Integrated analysis of root microbiomes of soybean and wheat from agricultural fields

Abstract

Root associated bacteria are critical for plant growth and health. Understanding the composition and role of root microbiota is crucial toward agricultural practices that are less dependent on chemical fertilization, which has known negative effects on the environment and human health. Here we analyzed the root-associated microbiomes of soybean and wheat under agricultural field conditions. We took samples from 11 different production fields across a large geographic area. We used 16S rRNA pyrosequencing to explore root microbial communities and also obtained 2,007 bacterial isolates from rhizospheres, which were tested for the presence of plant growth promoting (PGP) traits in-vitro. We observed that pH and nitrate content correlated with beta diversity variability of rhizospheric bacterial communities despite the variable field conditions. We described the dominant bacterial groups associated to roots from both crops at a large geographic scale and we found that a high proportion of them (60–70%) showed more than 97% similarity to bacteria from the isolated collection. Moreover, we observed that 55% of the screened isolates presented PGP activities in vitro. These results are a significant step forward in understanding crop-associated microbiomes and suggest that new directions can be taken to promote crop growth and health by modulating root microbiomes.

Metagenome-Wide Association Study and Machine Learning Prediction of Bulk Soil Microbiome and Crop Productivity

“…There were three samples (Greenfield 03, Auburn 07, and Urbana11) from high productivity areas and three samples (Greenfield 04, Auburn 08, Urbana 12) from low productivity areas located outside of the 90% confidence intervals (Figure 2A). Our observations in the PCoA were consistent to several publications that described the association between soil pH and microbiome (Rousk et al, 2010; Rascovan et al, 2016). However, the multicollinearity problem (such as the strong correlations between water pH and other characteristics) raises the possibility that water pH and crop productivity might be a confounding factor to PCo1 and PCo2, respectively.…”

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

“…Our results demonstrated that the soil and rhizosphere associated with Dioon coralloid roots are highly diverse. As with other plants [25,66,67], the soil (bulk soil and rhizosphere) is more diverse in the number of OTUs and genera than the root endosphere, although these differences are not significant in our study (alpha diversity metrics). When we compared the rhizosphere and endosphere from the six Dioon samples (set 3 comparison), we found significant differences in the alpha diversity, with higher diversity on the outside than the inside of coralloid root, a common pattern reported previously in 30 species of angiosperms [68].…”

Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions

“…Abiotic conditions should be measured across samples in case they affect the chosen phenotype for microbiome GWAS. For example, a study of soybean and wheat root microbiomes across many different field sites found that pH and nitrate content correlated with community diversity (Rascovan et al ., ).…”