Protein extraction and database construction in tea rhizosphere soil
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ORIGINAL ARTICLE
Protein extraction and database construction in tea rhizosphere soil Hai‑bin Wang1,2 · Chun‑lian Zhu1 · Yu‑hua Wang1 · Qing‑xu Zhang1,2 · Peng Wang1,2 · Ding Li1 · Xiao‑li Jia3 · Jiang‑hua Ye3 · Hai‑bin He2 Received: 7 August 2019 / Revised: 8 September 2020 / Accepted: 24 September 2020 / Published online: 30 September 2020 © Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2020
Abstract Soil protein extraction and database construction are the key points of soil proteomics research. In this paper, tea tree rhizosphere soil was used as material. The soil proteins were extracted three times by citrate, SDS, and mixture of citrate and SDS, respectively. The total proteins were separated by 2-DE electrophoresis and identified by Data Dependent Acquisition (DDA). The DDA data collection was further separated by High-Performance Liquid Chromatography (HPLC) and identified by LC–MS/MS, then to build the database of soil protein and microbial species using fungus and bacteria databases. The result showed soil protein was identified and reached 2741 points, and the molecular weight was mainly distributed in between 2.64 and 338.33 kDa, and Isoelectric point (pI) is mainly distributed in between 3.78 and 12.15. The soil protein was mainly from 138 families, 346 species of microorganisms. This optimization method could obtain more proteins than previous methods, with a wider range of molecular weight and pI. This study lays an important foundation for the research and development of soil metaproteomics. Keywords Tea tree (camellia sinensis) · Soil protein · Molecular weight · Isoelectric point · Microbe
Introduction The soil ecosystem in the rhizosphere plays an important role in the regulation of plant growth. Therefore, there are more and more researches on rhizosphere ecosystem in recent years, especially on rhizosphere microecosystem. The rhizosphere is a densely distributed area of the microbial community, and the richness of the microbial community is closely related to the distance from the rhizosphere Communicated by E. Schleiff. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11738-020-03146-5) contains supplementary material, which is available to authorized users. * Hai‑bin He [email protected] 1
College of Life Sciences, Longyan University, Longyan 364012, China
2
Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou 35002, China
3
College of Ecology and Resources Engineering, Wuyi University, Wuyishan 354300, China
(Mukerji 2006). Meanwhile, coevolution also exists between plants and soil microorganisms. For example, changes in plant root secretion affect the structure of the microbial community, while changes in microorganisms around roots affect the growth of plant roots (Harwkes 2007). These dynamic interactions indicate a close relationship between roots and microorganisms. Many researchers have studied soil
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