Metagenomic Analysis of Bacterial Communities in the Rhizosphere of Leguminous Crops and Trees.

Abstract

Legumes account for 27% of the world's primary crop production and contribute 33% to the dietary protein needs of humans. Important legume crops include clover, soybeans, alfalfa and peas. These plants are notable for their ability to form nitrogen‐fixing symbioses with bacteria of the genera rhizobia. These organisms live in the rhizosphere (the region of soil in the vicinity of plant roots) of legumes. Symbiotic nitrogen fixation in legume crops takes place in plant structures known as root nodules. Recent research suggests that certain tree species of the Leguminosae family do not form nodules but still possess nitrogen fixation capabilities (Bryan, 1996). The main objective of this study was to investigate the microbial communities associated with the rhizosphere of nodulating legume crops (alfalfa, clover and soybeans) and non‐nodulating leguminous trees (Honeylocust and Redbud). We hypothesized that examining the microbial communities in the rhizosphere of these plants will provide insights into the diversity of N2‐fixing microbes and the mechanisms of nitrogen fixation in non‐nodulating legumes. Total DNA was extracted from the rhizosphere and bacterial community analyzes were performed by sequencing the V4 region of the 16S rRNA gene. QIIME and UPARSE were used to analyze the sequencing reads and select operational taxonomic units (OTUs). A total of 441,587 qualified reads were obtained from the eight rhizosphere samples. Rarefaction curves obtained with the normalized OTUs number nearly reached saturation level for all the samples, indicating that bacterial communities from the rhizospheres were well covered by the sequence analysis. Phylogenetic analysis showed that Proteobacteria was the most abundant phylum in the rhizosphere of legumes covering 45–70% of the amplicons detected in the samples analyzed. Bacteriodes was the second major phylum followed by Acidobacteria and Actinobacteria. Regarding bacterial classes, the alphaproteobacteria and betaproteobacteria were abundant in crops while gammaproteobacteria and alphaproteobacteria were prevalent in leguminous trees. Principal component analysis indicated that bacterial communities could be separated into two groups according to their association with crops or trees. Rhizobium species were present in the rhizosphere of all the legumes analyzed. The presence of rhizobial species in the rhizosphere of non‐nodulating leguminous trees suggests that these microbes might have a role in the nitrogen fixation mechanisms utilized by these plants. This study provided valuable insights about the distribution of bacteria in the rhizosphere of agriculturally relevant leguminous crops and trees.