Comparative Metaproteomic Analysis on Consecutively Rehmannia glutinosa-Monocultured Rhizosphere Soil

Abstract

BackgroundThe 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 FindingsComparative 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/SignificanceOur 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.

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

“…In that study, microorganisms were sampled from leaf material, and parallel metagenomics and metaproteomics analyses were performed using one-dimensional protein separation followed by liquid chromatography high-accuracy mass spectrometry. Metaproteomic studies of rhizosphere samples are still at its beginning and first reports were only published very recently Wu et al, 2011). In those studies, proteins were directly extracted from rhizosphere samples (without a preceding physical enrichment step of microbial cells; Bastida et al, 2009), separated by twodimensional gel electrophoresis and identified by MALDI-TOF/TOF.…”

Environmental proteomics: A long march in the pedosphere

“…In the last decade environmental proteomics has broadened its analytical spectrum to various natural and polluted soil types, plant phyllosphere and rhizosphere, waters and other environmental matrices, such as organic wastes and mine spoils (Wilmes and Bond, 2004;Tyson et al, 2004;Ram et al, 2005;Schulze et al, 2005;Benndorf et al, 2007;Chourey et al, 2010;Williams et al, 2010;Wang et al, 2011;Wu et al, 2011). Early environmental proteomics aimed at developing efficient methods for increasing the yield of protein extraction in the direction 'the more the proteins the better', leading mostly to inventories of bulk soil proteins than to discovery of relevant protein expression profile of soil microbial communities.…”

“…The relative rarity of key function protein molecules against a background of abundant and diverse structural proteins may be responsible for the low rate of unique discoveries in soil metaproteomic studies, despite the rapid progress in protein extraction and detection methodologies. Even the most exhaustive studies are only able to identify 10e300 proteins (Benndorf et al, 2007;Chourey et al, 2010;Williams et al, 2010;Wang et al, 2011;Wu et al, 2011). Soil proteolytic activity (Renella et al, 2002) and geochemical denaturation are partially responsible for the low yield of protein extraction and identification.…”

Screening and Identification of Harmful and Beneficial Microorganisms Associated with Replanting Disease in Rhizosphere Soil of Pseudostellariae heterophylla

“…Previous studies showed that rhizospheric microbial dynamics largely governed proper soil ecosystem function and had close interaction with consecutive monoculture problems (Qu and Wang, 2008;Qi et al, 2009;Wu et al, 2009;Wu et al, 2011;Li et al, 2012b;Wu et al, 2013). Crop consecutive monoculture not only alters the physical and chemical properties of the soil, but also contributes to the development of diverse microbial groups in the rhizosphere (Minh, 2005;Lin et al, 2007;Yoneyama and Natsume, 2010;Berendsen et al, 2012;Ndabamenye et al, 2013).…”

“…The autotoxic compounds were often isolated from consecutive monoculture soil, such as phenolic acid and aliphatic acid compounds, which could selectively enhance specific microbial populations in the soil which then leads to a shift in microbial communities (Qu and Wang, 2008;Li et al, 2012b). Wu et al (2011) analyzed the rhizospheric biological properties of consecutively monocultured R. glutinosa using soil metaproteomics and found that consecutive monoculture can induce the changes of microbes in the expression of proteins.…”