Caffeine fostering of mycoparasitic fungi against phytopathogens

<p>Caffeine (1,3,7-trimethixanthine) is a typical purine alkaloid produced in more than 80 plant species. Its biological role is considered to strengthen plant's defense capabilities, directly as a toxicant to biotic attackers (allelopathy) and indirectly as an activator of defense system (priming). Caffeine is actively secreted into rhizosphere through primary root, and possibly affects the structure of microbe community nearby. The fungal community in coffee plant rhizosphere is enriched with particular species, including <i>Trichoderma</i> family, a mycoparasite that attacks and kills phytopathogens by coiling and destroying their hyphae. In the present study, the caffeine response of 8 filamentous fungi, 4 mycoparasitic <i>Trichoderma</i>, and 4 prey phytopathogens, was examined. Results showed that allelopathic effect of caffeine on fungal growth and development was differential, being stronger on pathogens than on <i>Trichoderma</i> species. Upon confronting, the prey immediately ceased the growth, whereas the predator continued to grow, indicating active mycoparasitism to have occurred. Caffeine enhanced mycoparasitism up to 1.7-fold. Caffeine thus functions in a double-track manner against fungal pathogens: first by direct suppression of growth and development, and second by assisting their natural enemy. These observations suggest that caffeine is a powerful weapon in the arms race between plants and pathogens by fostering enemy's enemy, and we propose the idea of "caffeine fostering" as the third role of caffeine.</p

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 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

Community level physiological profiling.

<p>The BioLog substrate utilization assay was performed to generate community-level substrate utilization profiles. Average well color development (AWCD) after a 96-hour incubation was recorded. Values are mean ± SD (n = 3). The effect of growth stage and interaction between both factors (growth stage and compartment) were not significant in two-way ANOVA, but significant difference was observed between bulk and rhizosphere soil, as shown by the different letters (p<0.05).</p

Bulk and rhizosphere sample preparation.

<p>Bulk and rhizosphere sample preparation.</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

Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions

<div><p>Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of <em>in vitro</em> grown <em>Arabidopsis</em> plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the <em>in vitro</em> root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p<0.05) between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development. In summary, our results suggest that the root exudation process of phytochemicals follows a developmental pattern that is genetically programmed.</p> </div

<i>Arabidopsis</i> root exudate composition across development.

<p>Identified compounds were grouped into chemical classes, and secretion levels were calculated based on cumulative peak area after normalization.</p