Field multi-omics analysis reveals a close association between bacterial communities and mineral properties in the soybean rhizosphere

Abstract

The plant root-associated environments such as the rhizosphere, rhizoplane, and endosphere are different from the outer soil region (bulk soil). They establish characteristic conditions including microbiota, metabolites, and minerals, and they can directly affect plant growth and development. However, comprehensive insights into those characteristic environments, especially the rhizosphere, and molecular mechanisms of their formation are not well understood. In the present study, we investigated the spatiotemporal dynamics of the root-associated environment in actual field conditions by multi-omics analyses (mineral, microbiome, and transcriptome) of soybean plants. Mineral and microbiome analyses demonstrated a characteristic rhizosphere environment in which most of the minerals were highly accumulated and bacterial communities were distinct from those in the bulk soil. Mantel’s test and co-abundance network analysis revealed that characteristic community structures and dominant bacterial taxa in the rhizosphere significantly interact with mineral contents in the rhizosphere, but not in the bulk soil. Our field multi-omics analysis suggests a rhizosphere-specific close association between the microbiota and mineral environment.

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

“…Rhizobium (each genus representing 30%), followed by Ochrobactrum (less than 1%) (Figure 3B). The beforementioned findings generally agree with those from other systems, reporting Proteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria as dominant phyla in the rhizosphere and further enrichment of Proteobacteria in the endosphere of diverse crops, including bean [4,9,10,16,[23][24][25]37,59,61,72,75], although Firmicutes dominated among endophytic bacteria cultured from seeds or roots [52,53]. However, the high abundances of the phyla Chloroflexi and Gemmatimonadetes and genera such as Flavisolibacter or Steroidobacter and the archaea, Candidatus Nitrososphaera, appear to be less common features of common bean rhizosphere microbiota: OTUs assigned to the Chloroflexi or Gemmatimonadetes reached abundances of <0.5% and 1-1.5%, respectively, in the rhizosphere of wild and cultivated common beans grown in agricultural soil from Columbia [59], and similarly low abundances were reported for the bean plants grown in several agricultural regions in the USA [37].…”

“…Ontogenetic effects on rhizosphere communities during the early stages of vegetative growth have been described, e.g., for soybean, maize, and rice [72,[86][87][88]. In our study, changes in the abundances of few, but functionally important taxa resulted in a dominance shift from Stenotrophomonas in the vegetative stage to taxa like Rhizobium, Aeromonas, or Paracoccus spp.…”

“…[9,71,78]. Moreover, among the same studies, high abundances of Chloroflexi were observed in the rhizosphere of soybean, oilseed rape, and wild grassland species [9,72,78], and-together with Flavisolibacter-even in the microbial community in the nodules of wild soybean [76]. OTUs assigned to the ammonia-oxidizing archaea Candidatus Nitrososphaera [81,82] were reported from the rhizosphere of oilseed rape and maize, and Rhizobium from the endosphere of oilseed rape, wheat, and canola roots [78,79].…”

“…A higher diversity of bacterial communities in the rhizosphere versus the endosphere has been reported, e.g., for rice, tomato, soybean, alfalfa, wheat, canola, poplar, pea, and lentil [4,5,23,65,[71][72][73][74], although a study using sunflower demonstrated that this pattern, although common, is not ubiquitous [20]. As an independent way to visualize the community differentiation we used an unconstrained principal coordinate analysis (PCoA) of Bray-Curtis distances to quantify β-diversity and observed a clear separation of rhizosphere versus endosphere samples along the Axis 1 (explaining 92.5% of the overall variation), while the ontogenetic stage had a minor effect (Figure 2).…”

“…Gemmatimonadetes were among the four dominant phyla in the rhizosphere of lentil, pea, soybean, wheat, maize, canola, oilseed rape, artichoke, and diverse grassland species from temperate zones in Europe or the Chinese tundra [9,26,72,[76][77][78][79][80]. Several of these studies demonstrated the enrichment of Gemmatimonadetes in the rhizosphere as compared to bulk soil [78] and linked this phylum to increased biomass production or increased resistance to salt stress [76,77,80], mainly due to abundant nitrogen-fixing Gemmatimonas spp.…”