Metaproteomic data of maize rhizosphere for deciphering functional diversity

Abstract

Metaproteomics is a powerful tool for obtaining data on all proteins recovered directly from environmental samples at a given time. It provides a direct evidence of functional diversity and structure among microbiota present in niches and significant insights into microbial activity together with metabolomics, which is the study of the intermediate and end-products of cellular processes. Metaproteomics is a comparatively new approach which is facing a number of empirical, technical, computational and experimental design challenges that needs to be addressed. Presently only little efforts have been made to have information on microbial proteins in rhizospheric soil of maize through metagemonics approach but there is no direct evidence on functions of microbial community in this very important niche. Since rhizosphere microbiome plays important role in plant growth and development the present study is conducted to optimize the metaproteomic extraction protocol from maize rhizosphere and analyse functionality of microbial communities.We present metaproteome data from maize rhizospheric soil. Isolation of metaproteome from maize rhizosphere collected from ICAR-IISS, Mau experimental Farm was done with the standardized protocol at our laboratory and metaproteome analysis was done with the standardized pipeline. In total 696 proteins with different functions representing 244 genus and 393 species were identified. The proteome data provides direct evidence on the biological processes in soil ecosystem and is the first reported reference data from maize rhizosphere. The LC MS/MS proteomic data are available via ProteomeXchange with identifier PXD014519.

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

“…The proteome information gives to coordinate prove on the biological processes in the soil environment and is the primary detailed reference information from the maize rhizosphere( Table 3). The LC-MS /MS proteomic information is accessible by ProteomeXchange with identifier PXD014519 [85]. The induction of proteins from the respective peptides and the confirmation of the source and function of these proteins are the major steps toward meta-proteomics information analysis.…”

Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights

“…The latter has proven to be a non-toxic, inexpensive, and viable approach for the purification of proteins from soils [ 19 ]. In one of the most recent works, an optimization of already cited protocols [ 21 , 23 ], with modifications at several steps, was done to improve the metaproteomic analysis of rhizospheric samples [ 69 ]. The use of polyvinylpolypyrrolidone (PVPP) to clean samples from humic acids and liquid nitrogen to minimize proteolysis was proposed again in this protocol.…”

“…The proteins were extracted with a double extraction, first with 10% TCA/acetone and then with phenol (pH 8.0) and SDS buffer. Although the mass spectrometry proteomics data showed a total of 696 proteins, the images on the SDS-PAGE showed a poor quantity and quality of the bands obtained [ 69 ].…”

“…In 2019, the first metaproteomics study on the maize rhizosphere was reported and identified 696 proteins with different functions from 393 different species. Most of these proteins belonged to three functional groups: carbon metabolism, glycine biosynthesis, and IMP (Inosine Mono Phosphate) biosynthesis [ 69 ].…”

Activities and molecular characterization of petroleum hydrocarbons degrading rhizobacteria from mangrove plants (Rhizophora sp.) in Kulon Progo, Yogyakarta, Indonesia

“…Rhizosphere is an ideal area for growth of soil microorganisms that are generally dominated by bacteria, actinomycetes and fungi (Renu et al 2019). This area is also rich exudates that are produced by plants through the process of root secretion.…”