Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details.
Horizontal_Positional_Accuracy_Report: No formal positional accuracy tests were conducted.
Vertical_Positional_Accuracy_Report: No formal positional accuracy tests were conducted.
Type_of_Source_Media: Digital and/or Hardcopy
Originator: Koty H. Sharp
Originator: Zoe A. Pratte
Originator: Allison H. Kerwin
Originator: Randi D. Rotjan
Originator: Frank J. Stewart
Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata
Issue_Identification: Vol. 5, issue 1
Publication_Place: London, United Kingdom
Publisher: BioMed Central, Springer Nature
Source_Currentness_Reference: publication date
The samples used to generate the sequences in this dataset were collected as part of the study reported in Sharp and others (2017). In addition, the DNA that was sequenced for this study was extracted from the samples by Sharp and others (2017) as part of their study.
Paired brown (symbiotic) and white (aposymbiotic) samples of A. poculata were collected as described in Sharp and others (2017). Briefly, samples were collected from Narragansett Bay in September 2015 and April 2016 by SCUBA at depths of 1-5 meters. Paired colonies were selected such that the brown and white members of the pair were no more than 10 centimeters apart. Samples were immediately brought to the surface, frozen in liquid nitrogen, and held at -80ºC until DNA extraction.
Eight samples--two sets of paired brown and white colonies collected in the fall (September) and two sets collected in the spring (April) were analyzed by USGS scientists. DNA was extracted from each sample of A. poculata as described in Sharp and others (2017). Briefly, the PowerSoil DNA Isolation Kit (Qiagen, Valencia, CA) was used according to the manufacturer’s protocol to extract DNA from a fragment of each sample comprising mucus, tissue, and skeleton.
Bacterial primers: DNA from each sample was amplified by PCR using primers 8F (5’–AGA GTT TGA TCC TGG CTC AG) and 1492R (5’–GGT TAC CTT GTT ACG ACT T) to target the 16S rRNA gene [9,10]. Each 25-microliter (µL) reaction contained 12.5 µL AmpliTaq Gold 360 Master Mix (Applied Biosystems, Foster City, CA), 0.4 µM concentration of each primer, and 10 µL of template DNA. The reaction conditions consisted of 15 minutes (min) of initial denaturation at 95ºC, 30 cycles of (i) 1 min denaturation at 95ºC, (ii) 1 min annealing at 54ºC, and (iii) 2 min extension at 72ºC, and 10 min of final extension at 72ºC. Amplicons were visualized on a 1.5% agarose gel, then extracted from the gel using the QIAquick Gel Extraction Kit (QIAGEN, Germantown, MD) according to the manufacturer’s instructions. Gel-extracted amplicons were quantitated using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) on a Qubit 3.0 fluorometer according to the manufacturer’s instructions.
Archaeal primers: DNA from two of the samples (FW1B8 and FW1W8) was also amplified using primers 21F (5’–TTC CGG TTG ATC CYG CCG GA) and 958R (5’–YCC GGC GTT GAM TCC AAT T) in order to amplify the 16S rRNA gene from Archaea (DeLong, 1992). Each 25-µL reaction contained 12.5 µL AmpliTaq Gold 360 Master Mix (Applied Biosystems, Foster City, CA), 0.4 µM concentration of each primer, and 10 µL of template DNA. The reaction conditions consisted of 15 min of initial denaturation at 95ºC, 30 cycles of (i) 95ºC for1.5 min, (ii) 55ºC for 1.5 min, and (iii) 72ºC for 1.5 min, and 10 min of final extension at 72ºC (DeLong, 1992). Amplicons were visualized, extracted, and quantitated as described above for the bacterial amplicons.
Amplicons were cloned into the pDrive vector using the PCR Cloning Plus kit (QIAGEN, Germantown, MD) and used to transform competent cells. After M13 screening, inserts in positive transformants were sequenced by the Clemson University Genomics Computational Laboratory (Clemson, SC). USGS staff received approximately 4,200 raw sequences from the sequencing facility (available, upon request) that were subsequently trimmed and checked for quality assurance/quality control (QA/QC). Those QA/QC procedures resulted in ~1,700 sequences, which are described in Goldsmith and others (2019) and provided in this data release.
Vector and ends were trimmed from the sequences using Geneious (version 11.1.4; Biomatters Ltd., Auckland, NZ).
Using QIIME version 1.9.1, all sequences less than 50 bp were removed. Greengenes version 13_8 (http://greengenes.secondgenome.com/
) was used through QIIME to perform a chimera check with usearch61 (https://www.drive5.com/usearch/)
, and to classify taxonomy using an open reference algorithm with a 97% similarity threshold . Singletons were retained, while all other default parameters were used. After chimeric, unclassified, chloroplast, and mitochondrial sequences were removed, 996 bacterial OTUs remained.
Upon submission of the sequences to NCBI’s GenBank, GenBank’s implementation of version 10 of usearch (64-bit version) using the uchime2_ref command in high confidence mode uncovered 190 additional chimeras. These sequences were removed, resulting in a dataset of 806 bacterial OTUs. Sequences representing each bacterial OTU have been deposited in GenBank under accession numbers MK175495 to MK176300. Sequences representing each archaeal OTU (18 OTUs) have been deposited in GenBank under accession numbers MH915525 to MH915542.
Added keywords section with USGS persistent identifier as theme keyword.
Contact_Organization: U.S. Geological Survey
Contact_Position: Marine Geologist
Contact_Person: VeeAnn A. Cross
Address_Type: Mailing and Physical
Contact_Voice_Telephone: 508-548-8700 x2251
Address: 384 Woods Hole Road
City: Woods Hole