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Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil.

Wu L, Wang H, Zhang Z, Lin R, Zhang Z, Lin W - PLoS ONE (2011)

Bottom Line: The consecutive monoculture for most of medicinal plants, such as Rehmannia glutinosa, results in a significant reduction in the yield and quality.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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 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.

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Related in: MedlinePlus

Functional classification of identified proteins.Identified proteins were classified according to their functions using KEGG database (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/).
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pone-0020611-g004: Functional classification of identified proteins.Identified proteins were classified according to their functions using KEGG database (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/).

Mentions: The identified proteins were classified by their functions using the KEGG database (Kyoto Encyclopedia of Genes and Genomes at http://www.genome.jp/kegg/). According to the putative physiological functions, they were categorized into 14 groups, as shown in Figure 4, by their association with (i) carbohydrate and energy metabolism, (ii) glycan biosynthesis and metabolism, (iii) xenobiotics biodegradation and metabolism, (iv) cofactors and vitamins metabolism, (v) secondary metabolism, (vi) amino acid metabolism, (vii) protein metabolism, (viii) nucleotide metabolism, (ix) signal transduction, (x) stress/defense response, (xi) genetic information processing, (xii) storage protein, (xiii) virulence factor and (xiv) membrane transport. Among them, 75.73% were derived from plants, 11.65% from bacteria and 12.62% from fungi (Table S1, S2 and S3). It demonstrated that the chemical-biological process in the rhizosphere ecosystem is driven by both the plants and the microbes, and even by the fauna. The largest functional group was the proteins involved in carbohydrate and energy metabolism (27.18%), followed by those associated with the amino acid metabolism (16.50%). They were associated with the soil nutrient cycles, including carbon (C) and N cycling. Sixteen proteins related to the stress/defense response (including the superoxide dismutase and catalase), 4 involved in the secondary metabolism (including the phenylalanine ammonia-lyase, geranylgeranyl pyrophosphate synthase and Pentalenene synthase), and 3 related to the xenobiotics metabolism (including the glutathione S-transferase and tellurite resistance protein) were also identified. Eight protein spots (including the chemotaxis signal transduction protein, methyl-accepting chemotaxis protein, GTP-binding protein, G-protein signaling regulator and TGF-beta receptor-interacting protein 1) from both the microbes and the plants relating to the signal transduction were detected.


Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil.

Wu L, Wang H, Zhang Z, Lin R, Zhang Z, Lin W - PLoS ONE (2011)

Functional classification of identified proteins.Identified proteins were classified according to their functions using KEGG database (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105091&req=5

pone-0020611-g004: Functional classification of identified proteins.Identified proteins were classified according to their functions using KEGG database (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/).
Mentions: The identified proteins were classified by their functions using the KEGG database (Kyoto Encyclopedia of Genes and Genomes at http://www.genome.jp/kegg/). According to the putative physiological functions, they were categorized into 14 groups, as shown in Figure 4, by their association with (i) carbohydrate and energy metabolism, (ii) glycan biosynthesis and metabolism, (iii) xenobiotics biodegradation and metabolism, (iv) cofactors and vitamins metabolism, (v) secondary metabolism, (vi) amino acid metabolism, (vii) protein metabolism, (viii) nucleotide metabolism, (ix) signal transduction, (x) stress/defense response, (xi) genetic information processing, (xii) storage protein, (xiii) virulence factor and (xiv) membrane transport. Among them, 75.73% were derived from plants, 11.65% from bacteria and 12.62% from fungi (Table S1, S2 and S3). It demonstrated that the chemical-biological process in the rhizosphere ecosystem is driven by both the plants and the microbes, and even by the fauna. The largest functional group was the proteins involved in carbohydrate and energy metabolism (27.18%), followed by those associated with the amino acid metabolism (16.50%). They were associated with the soil nutrient cycles, including carbon (C) and N cycling. Sixteen proteins related to the stress/defense response (including the superoxide dismutase and catalase), 4 involved in the secondary metabolism (including the phenylalanine ammonia-lyase, geranylgeranyl pyrophosphate synthase and Pentalenene synthase), and 3 related to the xenobiotics metabolism (including the glutathione S-transferase and tellurite resistance protein) were also identified. Eight protein spots (including the chemotaxis signal transduction protein, methyl-accepting chemotaxis protein, GTP-binding protein, G-protein signaling regulator and TGF-beta receptor-interacting protein 1) from both the microbes and the plants relating to the signal transduction were detected.

Bottom Line: The consecutive monoculture for most of medicinal plants, such as Rehmannia glutinosa, results in a significant reduction in the yield and quality.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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 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.

Show MeSH
Related in: MedlinePlus