http://lod.bco-dmo.org/id/dataset/765668 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 2019-04-24 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Accession numbers from acidification mesocosms and original in situ samples from coastal and offshore water station at the Pivers Island Coastal Observatory January to February 2017 2019-04-24 publication 2019-04-24 revision BCO-DMO Linked Data URI 2019-04-24 creation http://lod.bco-dmo.org/id/dataset/765668 Zackary I. Johnson Duke University principalInvestigator Kostas Konstantinidis Georgia Institute of Technology 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: Johnson, Z. I., Konstantinidis, K. (2019) Accession numbers from acidification mesocosms and original in situ samples from coastal and offshore water station at the Pivers Island Coastal Observatory January to February 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2019-04-24 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/765668 [access date] Accession numbers from acidification mesocosms and original in situ samples from coastal and offshore water station at the Pivers Island Coastal Observatory January to February 2017 Dataset Description: &lt;p&gt;This dataset contains Biosample and GenBank Short Read Archive (SRA) sequence accession numbers for metatranscriptomic samples obtained from acidified, warmed and control mesocosms from ocean and coastal waters.&amp;nbsp;&amp;nbsp;&lt;br /&gt; &lt;br /&gt; Ocean acidification (OA) is one of the major issues caused by the rising of atmospheric CO2 with immediate effects in the oceans carbonate chemistry. The oceanic microbial communities are key players in the biochemical cycles of the marine ecosystem and are expected to respond to the ocean’s changing chemistry in a feedback loop of intertwined microbial mediated processes. While the microbial response and effect to OA is challenging to predict due to the complexity of the system, experimental manipulations under controlled conditions can help us understand the major mechanisms of microbial adaptation to a changing oceanic chemistry. In this work we established replicated mesocosms in order to evaluate the effect of decreasing ph in the microbial community composition and gene expression using metatranscriptomics. We examined the effect of both decreasing ph and increasing temperature, one of the major parameters that is expected to have synergistic effects on the microbial response to OA. We examined the effect of both decreasing ph and increasing temperature, one of the major parameters that is expected to have synergistic effects on the microbial response to OA. Additionally, we established mesocosms with either coastal or ocean waters, with the expectation to observe less gene expression responses from the coastal communities which are adapted to a constantly changing water chemistry in comparison to the more sensitive to change ocean communities. In order to account for the variation in gene expression profiles from environmental samples we established two replicates for each of the following incubations (a) control (b) acidified (-0.3 from the in situ ph) (c) warmed (+3oC from the in situ temperature) (d) warmed and acidified. Each mesocosm was maintained under stable conditions for 5 days, after which we isolated samples for 16S rRNA amplicon sequencing and metatranscriptomic sequencing. Additionally, we sequenced the metatranscriptome of the original coastal and ocean samples in order to obtain a baseline gene expression profile of the in situ communities.&lt;/p&gt; Methods and Sampling: &lt;p&gt;In situ or mesocosms water samples were collected within less than 6min using a peristaltic pump. All samples were pre filtered through 3um porosity in line filters, and the bacterial biomass was collected on 0.22 um strive filters. The filters were immediately frozen in liquid nitrogen and store at -80oC until further processing.&lt;/p&gt; &lt;p&gt;Total RNA was extracted from the material collected on the filter using an organic extraction method described previously (Tsementzi et al, 2014; https://doi.org/10.1111/1758-2229.12180). Briefly Lysis buffer (50 mM Tris-HCl, 40 mM EDTA, 0.75 M sucrose) was added to the filters with 1 mg/ml lysozyme and subsequently incubated for 30 min at 37°C. A second 2-h incubation at 55°C was performed after the addition of 1% SDS and 10 mg/ml proteinase K. Acid phenol and chloroform extractions were performed twice on the lysates, and RNA was isolated using filter columns from the mirVANA RNA isolation kit (Ambion), washed twice by following the manufacturer’s instructions, and eluted in Tris-EDTA buffer. DNase treatment was performed using the TURBO DNA-free kit (Ambion, Austin, TX). Libraries were prepared from total RNA using the Ribo-Zero rRNA Removal Kit (Bacteria) following the manufacturer;s instructions&amp;nbsp; and without including the rRNA depletion step. The resulting cDNA libraries were sequenced (250-bp single-end reads) using the Illumina HiSeq 2500 sequencer at the Georgia Institute of Technology Genomics Facility.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1416673 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1416673 onGoing Zackary I. Johnson Duke University 1-252-504-7543 Marine Sciences and Conservation 135 Duke Marine Lab Rd. Beaufort NC 28516 USA zij@duke.edu pointOfContact Kostas Konstantinidis Georgia Institute of Technology 404-385-3628 Mason Building 790 Atlantic Drive Atlanta GA 30332 USA kostas@ce.gatech.edu pointOfContact asNeeded Unknown biosample_accession sample_name sample_title bioproject_accession organism host isolation_source collection_date geo_loc_name lat_lon samp_mat_process samp_size source_material_id description library_ID title library_strategy library_source library_selection library_layout platform instrument_model design_description filetype filename filename2 filename3 filename4 assembly ISO_datetime_UTC lat lon Illumina HiSeq 2500 sequencer theme None, User defined No BCO-DMO term ISO_DateTime_UTC latitude longitude featureType BCO-DMO Standard Parameters Automated DNA Sequencer 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. Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503477 Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707). In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean. Solicitations issued under this program: NSF 10-530, FY 2010-FY2011 NSF 12-500, FY 2012 NSF 12-600, FY 2013 NSF 13-586, FY 2014 NSF 13-586 was the final solicitation that will be released for this program. PI Meetings: 1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA) 2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC) 3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative) NSF media releases for the Ocean Acidification Program: Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long? Discovery nsf.gov - National Science Foundation (NSF) Discoveries - Trouble in Paradise: Ocean Acidification This Way Comes - US National Science Foundation (NSF) Press Release 12-179 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: Finding New Answers Through National Science Foundation Research Grants - US National Science Foundation (NSF) Press Release 13-102 World Oceans Month Brings Mixed News for Oysters Press Release 13-108 nsf.gov - National Science Foundation (NSF) News - Natural Underwater Springs Show How Coral Reefs Respond to Ocean Acidification - US National Science Foundation (NSF) Press Release 13-148 Ocean acidification: Making new discoveries through National Science Foundation research grants Press Release 13-148 - Video nsf.gov - News - Video - NSF Ocean Sciences Division Director David Conover answers questions about ocean acidification. - US National Science Foundation (NSF) Press Release 14-010 nsf.gov - National Science Foundation (NSF) News - Palau's coral reefs surprisingly resistant to ocean acidification - US National Science Foundation (NSF) Press Release 14-116 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: NSF awards $11.4 million in new grants to study effects on marine ecosystems - US National Science Foundation (NSF) SEES-OA largerWorkCitation program Collaborative Research: Ocean Acidification: microbes as sentinels of adaptive responses to multiple stressors: contrasting estuarine and open ocean environments https://osprey.bco-dmo.org/project/535566 Collaborative Research: Ocean Acidification: microbes as sentinels of adaptive responses to multiple stressors: contrasting estuarine and open ocean environments <p><em>Extracted from the NSF award abstract:</em></p> <p>This collaborative project by Duke University and Georgia Institute of Technology researchers will combine oceanographic and advanced molecular techniques to characterize the adaptive responses of microbial communities to multiple stressors associated with OA. In particular, microbial communities from estuarine and coastal ecosystems as well as open ocean waters will be incubated under conditions of increased acidity or temperature or both, and their activities will be measured and quantified. </p> <p> Preliminary data from time-series observations of a coastal temperate estuary shows that pH, temperature and other stressors vary over multiple space and time scales, and this variability is relatively higher than that observed in open ocean waters. Based on this evidence, the guiding hypothesis of this work is that microbes in coastal ecosystems are better adapted to ocean acidification as well as multiple stressors compared to similar microbes from the open ocean. To quantify the adaptive genetic, physiological and biogeochemical responses of microbes to OA, the team's specific goals are to: (1) characterize complex natural microbial community responses to multiple stressors using factorial mesocosm manipulations, (2) assemble a detailed view of genomic and physiological (including transcriptional) adaptations to OA at the single species level using cultured model marine microbes (e.g. Prochlorococcus, Synechococcus, Vibrio) identified as responsive to stressors in whole community mesocosm experiments, and (3) assess the power of model microbial strains and mesocosm experiments to predict microbial community responses to natural OA variability in a temporally dynamic, temperate estuary and along a trophic/pH gradient from the Neuse-Pamlico Sound to the Sargasso Sea. By comparing an estuarine ecosystem to its open ocean counterpart, this study will assess the sensitivity of microbial structure and function in response to ocean acidification.</p> <p>This project is associated with <a href="https://www.bco-dmo.org/project/2281" target="_blank">Pivers Island Coastal Observatory</a>.</p> OA microbe adaptation largerWorkCitation project eng; USA oceans -76.67 -76.19 34.04 34.72 2017-01-19 2017-02-12 Neuse-Pamlico Sound to the Sargasso Sea 0 BCO-DMO catalogue of parameters from Accession numbers from acidification mesocosms and original in situ samples from coastal and offshore water station at the Pivers Island Coastal Observatory January to February 2017 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/765677.rdf Name: biosample_accession Units: unitless Description: <p>biosample_accession</p> http://lod.bco-dmo.org/id/dataset-parameter/765678.rdf Name: sample_name Units: unitless Description: <p>sample_name</p> http://lod.bco-dmo.org/id/dataset-parameter/765679.rdf Name: sample_title Units: unitless Description: <p>sample_title</p> http://lod.bco-dmo.org/id/dataset-parameter/765680.rdf Name: bioproject_accession Units: unitless Description: <p>bioproject_accession</p> http://lod.bco-dmo.org/id/dataset-parameter/765681.rdf Name: organism Units: unitless Description: <p>organism</p> http://lod.bco-dmo.org/id/dataset-parameter/765682.rdf Name: host Units: unitless Description: <p>host</p> http://lod.bco-dmo.org/id/dataset-parameter/765683.rdf Name: isolation_source Units: unitless Description: <p>isolation_source</p> http://lod.bco-dmo.org/id/dataset-parameter/765684.rdf Name: collection_date Units: unitless Description: <p>collection_date</p> http://lod.bco-dmo.org/id/dataset-parameter/765685.rdf Name: geo_loc_name Units: unitless Description: <p>geo_loc_name</p> http://lod.bco-dmo.org/id/dataset-parameter/765686.rdf Name: lat_lon Units: unitless Description: <p>lat_lon</p> http://lod.bco-dmo.org/id/dataset-parameter/765687.rdf Name: samp_mat_process Units: unitless Description: <p>samp_mat_process</p> http://lod.bco-dmo.org/id/dataset-parameter/765688.rdf Name: samp_size Units: unitless Description: <p>samp_size</p> http://lod.bco-dmo.org/id/dataset-parameter/765689.rdf Name: source_material_id Units: unitless Description: <p>source_material_id</p> http://lod.bco-dmo.org/id/dataset-parameter/765690.rdf Name: description Units: unitless Description: <p>description</p> http://lod.bco-dmo.org/id/dataset-parameter/765691.rdf Name: library_ID Units: unitless Description: <p>library_ID</p> http://lod.bco-dmo.org/id/dataset-parameter/765692.rdf Name: title Units: unitless Description: <p>title</p> http://lod.bco-dmo.org/id/dataset-parameter/765693.rdf Name: library_strategy Units: unitless Description: <p>library_strategy</p> http://lod.bco-dmo.org/id/dataset-parameter/765694.rdf Name: library_source Units: unitless Description: <p>library_source</p> http://lod.bco-dmo.org/id/dataset-parameter/765695.rdf Name: library_selection Units: unitless Description: <p>library_selection</p> http://lod.bco-dmo.org/id/dataset-parameter/765696.rdf Name: library_layout Units: unitless Description: <p>library_layout</p> http://lod.bco-dmo.org/id/dataset-parameter/765697.rdf Name: platform Units: unitless Description: <p>platform</p> http://lod.bco-dmo.org/id/dataset-parameter/765698.rdf Name: instrument_model Units: unitless Description: <p>instrument_model</p> http://lod.bco-dmo.org/id/dataset-parameter/765699.rdf Name: design_description Units: unitless Description: <p>design_description</p> http://lod.bco-dmo.org/id/dataset-parameter/765700.rdf Name: filetype Units: unitless Description: <p>filetype</p> http://lod.bco-dmo.org/id/dataset-parameter/765701.rdf Name: filename Units: unitless Description: <p>filename</p> http://lod.bco-dmo.org/id/dataset-parameter/765702.rdf Name: filename2 Units: unitless Description: <p>filename2</p> http://lod.bco-dmo.org/id/dataset-parameter/765703.rdf Name: filename3 Units: unitless Description: <p>filename3</p> http://lod.bco-dmo.org/id/dataset-parameter/765704.rdf Name: filename4 Units: unitless Description: <p>filename4</p> http://lod.bco-dmo.org/id/dataset-parameter/765705.rdf Name: assembly Units: unitless Description: <p>assembly</p> http://lod.bco-dmo.org/id/dataset-parameter/765706.rdf Name: ISO_datetime_UTC Units: yyyy-MM-dd&#039;T&#039;HH:mm:ss&#039;Z&#039; Description: <p>ISO_datetime_UTC</p> http://lod.bco-dmo.org/id/dataset-parameter/765707.rdf Name: lat Units: degrees Description: <p>latitude with north positive</p> http://lod.bco-dmo.org/id/dataset-parameter/765708.rdf Name: lon Units: degrees Description: <p>longitude with east positive</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 https://osprey.bco-dmo.org/dataset/765668/data/download download onLine dataset &lt;p&gt;In situ or mesocosms water samples were collected within less than 6min using a peristaltic pump. All samples were pre filtered through 3um porosity in line filters, and the bacterial biomass was collected on 0.22 um strive filters. The filters were immediately frozen in liquid nitrogen and store at -80oC until further processing.&lt;/p&gt; &lt;p&gt;Total RNA was extracted from the material collected on the filter using an organic extraction method described previously (Tsementzi et al, 2014; https://doi.org/10.1111/1758-2229.12180). Briefly Lysis buffer (50 mM Tris-HCl, 40 mM EDTA, 0.75 M sucrose) was added to the filters with 1 mg/ml lysozyme and subsequently incubated for 30 min at 37°C. A second 2-h incubation at 55°C was performed after the addition of 1% SDS and 10 mg/ml proteinase K. Acid phenol and chloroform extractions were performed twice on the lysates, and RNA was isolated using filter columns from the mirVANA RNA isolation kit (Ambion), washed twice by following the manufacturer’s instructions, and eluted in Tris-EDTA buffer. DNase treatment was performed using the TURBO DNA-free kit (Ambion, Austin, TX). Libraries were prepared from total RNA using the Ribo-Zero rRNA Removal Kit (Bacteria) following the manufacturer;s instructions&amp;nbsp; and without including the rRNA depletion step. The resulting cDNA libraries were sequenced (250-bp single-end reads) using the Illumina HiSeq 2500 sequencer at the Georgia Institute of Technology Genomics Facility.&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 HiSeq 2500 sequencer Illumina HiSeq 2500 sequencer PI Supplied Instrument Name: Illumina HiSeq 2500 sequencer PI Supplied Instrument Description:The resulting cDNA libraries were sequenced (250-bp single-end reads) using the Illumina HiSeq 2500 sequencer at the Georgia Institute of Technology Genomics Facility. 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.