting Performances in Symbiotic Nitrogen Fixation

“…Our study has shown a higher relative abundance of genera in roots than in nodules, also confirmed in the alpha- and beta-diversity analyses. We should also comment that in a study with common bean [ 54 ], the microbiome of the rhizosphere was greater than in the endosphere, composed of seeds and roots, altogether indicating that diversity decreases to more specific communities from the rhizosphere to the nodule.…”

“…Several factors are required for introducing bacteria into the plant microbiome from the rhizosphere, including growth rate, competitiveness, chemotaxis, motility, quorum sensing, biofilm formation, adherence, carbon sources, and nutrient rates. In addition, to compose a plant´s microbiome, the bacteria need to be able to adhere and proliferate on the root surface and penetrate cell walls without being tied down by the plant’s immune system [ 54 ]. Our study identified a variety of rhizobia and non-rhizobia in the microbiomes of soybean and common bean roots.…”

The elite common beanPhaseolus vulgariscultivar Pinto Saltillo hosts a rich and diverse array of plant-growth promoting bacteria in its rhizosphere

“…Although the dominance of the phylum Proteobacteria in the rhizosphere of Pinto Saltillo bean was unexpected, species of Proteobacteria were abundant in the rhizosphere of other plants, sharing the niche with Actinobacteria and other less represented phyla (Supplementary Figure S6). Studies based on high-throughput 16S rRNA gene sequencing have shown that additional bacterial phyla, such as Acidobacteria, Bacteroidetes, and Verrucomicrobia, are found in the rhizosphere of diverse bean cultivars (22, 60, 61).…”

Contribution of Biofertilizers to Pulse Crops: From Single-Strain Inoculants to New Technologies Based on Microbiomes Strategies

“…Root architecture and exudation modified by plant domestication may have led to new microbial associations in the rhizosphere [ 232 ]. According to Medina-Paz et al [ 233 ] the common bean recruits specific taxa from the surrounding soil within its native area and in a domestication area. Using 16S rRNA amplicon gene sequencing for paired evaluations of rhizosphere and endosphere communities at three ontogenetic stages in common beans, they found that the rhizosphere bacterial community was dominated by six phyla: Proteobacteria (41%), Bacteroidetes (14%), Actinobacteria (13%), Gemmatimonadetes (6%), Chloroflexi (4%), and Acidobacteria (3.5%).…”