Soil and Rhizosphere Microbiome Proteomics and Metabolomics

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 in 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 “Soil and Rhizosphere Microbiome Proteomics and Metabolomics”, we welcome 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 yield and response 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 also to highlight the direct and indirect impacts 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