Transcriptome analysis reveals that barnyard grass exudates increase the allelopathic potential of allelopathic and non-allelopathic rice (Oryza sativa) accessions.

BACKGROUND: Allelopathy in rice (Oryza sativa) is a chemically induced response that is elevated by the exogenous application of chemical compounds and barnyard grass root exudates. An in-depth understanding of the response mechanisms of rice to chemical induction is necessary for the identification of target genes for increasing the allelopathic potential of rice. However, no previous studies have evaluated the transcriptomic changes associated with allelopathy in rice in response to barnyard grass exudates treatment. Thus, the aim of the present study was to reveal differentially expressed genes (DEGs) in allelopathic and non-allelopathic rice seedlings treated with barnyard grass exudates to identify target allelopathy genes. RESULTS: The inhibitory effect of the culture solutions on the allelopathic rice accession PI312777 (PI) and the non-allelopathic rice accession Lemont (LE) significantly increased (P < 0.05) after treatment with barnyard grass root exudates. The RNA sequencing results revealed that 14,891 genes in PI(+B) vs. LE(+B), 12,505 genes in PI(+B) vs. PI(-B), and 5857 genes in LE(+B) vs. LE(-B) were differentially expressed following root exudates treatment. These DEGs were classified into three categories and 32 functional groups, i.e., 12 groups in the biological process category, 12 groups in the cellular component category, and eight groups in the molecular function category. There were 5857 and 2846 upregulated genes and 135 and 50 upregulated Gene Ontology terms (P < 0.05) in the biological process category in PI(+B) vs. PI(-B) and LE(+B) vs. LE(-B), respectively. These results indicated that the allelopathic accession PI is more sensitive than the non-allelopathic accession LE to exogenous root exudates treatment. Genes related to rice allelochemical-related biosynthesis pathways, particularly the shikimic acid and acetic acid pathways, were significantly differentially expressed in both rice accessions. These findings suggested that phenolic acids, fatty acids, and flavonoids, which constitute the downstream metabolites of the shikimic acid and acetic acid pathways, are significantly expressed in response to root exudates of barnyard grass. CONCLUSIONS: The allelopathic potential of both rice accessions could be significantly enhanced by barnyard grass root exudates application. Furthermore, genes related to the biosynthesis pathways of reported rice allelochemicals were significantly differentially expressed in both accessions. Phenylalanine ammonia lyase was determined to be a potential target for the regulation of chemical induction.

[Characteristics of soil microbial community under different vegetation types in Wuyishan National Nature Reserve, East China].

By using Biolog Ecoplate system, this paper studied the structure and functional diversity of soil microbial community under different vegetation types in Wuyishan National Nature Reserve, aimed to probe into the effects of vegetation type on the diversity of soil microbial community. The results showed that the soil chemical properties, soil enzyme activities, and average well color development (AWCD) were higher in natural forest than in planted forest, and were the lowest in abandoned field. The AWCD reflecting soil microbial activity and functional diversity was increased with increasing incubation time, but there existed significant differences among different vegetation types. The carbon sources mostly used by soil microbes were carbohydrates and carboxylic acids, followed by amino acids, phenolic acids and polymers, and amines had the lowest utilization rate. The Simpson index, Shannon index, Richness index and McIntosh index in natural forest were holistically higher than those in planted forest. Principal component analysis (PCA) identified 2 principal component factors in relation to carbon sources, explaining 56.3% and 30.2% of the variation, respectively. The carbon sources used by soil microbial community differed with vegetation types. Amino acids and amides were the two main carbon sources separating the 2 principal component factors. The results of this study could provide basis for further approaching the relationships between vegetation diversity and soil microbial community diversity.

Separation of allelopathy from resource competition using rice/barnyardgrass mixed-cultures.

Plant-plant interference is the combined effect of allelopathy, resource competition, and many other factors. Separating allelopathy from resource competition is almost impossible in natural systems but it is important to evaluate the relative contribution of each of the two mechanisms on plant interference. Research on allelopathy in natural and cultivated plant communities has been hindered in the absence of a reliable method that can separate allelopathic effect from resource competition. In this paper, the interactions between allelopathic rice accession PI312777, non-allelopathic rice accession Lemont and barnyardgrass were explored respectively by using a target (rice)-neighbor (barnyardgrass) mixed-culture in hydroponic system. The relative competitive intensity (RCI), the relative neighbor effect (RNE) and the competitive ratio (CR) were used to quantify the intensity of competition between each of the two different potentially allelopathic rice accessions and barnyardgrass. Use of hydroponic culture system enabled us to exclude any uncontrolled factors that might operate in the soil and we were able to separate allelopathy from resource competition between each rice accession and barnyardgrass. The RCI and RNE values showed that the plant-plant interaction was positive (facilitation) for PI312777 but that was negative (competition) for Lemont and barnyardgrass in rice/barnyardgrass mixed-cultures. The CR values showed that one PI312777 plant was more competitive than 2 barnyardgrass plants. The allelopathic effects of PI312777 were much more intense than the resource competition in rice/barnyardgrass mixed cultures. The reverse was true for Lemont. These results demonstrate that the allelopathic effect of PI312777 was predominant in rice/barnyardgrass mixed-cultures. The most significant result of our study is the discovery of an experimental design, target-neighbor mixed-culture in combination with competition indices, can successfully separate allelopathic effects from competition.

Characterization of metaproteomics in crop rhizospheric soil.

Soil rhizospheric metaproteomics is a powerful scientific tool to uncover the interactions between plants and microorganisms in the soil ecosystem. The present study established an extraction method suitable for different soils that could increase the extracted protein content. Close to 1000 separate spots with high reproducibility could be identified in the stained 2-DE gels. Among the spots, 189 spots representing 122 proteins on a 2-DE gel of rice soil samples were successfully identified by MALDI-TOF/TOF-MS. These proteins mainly originated from rice and microorganisms. They were involved in protein, energy, nucleotide, and secondary metabolisms, as well as signal transduction and resistance. Three characteristics of the crop rhizospheric metaproteomics seemed apparent: (1) approximately one-third of the protein spots could not be identified by MALDI-TOF/TOF/MS, (2) the conservative proteins from plants formed a feature distribution of crop rhizospheric metaproteome, and (3) there were very complex interactions between plants and microorganisms existing in a crop rhizospheric soil. Further functional analysis on the identified proteins unveiled various metabolic pathways and signal transductions involved in the soil biotic community. This study provides a paradigm for metaproteomic research on soil biology.

[Regulation effect of exogenous salicylic acid on weed suppression and molecular physiological characteristics of allelopathic rice].

To investigate the feasibility of using exogenous salicylic acid (SA) to regulate the allelopathic weed suppression of rice, this paper studied the effects of different concentrations exogenous SA on the weed-suppression and physiological-biochemical characteristics of allelopathic rice PI312777, and the relative expression quantity of gene ZB8 in the rice by real time quantitative RT-PCR (FQ-PCR). The results showed that exogenous SA induced the enhancement of the allelopathic potential of donor rice in suppressing target weed plants, and this inducing effect was SA dose and treatment time dependent. After foliar spraying SA, the inhibitory effect of PI312777 on barnyardgrass increased significantly, and the root vigor and superoxide dismutase (SOD) and peroxidase (POD) activities of PI312777 increased, while its catalase (CAT) activity decreased. The reverse was true for the target weed barnyardgrass. At the same time, the phenylalanine ammonialyase (PAL) activity of PI312777 increased significantly, leading to an increase of the total content of phenols. Among the test concentrations of SA, 0.2 mmol x L(-1) had the best inducing effect, under which, the relative expression quantity of ZB8 increased first and decreased then, with a peak at 24 hours after treatment.

[The differential expression of the genes of the key enzymes involved in phenolic compound metabolism in rice (Oryza sativa L.) under different nitrogen supply].

Differential expression of the key genes controlling phenolic metabolism in allelopathic and non-allelopathic rice accessions was investigated under two nitrogen supply levels (lower and normal) using fluorescence quantitative-polymerase chain reaction (FQ-PCR) (Figs.2, 3). The results indicated that 9 key enzyme genes concerned were mediated by lower nitrogen level (Table 2). All of the nine genes (Table 1, Fig.4), were up-regulated by 1.9-5.4 times of the relative gene expression amounts in allelopathic rice accession, 'PI312777' under the lower nitrogen condition compared with their controls, of which PAL gene showed the highest relative gene expression amount with 5.4 times of the relative gene expressions compared with the control, while in non-allelopathic rice Lemont, seven genes were down-regulated by 29%-72% under lower nitrogen supplies compared with their controls and only two genes, i.e., phenylalanine ammonia-lyase and cinnamoyl-CoA genes were up-regulated, which however were a decrease of 22% and 74% over those in allelopathic rice accession (Table 2). These findings strongly suggest that the increase of allelopathic potential induced by 1/4 nutrient stress was responsible for enhanced phenolic compound synthesis metabolism.