http://lod.bco-dmo.org/id/dataset/860347 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2021-09-09 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) T. rotula microbiome global sample 2021-09-13 publication 2021-09-13 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2021-09-13 publication https://doi.org/10.26008/1912/bco-dmo.860347.1 Tatiana A. Rynearson University of Rhode Island principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Rynearson, T. A. (2021) T. rotula microbiome global sample. 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.860347.1 [access date] T. rotula microbiome global sample Dataset Description: Methods and Sampling: &lt;p&gt;Single cells and chains of &lt;em&gt;T. rotula&lt;/em&gt; were subjected to three serial washes in separate aliquots of 200 μl sterile seawater, with &amp;lt;2 μl seawater carried between washes. Individual cells or chains were then cultured with associated bacteria in 1ml f/20 in sterile polystyrene plates at ~&lt;em&gt;in situ&lt;/em&gt; temperature and 90-120 μmol photons m⁻² s⁻¹ on a 12:12-h light:dark cycle. Isolates were grown for two weeks, or until the phytoplankton concentration reached ~1,000 cells mL⁻¹, whichever occurred sooner. Single cell isolates were filtered onto 0.2-μm filters (Millipore) and stored at -80 °C until DNA extraction. DNA was extracted from &lt;em&gt;T. rotula&lt;/em&gt; isolates and bacterial co-cultures following Whittaker and Rynearson (2017).&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0727227 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0727227 completed Tatiana A. Rynearson University of Rhode Island 401-874-6022 Graduate School of Oceanography, University of Rhode Island 215 South Ferry Rd. Narragansett RI 02882 USA rynearson@uri.edu pointOfContact asNeeded Dataset Version: 1 Unknown SRA_Library_Name Desc Sample_Site Sample_Name Sample_date Lat Long Chl_a Salinity SST T_rotula_Cell_Abundance Study_Accession Bioproject SRA_Accession Illumina MiSeq 2x250 bp PE reads YSI theme None, User defined sample identification sample description site date latitude longitude chlorophyll a sea surface salinity sea surface temperature abundance NCBI SRA study accession (SRP) NCBI BioProject accession NCBI SRA Sample accession (SRS) featureType BCO-DMO Standard Parameters Automated DNA Sequencer Microscope - Optical Spectrophotometer Thermal Cycler Water Quality Multiprobe instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Connecting local, regional and global scales of gene flow in planktonic marine diatoms https://osprey.bco-dmo.org/project/511708 Connecting local, regional and global scales of gene flow in planktonic marine diatoms <p><em>Description from NSF award abstract:</em><br /> Diatoms are ubiquitous, unicellular, eukaryotes that generate about 40% of the organic carbon fixed annually in the sea. Interpretation of diatom species distributions and abundances in relation to environmental conditions has relied on two assumptions: (1) cells with identical morphologies represent the same species and (2) high potentials for dispersal and gene flow in passively drifting diatoms prevent local adaptation. Recent studies have challenged both assumptions, suggesting diatoms possess rich patterns of genetic and physiological variation both within and between species. Although there is emerging evidence of intra-specific population differentiation on local scales (~100km), it is commonly assumed that planktonic microbes are homogenously distributed on global scales (e.g. Fenchel and Finlay 2004). There is currently no data on diatoms to support this assumption. Aside from intriguing data on local scales, nothing is known about regional and global-scale population genetics and biogeography of diatoms.</p> <p>The research proposed here will focus on the essential questions of if and how populations of planktonic diatoms are connected at local, regional and global scales. Connectivity among populations can influence a species'' ecology, adaptive potential, evolutionary longevity and ultimately speciation potential. The proposed research will examine how local populations are connected to each other on regional scales and how regional dynamics connect to global-scale biogeographies using two model diatom species. rDNA sequence variation will be used to test whether broad species distributions observed in diatoms result from cryptic speciation. Within species, microsatellite markers will be used to identify genetically distinct populations, determine their relatedness to each other and examine spatial patterns of differentiation. The degree of physiological variation that accompanies genetic differentiation between populations will also be examined. Samples will be collected in a framework of existing oceanography and biodiversity programs, permitting genetic data to be interpreted in the context of larger, often long-term, studies. Because little is known about diatom biogeography, this work will begin to shed light on the connections between local and global population dynamics. Because the proposed research will represent the first large-scale sampling of diatom population genetics, it will also serve to generate many new hypotheses about the mechanisms that regulate ecological processes such as bloom formation over space and time and evolutionary processes such as the development of reproductive isolation and eventual speciation in planktonic organisms.</p> <p><em>Related publications:</em><br /> Rynearson, T.A., E.O. Lin and E.V. Armbrust. 2009. Metapopulation structure in the planktonic diatom <em>Ditylum brightwellii </em>(Bacillariophyceae)<em>. Protist</em>, 160(1):111-121. doi:<a href="http://dx.doi.org/10.1016/j.protis.2008.10.003" target="_blank">10.1016/j.protis.2008.10.003</a></p> <p>Whittaker, K., Rignanese, D., Olson, R., Rynearson, T., 2012. Molecular subdivision of the marine diatom <em>Thalassiosira rotula</em> in relation to geographic distribution, genome size, and physiology. <em>BMC Evolutionary Biology,</em> 12:209. doi:<a href="http://dx.doi.org/10.1186/1471-2148-12-209" target="_blank">10.1186/1471-2148-12-209</a></p> <p>Boyd, P.W., Rynearson, T.A., Armstrong, E.A., Fu, F., Hayashi, K., Hu, Z., Hutchins, D.A., Kudela, R.M., Litchman, E., Mulholland, M.R., Passow, U., Strzepek, R.F., Whittaker, K.A., Yu, E., Thomas, M.K., 2013. Marine Phytoplankton Temperature versus Growth Responses from Polar to Tropical Waters - Outcome of a Scientific Community-Wide Study. <em>PLoS One</em>, 8(5), e63091. doi:<a href="http://dx.doi.org/10.1371/journal.pone.0063091" target="_blank">10.1371/journal.pone.0063091</a></p> Diatom Gene Flow largerWorkCitation project eng; USA oceans -125.09 174.81 -41.3 51.18 2010-01-26 2010-11-19 global diatom samples; laboratory-based analyses 0 BCO-DMO catalogue of parameters from T. rotula microbiome global sample Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/860362.rdf Name: SRA_Library_Name Units: unitless Description: <p>Sample ID</p> http://lod.bco-dmo.org/id/dataset-parameter/860363.rdf Name: Desc Units: unitless Description: <p>Library description</p> http://lod.bco-dmo.org/id/dataset-parameter/860364.rdf Name: Sample_Site Units: unitless Description: <p>Sample site</p> http://lod.bco-dmo.org/id/dataset-parameter/860365.rdf Name: Sample_Name Units: unitless Description: <p>Timepoint identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/860366.rdf Name: Sample_date Units: unitless Description: <p>Date of collection; format: YYYY-MM-DD</p> http://lod.bco-dmo.org/id/dataset-parameter/860367.rdf Name: Lat Units: degrees North Description: <p>Latitude</p> http://lod.bco-dmo.org/id/dataset-parameter/860368.rdf Name: Long Units: degrees East Description: <p>Longitude</p> http://lod.bco-dmo.org/id/dataset-parameter/860369.rdf Name: Chl_a Units: milligrams per liter (mg/L) Description: <p>Chlorophyll a concentration</p> http://lod.bco-dmo.org/id/dataset-parameter/860370.rdf Name: Salinity Units: parts per thousand (ppt) Description: <p>Sea surface salinity</p> http://lod.bco-dmo.org/id/dataset-parameter/860371.rdf Name: SST Units: degrees Celsius Description: <p>Sea surface temperature</p> http://lod.bco-dmo.org/id/dataset-parameter/860372.rdf Name: T_rotula_Cell_Abundance Units: cells per milliliter (cells/mL) Description: <p>T. rotula cell abundance at time of collection</p> http://lod.bco-dmo.org/id/dataset-parameter/860373.rdf Name: Study_Accession Units: unitless Description: <p>NCBI SRA accession for the projct</p> http://lod.bco-dmo.org/id/dataset-parameter/860374.rdf Name: Bioproject Units: unitless Description: <p>NCBI BioProject ID number</p> http://lod.bco-dmo.org/id/dataset-parameter/860375.rdf Name: SRA_Accession Units: unitless Description: <p>NCBI SRA accession numbers</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 12882 https://darchive.mblwhoilibrary.org/bitstream/1912/27543/1/dataset-860347_t-rotula-microbiome-global-sample__v1.tsv download https://doi.org/10.26008/1912/bco-dmo.860347.1 download onLine dataset &lt;p&gt;Single cells and chains of &lt;em&gt;T. rotula&lt;/em&gt; were subjected to three serial washes in separate aliquots of 200 μl sterile seawater, with &amp;lt;2 μl seawater carried between washes. Individual cells or chains were then cultured with associated bacteria in 1ml f/20 in sterile polystyrene plates at ~&lt;em&gt;in situ&lt;/em&gt; temperature and 90-120 μmol photons m⁻² s⁻¹ on a 12:12-h light:dark cycle. Isolates were grown for two weeks, or until the phytoplankton concentration reached ~1,000 cells mL⁻¹, whichever occurred sooner. Single cell isolates were filtered onto 0.2-μm filters (Millipore) and stored at -80 °C until DNA extraction. DNA was extracted from &lt;em&gt;T. rotula&lt;/em&gt; isolates and bacterial co-cultures following Whittaker and Rynearson (2017).&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;The V3-V4 rDNA region of the 16S rRNA gene was amplified from all samples using a dual index approach in 20 µl reactions containing 1µl genomic DNA, 0.4 U of Taq (Lucigen) polymerase, and a final concentration of 200 μM dNTPs, 2 mM MgCl₂, and 0.5 μM of each primer (16S V3 Forward – CCTACGGGNGGCWSCAG and 16S V4 Reverse – GGACTACNVGGGTWTCTAAT). The PCR was run for 30 seconds at 98 °C, followed by 30-35 cycles at 98 °C for 10 seconds, 55 °C for 30 sec and 72 °C for 30 sec, with a final extension at 72 °C for 2 min. Triplicate 20 µl reactions were pooled and gel-purified for each sample.&lt;/p&gt; &lt;p&gt;Raw paired-end libraries were quality controlled using the ea-utils V.1.04.807 script fastq-mcf 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 fastq_mergepairs 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 filter_fasta.py followed by an additional clustering step in MED with a minimum substantive abundance (-M) of 53 sequences required to form a single node. Chimeras were identified and removed using the USEARCH V.11.0.667 script uchime2_ref 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 multiple_rarefactions_even_depth.py ten times to an even depth of 501 sequences per sample and OTU tables were merged using merge_otu_tables.py in QIIME V.1.9.1.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;BCO-DMO Processing:&lt;/strong&gt;&lt;br /&gt; - flagged N/A as missing data identifier (replaced ;with&amp;nbsp;nd);&lt;br /&gt; - converted date format to YYYY-MM-DD&lt;br /&gt; - renamed fields to conform with BCO-DMO naming conventions;&lt;br /&gt; - removed commas from the Sample_Site column.&lt;/p&gt; Specified by the Principal Investigator(s) asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact Illumina MiSeq 2x250 bp PE reads Illumina MiSeq 2x250 bp PE reads PI Supplied Instrument Name: Illumina MiSeq 2x250 bp PE reads Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. PI Supplied Instrument Name: Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/ PI Supplied Instrument Name: Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/ PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html) YSI YSI PI Supplied Instrument Name: YSI PI Supplied Instrument Description:A YSI instrument measured SST and salinity. Instrument Name: Water Quality Multiprobe Instrument Short Name:Water Quality Multiprobe Instrument Description: An instrument which measures multiple water quality parameters based on the sensor configuration.