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Rehmannia Glutinosa-Monocultured Rhizosphere Soil

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Rehmannia Glutinosa-Monocultured Rhizosphere Soil Comparative Metaproteomic Analysis on Consecutively Rehmannia glutinosa-Monocultured Rhizosphere Soil Linkun Wu1,2, Haibin Wang1,2., Zhixing Zhang1,2., Rui Lin2,3, Zhongyi Zhang1,4, Wenxiong Lin1,2* 1 School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China, 2 Agroecological Institute, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China, 3 College of Oceanography and Environmental Science, Xiamen University, Xiamen, Fujian, China, 4 Institute of Chinese Medicinal Materials, Henan Agriculture University, Zhengzhou, Henan, China Abstract Background: The consecutive monoculture for most of medicinal plants, such as Rehmannia glutinosa, results in a significant reduction in the yield and quality. There is an urgent need to study for the sustainable development of Chinese herbaceous medicine. Methodology/Principal Findings: Comparative metaproteomics of rhizosphere soil was developed and used to analyze the underlying mechanism of the consecutive monoculture problems of R. glutinosa. The 2D-gel patterns of protein spots for the soil samples showed a strong matrix dependency. Among the spots, 103 spots with high resolution and repeatability were randomly selected and successfully identified by MALDI TOF-TOF MS for a rhizosphere soil metaproteomic profile analysis. These proteins originating from plants and microorganisms play important roles in nutrient cycles and energy flow in rhizospheric soil ecosystem. They function in protein, nucleotide and secondary metabolisms, signal transduction and resistance. Comparative metaproteomics analysis revealed 33 differentially expressed protein spots in rhizosphere soil in response to increasing years of monoculture. Among them, plant proteins related to carbon and nitrogen metabolism and stress response, were mostly up-regulated except a down-regulated protein (glutathione S-transferase) involving detoxification. The phenylalanine ammonia-lyase was believed to participate in the phenylpropanoid metabolism as shown with a considerable increase in total phenolic acid content with increasing years of monoculture. Microbial proteins related to protein metabolism and cell wall biosynthesis, were up-regulated except a down-regulated protein (geranylgeranyl pyrophosphate synthase) functioning in diterpenoid synthesis. The results suggest that the consecutive monoculture of R. glutinosa changes the soil microbial ecology due to the exudates accumulation, as a result, the nutrient cycles are affected, leading to the retardation of plant growth and development. Conclusions/Significance: Our results demonstrated the interactions among plant, soil and microflora in the proteomic level are crucial for the productivity and quality of R. glutinosa in consecutive monoculture system. Citation: Wu L, Wang H, Zhang Z, Lin R, Zhang Z, et al. (2011) Comparative Metaproteomic Analysis on Consecutively Rehmannia glutinosa-Monocultured Rhizosphere Soil. PLoS ONE 6(5): e20611. doi:10.1371/journal.pone.0020611 Editor: Jack Anthony Gilbert, Argonne National Laboratory, United States of America Received February 7, 2011; Accepted May 5, 2011; Published May 31, 2011 Copyright: ß 2011 Wu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the National Natural Science Foundation of China (Grant no. 30772729, 30671220, 31070403) and the Natural Science Foundation of Fujian province, China (Grant no. 2008J0051). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] . These authors contributed equally to this work. Introduction eight years on a same lot [3]. Therefore, the farmers have to plant R. glutinosa in the less desirable areas outside Jiaozuo, and inevitably Tuberous root of Rehmannia glutinosa Libosch in the family of have a poor harvest in yield and quality [4]. Scrophulariaceae is used as one of the important and highly demanded Previous studies pointed out some possible consequences of the traditional Chinese medicines. High quality R. glutinosa is mainly consecutive monoculture, including soil nutrient imbalance, produced in Jiaozuo, Henan province (35u199N, 113u519E) of autotoxic substance generation and/or soil borne diseases [4]. central China, where the climatic and soil conditions for its For instance, the relative nitrogen (N), phosphorus (P) and cultivation are the most desirable. However, the productivity potassium (K) contributions to R. glutinosa’s biomass production and quality of the tuberous products substantially decline after were N.P.K [5]. In addition, the nutritional decline in soil was consecutive monoculture. This phenomenon is known as soil not the fundamental reason for the ill-effects caused by consecutive sickness (replanting disease) [1] and/or consecutive monoculture monoculture [6]. Rather, the main culprit was believed to be the problems [2]. The consecutively monocultured medicinal plants autotoxicity generated by the plant’s root exudates [3,7]. The GC- tend to suffer from severe diseases, which result in reduced biomass, MS analysis on the aqueous extracts of R. glutinosa rhizosphere soil especially decreased tuberous products. To curb the ill-effects, the showed that the allelochemicals, including organic acids, alde- common practice is to cultivate the medicinal plants only once every hydes and phenolics, were potentially harmful for plant growth PLoS ONE | www.plosone.org 1 May 2011 | Volume 6 | Issue 5 | e20611 Metaproteomic Analysis on Crop Rhizosphere Soil [8]. There are reports on the negative effects of phenolic acids on one- and two-year monoculture soils was performed on the the soil microorganisms, indicating that the allelochemicals (e.g., protein extracts obtained. It was speculated that the R. glutinosa cinnamic acid, 2,4-di-tert-butylphenol and vanillic acid) can affect biomasses, both above- and below-ground, would be reduced the microbial genetic diversity and ecology in soil [1,2]. More when the monoculture was extended from one year to two years, recent studies have revealed that the consecutive monoculture owing to the imbalance among the community members (i.e., practice influences the structure and populations of R. glutinosa plants, microflora and fauna), and the inhibition of nutrient rhizoshpere community [9,10]. However, there is no report cycling in the rhizosphere soil. In this study, we aimed to: (i) hitherto focusing on the relationship among the soil ecosystem, extract proteins directly from the rhizoshpere soil, (ii) determine microbial community and consecutive monoculture in a proteomic changes on soil protein abundance under consecutive monocul- perspective. ture, and (iii) understand the interactions between the root There has been an increasing interest on the biological system and the rhizospheric microorganisms. The result might properties of rhizosphere in situ [11]. Various approaches can be provide a theoretical basis and technological support for re- utilized to obtain the biological information within rhizosphere. storation of soil damage, improvement of soil ecological However, the complexity due to the numerous and diverse environment, and establishment of an effective cropping practice interactions among the soil’s physical, chemical, and biological to resolve the problems associated with R. glutinosa consecutive components seems to have hampered the progress [12]. For monoculture. example, the microbial biomass carbon [13], microbial respiration [14], lipids [15] and nucleic acids [16] that are frequently used as Results indicators for the microbial activities, fall short of explaining the functions of soil microbes in situ. Metaproteomic analysis is capable Dried weight of R. glutinosa biomasses of providing information to show the actual functionality with Consecutive monoculture significantly inhibited the growth of respect to the metabolic reactions and regulatory cascades. The R. glutinosa, as indicated by the reduced above- and below-ground methodology, therefore, may offer a greater potential than the biomasses after the two-year consecutive monoculture (Table 1). conventional means for functional analysis on the microbial The two-year consecutive monoculture significantly lowered the communities. dry weights of the above-ground R. glutinosa plant on the 70th, Metaproteomics is a study of all proteins recovered directly from 80th and 90th day after planting, and those of the below-ground environmental samples at a given time [17]. It has some superior tuber on the 60th, 70th, 80th and 90th day after planting. The advantages for soil studies. First of all, the rhizosphere soil plant’s root to shoot ratios (R/S) on the 50th, 60th, 70th, 80th metaproteomics provides a direct evidence on the biological and 90th day were significantly lowered by the extended processes in soil ecosystem at the proteomic level. Even the nucleic monoculture. acids-based approaches are greatly restricted due to the weak correlation between mRNA and protein abundances, and the Root activity and N, P and K contents of R. glutinosa complexity of mRNA post-transcriptional processing and modifi- The consecutive monoculture significantly retarded the R. cation [18]. Moreover, the biological process in rhizosphere
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