<div><p>Eight of the freshly-isolated <em>T. rotula</em> cells (3 cells each from PopA and PopB, 2 from PopC) were brought into culture and maintained at 18°C, ~100 μmol photons m⁻²s⁻¹, and an 18:6 light to dark cycle. The isolates underwent antibiotic treatment 1-4 months before the start of the experiment. Antibiotic treatment consisted of 1.5 mL of culture and 150 mL of F/2 media with 100 μg L⁻¹ of imipenem (Fisher Scientific) in 250 mL flasks on shaker tables at about 70 RPM for up to 96 hours before being transferred into F/2 media. Successful antibiotic treatment was identified by staining live cultures with 1% SYBR and visually verifying the absence of bacteria on a Nikon inverted Epifluorescent microscope both after the initial antibiotic treatments and before the start of the experiment. Isolates were maintained in exponential growth prior in F/2 media to the beginning of the experiment.</p>
<p>To begin the common garden experiment, 10L of whole seawater was collected from the pier from the URI Graduate School of Oceanography (41.49°, - 71.42°) on September 15, 2018. Whole seawater was filtered twice through 1μm polycarbonate track etch membrane filters (PCTE; Sterlitech) into autoclaved flasks to capture the free-living <em>in situ</em> bacterial community and remove grazers and large phytoplankton. Following filtration, 150 mL aliquots of the 1μm filtered seawater were added to sterile 250 mL Erlenmeyer flasks and amended with sterile F/10 vitamins and nutrients. All treatments were conducted in triplicate and included single strain flasks that were inoculated with a final concentration of 1,000 <em>T. rotula </em>cells mL⁻¹. We also had two control treatments: a bacterial control consisting of 150mL quadruplicates of the <em>in situ </em>bacterial community amended with F/10 vitamins and nutrients and a media control consisting of 150 mL triplicates of sterile seawater amended with F/10 vitamins and nutrients. All treatments were maintained at 18°C, 100 μmol photons m⁻²s⁻¹, an 18:6 light:dark cycle, and 70 RPM on shaker tables.</p>
<p>On day 5, 100 mL of each culture flask was filtered onto a 0.2-μm Express Filter (Millipore), flash frozen in liquid nitrogen and kept at -80°C until DNA extraction using the Gentra Puregene Yeast/Bacteria kit (Qiagen) following the manufacturer’s protocol.</p>
<p>The V4-V5 region of the bacterial 16S rRNA gene was amplified using the 515F-Y and 926R primers. PCR reactions were performed in triplicate 20 μl reactions containing 20 ng template DNA, 1X Taq Buffer, 0.5 μM of each primer, 200 μM of dNTPs, and 0.4 U of Taq DNA polymerase (Lucigen). The thermal cycling conditions were 2 min at 95°C, followed by 30 cycles of 1 min at 95°C, 1 min at 50°C, 30 s at 72°C, a final extension of 72°C for 10 min. Triplicate PCR reactions were pooled and gel purified. Libraries were sequenced at the Duke Center for Genomic and Computational Biology on a MiSeq 2x250bp run (Illumina).</p></div>
T. rotula Common Garden Experiment
T. rotula Common Garden Experiment
<div><p>Raw paired-end libraries were quality controlled using the ea-utils V.1.04.807 script <em>fastq-mcf</em> to a mate-pair quality mean of 25 with a 10 basepair (bp) sliding window and a minimum length of 150 bp. Forward and reverse reads were merged using the USEARCH V.8.1.1861 script <em>fastq_mergepairs</em> with a minimum overlap length of 10 bp and zero differences in the overlap region followed by clustering using Minimum Entropy Decomposition (MED) V.2.0 with standard settings. Chloroplasts were filtered using the QIIME V.1.9.1 script <em>filter_fasta.py</em>. Chimeras were identified and removed using the USEARCH V.11.0.667 script <em>uchime2_ref</em> in sensitive mode against the Silva v128 database. Silva database v128 was used to assign taxonomy to OTUs and libraries were then rarefied using the script <em>multiple_rarefactions_even_depth.py</em> ten times to an even depth of 5,827 sequences per sample and OTU tables were merged using <em>merge_otu_tables.py</em> in QIIME V.1.9.1 (10).</p>
<p><strong>BCO-DMO Processing:</strong><br />
- renamed fields to conform with BCO-DMO naming conventions.</p></div>
860381
T. rotula Common Garden Experiment
2021-09-09T14:30:59-04:00
2021-09-09T14:30:59-04:00
2023-07-07T16:10:26-04:00
urn:bcodmo:dataset:860381
Data from common garden experiment containing three populations of T. rotula
This dataset includes NCBI identifiers and sample descriptions from the common garden experiment containing three populations of T. rotula.
false
Rynearson, T. A. (2021) Data from common garden experiment containing three populations of T. rotula. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-09-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.860381.1 [access date]
true
1
10.26008/1912/bco-dmo.860381.1
false
2021-09-13
Datapackage.json
Frictionless Data Package
https://www.bco-dmo.org/dataset/860381/datapackage.json
application/vnd.datapackage+json
PDF
https://www.bco-dmo.org/dataset/860381/Dataset_description.pdf
application/pdf
ISO 19115-2 (NOAA Profile)
https://www.bco-dmo.org/dataset/860381/iso
application/xml
http://www.isotc211.org/2005/gmd-noaa
Dublin Core
https://www.bco-dmo.org/dataset/860381/dublin-core
application/xml
http://purl.org/dc/elements/1.1/
860381
http://lod.bco-dmo.org/id/dataset/860381
2018-09 - 2018-09
2018-09
--09
2018
2018-09
--09
2018
OSPREY
http://www.opengis.net/def/crs/OGC/1.3/CRS84
<http://www.opengis.net/def/crs/OGC/1.3/CRS84> POINT (-71.38 41.57)
41.57
-71.38
41.570000000000
-71.380000000000