http://lod.bco-dmo.org/id/dataset/745645 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 2018-09-06 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Coastal eastern subtropical pacific 2018-09-06 publication 2018-09-06 revision BCO-DMO Linked Data URI 2018-09-06 creation http://lod.bco-dmo.org/id/dataset/745645 Christopher Dupont J. Craig Venter Institute principalInvestigator Alyson E. Santoro University of California-Santa Barbara 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: Dupont, C., Santoro, A. E. (2018) Coastal eastern subtropical pacific. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-09-06 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/745645 [access date] Dataset Description: &lt;p&gt;These data were published in&amp;nbsp;Carini et al., 2018.&lt;/p&gt; Methods and Sampling: Organism sources and cultivation conditions: ‘Candidatus Nitrosopelagicus brevis’ str. CN25 (Santoro et al., 2015), was propagated in ONP medium (Santoro and Casciotti, 2011), consisting of aged natural seawater (collected from 10 m depth at 15°S, 173°W on 23 October 2011; 0.2 μm pore size filtered at sea) amended with a chemolithoautotrophic nitrogen source (NH4Cl or urea, described in ‘Experimental design’), ampicillin (10.8 μM), streptomycin (68.6 μM), potassium phosphate (29.4 μM), and a chelated trace metal mix consisting of disodium ethylenediaminetetraacetic acid (14 μM), FeCl2 (7.25 μM), ZnCl2 (0.5 μM), MnCl2 (0.5 μM), H3BO3 (1 μM), CoCl2-6H2O (0.8 μM), CuCl2-2H2O (0.1 μM), NiCl2-H2O (0.1 μM), Na2MoO4-2H2O (0.15 μM). ‘Ca. N. brevis’ str. U25 was enriched from the original CN25 enrichment culture (Santoro and Casciotti, 2011) using sequential transfers of the initial enrichment into ONP medium amended with 50-100 μM urea, instead of NH4Cl, over a period of ~48 months. All enrichments were propagated in 250 mL polycarbonate flasks at 22°C in the dark and monitored for NO2- production using the Griess reagent colorimetric method (Strickland and Parsons, 1972). Cell counts were obtained with a Millipore Guava EasyCyte 5HT flow cytometer as described previously (Tripp, 2008). Cell harvesting for and genome sequencing of ‘Ca. N. brevis’ str. U25: A Ca. N. brevis U25 enrichment culture that was grown exclusively with urea as the sole chemolithoautotrophic growth substrate for &gt;50 generations, was harvested by filtration on to 25 mm diameter, 0.22 μm pore-size Supor-200 filters and frozen at -80°C. DNA was extracted using a DNeasy blood &amp; Tissue DNA extraction kit (Qiagen, Valencia, CA, USA), following the manufacturer’s instructions. The DNA was treated with RNAse and examined using a Bioanlayzer 2100 (Agilent) with 500 ng serving as the input for library construction (NEBNext paired-end DNA Library Prep kit, New England Biolabs). Instruments: The sample was sequenced on an Illumina MiSEQ (v2 chemistry, paired 250 bp reads). Reads were quality trimmed and served as the inputs to assembly with metaSPAdes (v 0.5, 70mer) (Nurk et al., 2017). The K-mer usage of and phylogenetic annotation of the assembled contigs were then used to visually identify a putative thaumarchaeal bin (Supplementary Figure 1a) (Laczny et al., 2015). The 3 contig genome was annotated using the JGI IMG pipeline and the PGAP pipeline at NCBI. Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1259994 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1259994 Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260006 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1260006 onGoing Christopher Dupont J. Craig Venter Institute 858-200-1886 9704 Medical Center Drive Rockville MD 20850 USA cdupont@jcvi.org pointOfContact Alyson E. Santoro University of California-Santa Barbara 805-893-5318 2155 Marine Biotech Lab Santa Barbara CA 93106 USA asantoro@ucsb.edu pointOfContact asNeeded Dataset Version: 1 Unknown llumina MiSEQ Millipore Guava EasyCyte 5HT flow cytometer theme None, User defined Automated DNA Sequencer Flow Cytometer 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. Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea https://osprey.bco-dmo.org/project/555307 Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea <p><em>NSF award abstract:</em></p> <p>Intellectual Merit. How organisms respond to their physical and chemical and environment is a central question in marine ecology. For microbes living in the mesopelagic - the ocean's "twilight zone" - an efficient response is particularly important to capitalize on the intermittent delivery of organic and inorganic compounds sinking from the surface ocean. These organisms must have a suite of metabolic and regulatory strategies used to cope with environmental variability, but these strategies are largely unknown. Understanding when and why metabolic genes are expressed is critical to our understanding of nutrient remineralization in the ocean. Marine group 1 (MG1) archaea are ubiquitous, abundant microbes in the meso- and bathypelagic and promising model organisms for investigating these questions. MG1 archaea are chemolithoautotrophs that oxidize ammonia for energy and fix carbon for biomass, and as such, play a central role in the ocean's coupled carbon and nitrogen cycles. Though MG1 have historically eluded cultivation, recent efforts have been successful at bringing representative MG1 archaea from the open ocean into culture and demonstrating their importance in the production of the greenhouse gas nitrous oxide. This project takes advantage of unique MG1 cultures and the recently sequenced draft genome of one of the organisms - strain CN25 - to investigate the physiological and transcriptional responses of MG1 archaea to variations in their chemical environment, specifically:</p> <p>1. Comparative transcriptomics of CN25 cells grown under a range of energy availability and nitrosative stress will identify select genes that can be used to diagnose the physiological state of natural populations</p> <p>2. Improvements in the genomic and transcriptomic knowledge of MG1 archaea will facilitate a thorough reinterpretation of existing metagenomic and metatranscriptomic datasets, as well as provide a better contextual understanding in future studies</p> <p>The investigators will conduct comparative transcriptomics of CN25 cells harvested in mid-exponential growth and stationary phase versus starved cells. Transcriptomes of cells grown at high nitrate concentrations and low pO2 with those grown in standard conditions will be characterized. A strand-specific, high-density RNAseq approach will be used to examine the expression of putative ORFs, polycistronic operons, and small RNAs, which, in addition to gene expression profiling, has the ancillary benefit of improving genome annotation. Finally, the investigators will sequence the genomes of two additional MG1 strains isolated from the open ocean, as well as single cells from environmental surveys, and leverage the combination with the CN25 genome to reanalyze available metagenomic and metatranscriptomic datasets. The results will define the transcriptional response of a model mesopelagic microbe to a range of chemical environments, and show how the physicochemical environment induces changes in gene expression and gene content that result in greenhouse gas production. This work will rapidly generate new knowledge of how some of the most ubiquitous, yet heretofore elusive, microorganisms respond to geochemical variability and shape our evolving understanding of the marine nitrogen cycle.</p> <p>Broader Impacts. The scientific and societal impact of the project will be to elucidate the mechanisms of greenhouse gas production in a model marine organism that is of broad interest to biological and chemical oceanographers. Transcriptome sequencing will improve the assembly of the CN25 genome, the first genome of an MG1 archaeon from the open ocean. Both the genome and transcriptomes will be important references for researchers using metagenomics, metatranscriptomics, and metaproteomics in the ocean, as these techniques are reliant on a knowledgebase composed of both DNA sequence and physiology. Thus, the results add value to both existing and future studies. The proposed research will advance education, teaching, and training for the next generation of marine scientists by providing support for two early-career investigators, one postdoctoral researcher, and a secondary school teacher.</p> AmoA Archaea largerWorkCitation project eng; USA oceans -173 -173 15 15 2011-10-23 2011-10-23 Epipelagic and mesopelagic, Equatorial Pacific 0 BCO-DMO catalogue of parameters from Coastal eastern subtropical pacific 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 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/745645/data/download download onLine dataset Organism sources and cultivation conditions: ‘Candidatus Nitrosopelagicus brevis’ str. CN25 (Santoro et al., 2015), was propagated in ONP medium (Santoro and Casciotti, 2011), consisting of aged natural seawater (collected from 10 m depth at 15°S, 173°W on 23 October 2011; 0.2 μm pore size filtered at sea) amended with a chemolithoautotrophic nitrogen source (NH4Cl or urea, described in ‘Experimental design’), ampicillin (10.8 μM), streptomycin (68.6 μM), potassium phosphate (29.4 μM), and a chelated trace metal mix consisting of disodium ethylenediaminetetraacetic acid (14 μM), FeCl2 (7.25 μM), ZnCl2 (0.5 μM), MnCl2 (0.5 μM), H3BO3 (1 μM), CoCl2-6H2O (0.8 μM), CuCl2-2H2O (0.1 μM), NiCl2-H2O (0.1 μM), Na2MoO4-2H2O (0.15 μM). ‘Ca. N. brevis’ str. U25 was enriched from the original CN25 enrichment culture (Santoro and Casciotti, 2011) using sequential transfers of the initial enrichment into ONP medium amended with 50-100 μM urea, instead of NH4Cl, over a period of ~48 months. All enrichments were propagated in 250 mL polycarbonate flasks at 22°C in the dark and monitored for NO2- production using the Griess reagent colorimetric method (Strickland and Parsons, 1972). Cell counts were obtained with a Millipore Guava EasyCyte 5HT flow cytometer as described previously (Tripp, 2008). Cell harvesting for and genome sequencing of ‘Ca. N. brevis’ str. U25: A Ca. N. brevis U25 enrichment culture that was grown exclusively with urea as the sole chemolithoautotrophic growth substrate for &gt;50 generations, was harvested by filtration on to 25 mm diameter, 0.22 μm pore-size Supor-200 filters and frozen at -80°C. DNA was extracted using a DNeasy blood &amp; Tissue DNA extraction kit (Qiagen, Valencia, CA, USA), following the manufacturer’s instructions. The DNA was treated with RNAse and examined using a Bioanlayzer 2100 (Agilent) with 500 ng serving as the input for library construction (NEBNext paired-end DNA Library Prep kit, New England Biolabs). Instruments: The sample was sequenced on an Illumina MiSEQ (v2 chemistry, paired 250 bp reads). Reads were quality trimmed and served as the inputs to assembly with metaSPAdes (v 0.5, 70mer) (Nurk et al., 2017). The K-mer usage of and phylogenetic annotation of the assembled contigs were then used to visually identify a putative thaumarchaeal bin (Supplementary Figure 1a) (Laczny et al., 2015). The 3 contig genome was annotated using the JGI IMG pipeline and the PGAP pipeline at NCBI. 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 llumina MiSEQ llumina MiSEQ PI Supplied Instrument Name: llumina MiSEQ PI Supplied Instrument Description:llumina MiSEQ (v2 chemistry, paired 250 bp 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. Millipore Guava EasyCyte 5HT flow cytometer Millipore Guava EasyCyte 5HT flow cytometer PI Supplied Instrument Name: Millipore Guava EasyCyte 5HT flow cytometer Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. (from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/