Enhancement of developmentally regulated daidzein secretion from soybean roots in field conditions as compared with hydroponic culture

Analyses of metabolite secretions by field-grown plants remain scarce. We analyzed daidzein secretion by field-grown soybean. Daidzein secretion was higher during early vegetative stages than reproductive stages, a trend that was also seen for hydroponically grown soybean. Daidzein secretion was up to 10 000-fold higher under field conditions than hydroponic conditions, leading to a more accurate simulation of rhizosphere daidzein content

Do soybeans select specific species of Bradyrhizobium during growth?

Soybean is an important crop, with processed soybeans being the second largest source of vegetable oil and the largest source of animal protein feed in the world. Nodules on soybean roots are responsible for symbiotic nitrogen fixation, enabling soybean plants to obtain sufficient nitrogen for growth and seed production. Because nitrogen is an essential, but often limiting, nutrient for plant growth, improvements in nitrogen fixation are highly required in agriculture. We recently reported a comprehensive analysis of rhizosphere bacterial communities during soybean growth in a field in Kyoto prefecture, Japan. The bacterial communities of the rhizosphere changed significantly during growth, with potential plant growth-promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, increasing in a stage-specific manner. In this addendum, we focus on changes in Bradyrhizobium during soybean growth, suggesting that soybean plants select for symbiotic partners

Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field

<div><p>Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including <i>Bacillus</i>, <i>Bradyrhizobium,</i> and <i>Rhizobium</i>, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field.</p></div

Relative abundance of major bacterial phyla present in bulk and rhizosphere soil during soybean growth, as revealed by pyrosequencing.

<p>Each bar represents the average relative abundance of triplicates.</p

Relative abundance of OTUs with high absolute loading on Principal Component 1 (PC1).

<p>(A) OTUs with high positive loading on PC1; (B) OTUs with high negative loading on PC1. White bars represent bulk soil and black bars represent rhizosphere soil. The relative abundance was calculated using the data from pyrosequencing analysis. The numbers in parentheses are loading values. □; initial soil, ▪; vegetative stage, ▪; flowering stage, ▪; mature stage. Values are mean ± SD (n = 3), with significant differences by Tukey's HDS test (P<0.05) indicated.</p

Principal component analysis of the relative abundance of OTUs.

<p>Principal component analysis of the relative abundance of OTUs.</p

Relative abundance of eight different genera during soybean growth.

<p>The relative abundance of the eight genera shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100709#pone-0100709-g004" target="_blank">Figure 4</a> was compared. □; initial soil, ▪; vegetative stage, ▪; flowering stage, ▪; mature stage. Values are mean ± SD (n = 3), with significant differences by Tukey's HDS test (P<0.05) indicated.</p

A Phosphofructokinase B-Type Carbohydrate Kinase Family Protein, NARA5, for Massive Expressions of Plastid-Encoded Photosynthetic Genes in Arabidopsis1[W][OA]

To date, there have been no reports on screening for mutants defective in the massive accumulation of Rubisco in higher plants. Here, we describe a screening method based on the toxic accumulation of ammonia in the presence of methionine sulfoximine, a specific inhibitor of glutamine synthetase, during photorespiration initiated by the oxygenase reaction of Rubisco in Arabidopsis (Arabidopsis thaliana). Five recessive mutants with decreased amounts of Rubisco were identified and designated as nara mutants, as they contained a mutation in genes necessary for the achievement of Rubisco accumulation. The nara5-1 mutant showed markedly lower levels of plastid-encoded photosynthetic proteins, including Rubisco. Map-based cloning revealed that NARA5 encoded a chloroplast phosphofructokinase B-type carbohydrate kinase family protein of unknown function. The NARA5 protein fused to green fluorescent protein localized in chloroplasts. We conducted expression analyses of photosynthetic genes during light-induced greening of etiolated seedlings of nara5-1 and the T-DNA insertion mutant, nara5-2. Our results strongly suggest that NARA5 is indispensable for hyperexpression of photosynthetic genes encoded in the plastid genome, particularly rbcL