Special Issue "Mass Spectrometry-Based Omics of Soil and Plant Microbiomes"

A special issue of Methods and Protocols (ISSN 2409-9279).

Deadline for manuscript submissions: closed (30 June 2019) | Viewed by 3117

Special Issue Editor

Proteomics and Metabolomics Facility, Center for Biotechnology, Institute of Agriculture and Natural Resources, University of Nebraska-Lincoln N300, Beadle Center, 1901 Vine St, Lincoln, NE 68588-0665, USA
Interests: proteomics; mass spectrometry; post-translational modifications; phosphoproteomics; redox proteomics; targeted metabolomics; liquid chromatography; electrophoresis
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Special Issue Information

Dear Colleagues,

Microorganisms in the soil are responsible for important biogeochemical processes, including nutrient and water mobilization. By directly interacting with plant roots and the rhizosphere, the microbiome has a profound beneficial or detrimental impact on plant growth. This regulation of biogeochemical processes occurs at the enzymatic level, but little is understood regarding protein diversity and function in soil.

Metagenomics and metatranscriptomics have emerged as very powerful analytical tools for determining the taxonomic and functional components of microbial communities. However, especially in the soil microbiome, it is proteins with enzymatic activity that are the final key operational components in metabolic pathways. The identification and quantification of proteins expressed by the microbiome, and the release of metabolites into the soil and the rhizosphere of plants growing in a field, is essential to understanding the mechanisms involved in microbiome interaction with plants. This type of metaproteomic analysis has only recently become possible thanks to the growth in genomic data and the bioinformatics tools used to build more comprehensive databases. In addition, proteomics and metabolomics have gained momentum from the increased mass accuracy and sensitivity of commercialized mass spectrometers that are now available. However, there are still many methodological challenges to overcome for the study of proteins and metabolites contained in soils, due to the diversity and complexity of the matrix and the high dilution of compounds in soil samples and root exudates, as well as the lack of bioinformatic data analysis workflows to address the specific needs for mining proteomic and metabolomic data.

In this Special Issue on “Mass Spectrometry-Based Omics of Soil and Plant Microbiomes”, we encourage researchers to submit original research or review articles on advanced methods to study the interactions between plant roots and the soil microbiome at the protein and metabolite levels. The goal is to collect the most recent developments in sample processing and data analysis workflows, with a particular interest in the identification and quantification of proteins and/or metabolites involved in root–microbiome interactions and their impact on crop yields and responses to climate change. This Special Issue intends to provide a better understanding of the soil–rhizosphere interaction with respect to crop improvement and food and fuel sustainability and to highlight the direct and indirect impact of climate change on soil communities and what this may mean for plant productivity.

Dr. Sophie Alvarez
Guest Editor

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  • soil
  • crop
  • climate change
  • proteome
  • metabolome
  • microbiome
  • mass spectrometry
  • bioinformatics

Published Papers (1 paper)

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9 pages, 1272 KiB  
Solvation Free Energy Simulation for Rosmarinic Acid Extraction from Orthosiphon stamineus
Methods Protoc. 2019, 2(3), 64; https://doi.org/10.3390/mps2030064 - 27 Jul 2019
Cited by 4 | Viewed by 2753
This study was aimed to extract rosmarinic acid from Orthosiphon stamineus Benth. (Lamiaceae) in high yield. The mixture of chloroform–ethyl acetate (70:30) was chosen as the solvent system because rosmarinic acid gave the lowest solvation free energy in that solvent system [...] Read more.
This study was aimed to extract rosmarinic acid from Orthosiphon stamineus Benth. (Lamiaceae) in high yield. The mixture of chloroform–ethyl acetate (70:30) was chosen as the solvent system because rosmarinic acid gave the lowest solvation free energy in that solvent system based on the computational solubility prediction. The crude extract of the plant was fractionated by C18 reversed phase absorbent to recover rosmarinic acid. The content of rosmarinic acid was increased from 4.0% w/w to 6.7% w/w after fractionation. The radical scavenging activity of rosmarinic acid rich fraction (IC50 = 38.3 μg/mL) was higher than the crude extract (IC50 = 58.85 μg/mL) based on the DPPH assay. Several phytochemicals were also identified based on the detection of fragment ions of target compounds. Fractions 1 to 3 could be combined to be a rosmarinic acid rich fraction. Simultaneously, the combination of fractions 4 to 6 could obtain a plant fraction rich in rosmarinic acid, sinensetin and eupatorin, whereas fractions 7 to 9 could be combined as a sinensetin rich fraction. The preparation of known phytochemical profile of O. stamineus fraction is highly required for value added product formulation and pharmacological studies, particularly for anti-diabetes and kidney related diseases which had previously been reported attributed to this herbal plant. This is the first study using solvation free energy to predict the suitable solvent system for rosmarinic acid extraction from highly complex herbal sample using the technology of solid phase extraction. The use of solvation free energy simulation is convenient and reliable before wet experiments for time and cost saving. Full article
(This article belongs to the Special Issue Mass Spectrometry-Based Omics of Soil and Plant Microbiomes)
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