{"links":{"first":"https://www.ebi.ac.uk/metagenomics/api/v1/samples/SRS003189/studies?format=json&page=1","last":"https://www.ebi.ac.uk/metagenomics/api/v1/samples/SRS003189/studies?format=json&page=1","next":null,"prev":null},"data":[{"type":"studies","id":"MGYS00004563","attributes":{"bioproject":null,"accession":"MGYS00004563","samples-count":2,"is-private":false,"last-update":"2019-04-12T16:20:34","secondary-accession":"SRP000815","centre-name":"University of Georgia","public-release-date":null,"study-abstract":"Ten primer pairs targeting environmental clades of the dimethylsulfoniopropionate (DMSP) demethylase protein, DmdA, were designed using an iterative bioinformatic approach that took advantage of >1700 dmdA sequences captured in marine metagenomic datasets.  Using the bioinformatically-optimized primer pairs, dmdA genes were amplified from free-living coastal bacterioplankton samples and sequenced using 454 technology.  An average of 6,400 amplicons per primer pair represented almost 800 clusters of environmental dmdA sequences, with clusters defined conservatively at >90% nucleotide sequence identity (~95% protein identity).  Systematic comparisons of primer performance showed that degenerate and inosine-based primers did not perform better than specific primer sets in retrieving dmdA diversity, and sometimes captured a lower diversity of sequences from the same DNA sample.  The specific primer sets were used to compare dmdA diversity in free-living versus particle-associated bacteria in southeastern U.S. coastal waters.  Hundreds of different dmdA clusters were found in both size fractions, with Roseobacter-like and SAR11-like sequences dominating both. The free-living fraction had a higher diversity of dmdA clusters overall, though clusters retrieved by a given primer set were largely shared (52-88%) across the two size fractions, and most sequences were affiliated with these shared clusters (~90%). Despite evidence from 16S rRNA-based taxonomic surveys that free-living bacterioplankton are a considerably less diverse subset of particle-associated bacteria at this site, this seems not to be the case for a widespread bacterial gene mediating sulfur transformations.","study-name":"Deep sequencing of a DMSP-degrading gene (dmdA) in a coastal bacterioplankton community","data-origination":"HARVESTED"},"relationships":{"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00004563/analyses?format=json"}},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00004563/publications?format=json"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00004563/biomes?format=json"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Marine","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine?format=json"}}]},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00004563/downloads?format=json"}},"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00004563/geocoordinates?format=json"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00004563/samples?format=json"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00004563?format=json"}}],"meta":{"pagination":{"page":1,"pages":1,"count":1}}}