GNPS - Iron Oxidizing Bacteria Exo-Metabolomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Unkown
SUBMITTER: 
Daniel Petras
PROVIDER: MSV000088519 | GNPS | Mon Dec 06 02:38:00 GMT 2021
REPOSITORIES: GNPS
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Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
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Project description:Nitrate-reducing iron(II)-oxidizing (NDFO) bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. A second NDFO culture, culture BP, was obtained with a sample taken in 2015 at the same pond and cultured in a similar way. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture BP. Raw sequencing data of 16S rRNA amplicon sequencing (V4 region with Illumina and near full-length with PacBio), shotgun metagenomics, metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA693457. This dataset contains proteomics data for 2 conditions in triplicates. Samples R23, R24, and R25 are grown in autotrophic conditions, samples R26, R27, and R28 in heterotrophic conditions.
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Project description:Iron-oxidizing bacteria are widely found in natural and man-made environments where they influence varied biogeochemical cycles. Despite their prevalence, the mechanisms and Fe(II) substrates used by these organisms remain understudied. To date, there has been limited exploration of the ability of iron-oxidizing bacteria to utilize solid minerals as electron donors. Sideroxydans lithotrophicus ES-1 is a robust, facultative iron oxidizer with multiple enzymatic pathways for iron oxidation, making it a prime candidate for evaluating extracellular electron uptake mechanisms. In this study, S. lithotrophicus ES-1 was grown on dissolved Fe(II)-citrate and three preparations of magnetite that provided different ratios of soluble and solid Fe(II). S. lithotrophicus ES-1 grew equally well on the different batches of magnetite, suggesting it can adapt to the type of iron present during growth. S. lithotrophicus ES-1 oxidized all available dissolved Fe2+ released from magnetite, and continued to build biomass when only solid Fe(II) remained. Quantitative proteomic analyses of S. lithotrophicus ES-1 grown on these substrates revealed proteome remodeling in response to electron donor and growth state, and uncovered potential proteins and metabolic pathways involved in the oxidation of solid magnetite. While the Cyc2 iron oxidases were highly expressed on both dissolved and solid substrates, the MtoAB complex was only expressed during growth on the solid magnetite, suggesting these proteins play a role in oxidation of solid minerals in S. lithotrophicus ES-1. A set of cupredoxin domain-containing proteins were also identified that were specifically expressed during solid iron oxidation. This work confirmed the iron oxidizer, S. lithotrophicus ES-1, utilized distinct extracellular electron transfer pathways when growing on solid mineral electron donors compared to dissolved Fe(II)-citrate. The presence of multiple pathways, and the ability to regulate their expression and use, could benefit iron-oxidizing bacteria that encounter various electron donors in their environments.
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