Santa Barbara Channel Marine BON: genomics study on 16S primer comparison

This project examined the effects of 16S rRNA gene primer selection on
population representation and community ecology of bacteria and
archaea in the Santa Barbara Channel. Four 16S rRNA primer sets
targeting different hypervariable regions of the gene were compared
using both mock communities of known composition constructed from
cloned 16S rRNA genes and field samples covering the annual cycle.
Amplicon results were compared with shotgun metagenomes prepared from
a subset of the field samples. The field samples included in the comparison study are subsets of two
more extensive field programs in the Santa Barbara Channel. Samples
included from the Plumes and Blooms transect times-series program were
collected between February 2012 and August 2014. Samples from
University-National Oceanographic Laboratory Systems cruise PS1103
(Wear et al. 2015; DOI: 10.1002/lno.10042) were collected in May 2011. All datasheets represent curated, processed output of the
bioinformatics pipeline. Unprocessed sequencing data are archived with
the National Center for Biotechnology Information, with accession
numbers specified in the individual datasheets. Four dataset entities included primer testing on a known mock
community (Entity #1 and #2) as well as the application of the primers
to field samples (Entity #3) and shotgun metagenomes from a subset of
field samples (Entity #4): 1) Cloned 16S genes used to construct the mock community. 2) Mock community sequencing results - relative abundance of each
clone with each of 4 primer sets. 3) Field sequencing results - relative abundance of operational
taxonomic units (OTUs) and weighted UniFrac distance matrices. 4) Metagenome results – taxonomic identities of individual 16S rRNA
sequences identified in each metagenome. The funding source for this project is: the National Aeronautics and
Space Administration Biodiversity and Ecological Forecasting program
(Grant NNX14AR62A), the Bureau of Ocean and Energy Management
Ecosystem Studies program (BOEM award MC15AC00006), and NOAA in
support of the Santa Barbara Channel Biodiversity Observation
Network. Samples were originally collected under the NASA Earth and
Space Science Fellowship Program – Grant NNX12AO13H and National
Science Foundation Award OCE-0850857. Additional support came from a
NASA Postdoctoral Fellowship to EGW and NSF OCE-1538428 to CEN. Data
were collected using instruments provided by the Santa Barbara Coastal
LTER, funded by NSF OCE-1232779.