Jacoby, Richard P., Succurro, Antonella and Kopriva, Stanislav (2020). Nitrogen Substrate Utilization in Three Rhizosphere Bacterial Strains Investigated Using Proteomics. Front. Microbiol., 11. LAUSANNE: FRONTIERS MEDIA SA. ISSN 1664-302X

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Abstract

Nitrogen metabolism in the rhizosphere microbiome plays an important role in mediating plant nutrition, particularly under low inputs of mineral fertilizers. However, there is relatively little mechanistic information about which genes and metabolic pathways are induced by rhizosphere bacterial strains to utilize diverse nitrogen substrates. Here we investigate nitrogen substrate utilization in three taxonomically diverse bacterial strains previously isolated from Arabidopsis roots. The three strains represent taxa that are consistently detected as core members of the plant microbiome: Pseudomonas, Streptomyces, and Rhizobium. We use phenotype microarrays to determine the nitrogen substrate preferences of these strains, and compare the experimental results vs. computational simulations of genome-scale metabolic network models obtained with EnsembleFBA. Results show that all three strains exhibit generalistic nitrogen substrate preferences, with substrate utilization being well predicted by EnsembleFBA. Using label-free quantitative proteomics, we document hundreds of proteins in each strain that exhibit differential abundance values following cultivation on five different nitrogen sources: ammonium, glutamate, lysine, serine, and urea. The proteomic response to these nitrogen sources was strongly strain-dependent, with lysine nutrition eliciting widespread protein-level changes in Pseudomonas sp. Root9, whereas Rhizobium sp. Root491 showed relatively stable proteome composition across different nitrogen sources. Our results give new protein-level information about the specific transporters and enzymes induced by diverse rhizosphere bacterial strains to utilize organic nitrogen substrates.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Jacoby, Richard P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Succurro, AntonellaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kopriva, StanislavUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-336267
DOI: 10.3389/fmicb.2020.00784
Journal or Publication Title: Front. Microbiol.
Volume: 11
Date: 2020
Publisher: FRONTIERS MEDIA SA
Place of Publication: LAUSANNE
ISSN: 1664-302X
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
PLANT; SOIL; MICROBES; GENOME; GENE; MICROORGANISMS; PRODUCTIVITY; COMPETITION; METABOLISM; NUTRITIONMultiple languages
MicrobiologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/33626

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