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Study

Study Name: Marine bacterioplanktonic communities from the University of Georgia, USA for heterotrophic carbon processing in the sea

Projects

Biosamples

Organisms

Biosamples: 26 Seq. Projects: 62
STUDY INFORMATION
GOLD Study ID Gs0102994
Study Name Marine bacterioplanktonic communities from the University of Georgia, USA for heterotrophic carbon processing in the sea
Other Names The Genetic Basis for Heterotrophic Carbon Processing in the Sea
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
SRA Studies
Legacy ER Study ID 57994
Legacy GOLD ID Gm0057994
Added By Tatiparthi Reddy on 2013-10-21
Last Modified By JGI automated process on 2019-09-06
PI Mary Ann Moran
Description Heterotrophic marine bacterioplankton are the principal consumers of dissolved organic matter (DOM) in the oceans. As the largest living surface area in the sea, they detect, transport, and assimilate bioreactive constituents from the DOM pool, transforming these compounds to particulate matter or recycling them back to their inorganic forms. Despite the importance of this activity on a global scale, progress in understanding bacterioplankton-mediated DOM flux has been slow. Functional genomic/metagenomic approaches have the potential to uncover major insights into DOM fate, but are limited by the mismatch between the pace of finding new genes and the pace of determining their function.

We would leverage an existing model organism system based on the marine Roseobacter Ruegeria (formerly Silicibacter) pomeroyi DSS-3 to improve understanding of the genetic basis of bacterial DOM cycling in the ocean. A whole genome negative selection framework will be applied to R. pomeroyi DSS-3 to identify genes required for transformation of selected compounds or compound classes representative of the DOM pool. Since this is a 'negative selection' approach, it is restricted to DOM compounds that can support growth of the model bacterium (making the large genome and substrate promiscuity of R. pomeroyi advantageous) and compounds that are degraded by only one pathway in the bacterium.

Transposon mutant libraries of R. pomeroyi DSS-3 will be challenged in batch culture for the ability to grow on organic compounds representative of the marine DOM pool (for example, selected sugars, organic acids, aromatic compounds, and amino acids). The surviving mutant pool for each compound will be screened with Illumina sequencing, using deep sequencing of the transposon-gene junctions. When mapped to the R. pomeroyi DSS-3 genome, coverage gaps will indicate the location of essential genes, since mutants with a transposon insertion in an essential gene will be unable to grow. Enrichment of the transposon-gene junctions prior to sequencing will be carried out by affinity purification. This whole-genome negative selection approach has been given the acronym 'HITS' for 'high-throughput insertion tracking by deep sequencing'. Mutants absent in all surviving mutant pools will allow ust to distinguish core genes (which are not of interest here) from genes necessary for the selected DOM transformations.

Genes identified by HITS in the R. pomeroyi model system will be evaluated for their ecological relevance. For a selected subset of compounds, quantitative metatranscriptomic analyses will be carried out using natural marine bacterial communities and experimental manipulation of the concentration of the compounds. Transcriptional response of the natural marine community for the candidate genes and associated pathways will be characterized.
Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study Yes
Publication
Is GEBA No
Is HMP No
ECOSYSTEM CLASSIFICATION
Ecosystem Environmental
Ecosystem Category Aquatic
Ecosystem Type Marine
Ecosystem Subtype Unclassified
Specific Ecosystem Unclassified
STUDY COMPOSITION
Number of Biosamples 26
Number of Organisms 1
Number of Seq Projects 62
Number of Analysis Projects 0
Number of Related Studies 0

 

 

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