MassIVE MSV000090377

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Microbial Consortium Interactions Driving Chitin Degradation in Soil

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Description

These data are part of a multi-omics (genomics, transcriptomics, proteomics, and metabolomics) study to understand population dynamics and community interactions of an 8-member naturally co-adapted soil microbial consortia inoculated into autoclaved soil collected from our field site in Prosser, WA and analyzed at four time points (0, 4, 8, and 12 weeks post-inoculation). Chitin amendment at 0.5 mg/g of soil was used as a carbon and nitrogen source for this bacterial consortium. Two inoculation concentrations (10^8 and 10^9) along with a a control of no inoculum addition was studied. These data will be used for correlative molecular networking and metagenomics based metabolic modeling. The 8-member consortium was composed of a Streptomyces sp., Neorhizobium tomejilense, a Dyadobacter sp., a Sphingopyxis sp., Ensifer adhaerens, Variovorax beijingensis, Sinorhizobium meliloti, and a Rhodococcus sp. Isolate. These data deposited to MassIVE represent the LC-MS/MS proteomics and LC-MS metabolomics portions of the project. The proteomics data is label-free analyses of peptides obtained after a trypsin digestion. Each sample was first fractionated off-line into 6 fractions using a high pH C-18 separation and each of those 6 fractions were then analyzed using a low pH C-18 separation directly coupled to a Thermo Scientific Q-Exactive Orbitrap for analysis. The LC-MS metabolomics analysis was based on a water:methanol soluble metabolite extraction followed by both negative and positive ion mode analysis of the metabolites separated by low pH C-18 and analyzed using a Q-Exactive HF-X Quadrupole-Orbitrap mass spectrometer. The GC-MS metabolomics analysis was based on the same water:methanol soluble metabolite fraction as analyzed in the LC-MS analysis but which has been derivatized and analyzed by gas chromatography and analyzed by an Agilent mass spectrometer. [doi:10.25345/C5PG1HS89] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: soil microbiome ; chitin ; community interactions ; population dynamics ; multi-omics ; bacteria

Contact

Principal Investigators:
(in alphabetical order) 		Janet K. Jansson, Pacific Northwest National Laboratory, United States
Submitting User: alchemistmatt
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