http://lod.bco-dmo.org/id/dataset/871075 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 2022-03-11 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Cellular carbon (C) and nitrogen (N) measurements of marine nitrifiers 2022-03-11 publication 2022-03-11 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2022-03-17 publication https://doi.org/10.26008/1912/bco-dmo.871075.1 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: Bayer, B., Santoro, A. E. (2022) Cellular carbon (C) and nitrogen (N) measurements of marine nitrifiers. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-03-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.871075.1 [access date] Nitrifier CN Dataset Description: Methods and Sampling: &lt;p&gt;100-500 mL of culture was filtered onto combusted (450°C, 4h) glass fiber filters (Advantec, GF-75, 25mm). Filters were acidified with HCl (10% v/v), dried (60°C, 24 h), and packed into tin capsules prior to being analyzed on a CHN elemental analyzer (Exeter Analytical, CEC 440HA). The instrument was calibrated with acetanilide following manufacturer protocols.&lt;/p&gt; &lt;p&gt;A detailed description of materials and methods can be found in Bayer et al. 2022.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924512 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924512 completed 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 Nitrifier_strain Growth_phase Filtered_volume Blank_corrected_C Blank_corrected_N C_to_N_molar Cell_abundance C_content CHN elemental analyzer (Exeter Analytical, CEC 440HA) theme None, User defined taxon growth volume Elemental carbon (C) Nitrogen mole_ratio abundance featureType BCO-DMO Standard Parameters CHN Elemental Analyzer 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. Collaborative Research: Underexplored Connections between Nitrogen and Trace Metal Cycling in Oxygen Minimum Zones Mediated by Metalloenzyme Inventories https://osprey.bco-dmo.org/project/806565 Collaborative Research: Underexplored Connections between Nitrogen and Trace Metal Cycling in Oxygen Minimum Zones Mediated by Metalloenzyme Inventories <p><em>NSF abstract:</em><br /> Though scarce and largely insoluble, trace metals are key components of sophisticated enzymes (protein molecules that speed up biochemical reactions) involved in biogeochemical cycles in the dark ocean (below 1000m). For example, metalloenzymes are involved in nearly every reaction in the nitrogen cycle. Yet, despite direct connections between trace metal and nitrogen cycles, the relationship between trace metal distributions and biological nitrogen cycling processes in the dark ocean have rarely been explored, likely due to the technical challenges associated with their study. Availability of the autonomous underwater vehicle (AUV) Clio, a sampling platform capable of collecting high-resolution vertical profile samples for biochemical and microbial measurements by large volume filtration of microbial particulate material, has overcome this challenge. Thus, this research project plans an interdisciplinary chemistry, biology, and engineering effort to test the hypothesis that certain chemical reactions, such as nitrite oxidation, could become limited by metal availability within the upper mesopelagic and that trace metal demands for nitrite-oxidizing bacteria may be increased under low oxygen conditions. Broader impacts of this study include the continued development and application of the Clio Biogeochemical AUV as a community resource by developing and testing its high-resolution and adaptive sampling capabilities. In addition, metaproteomic data will be deposited into the recently launched Ocean Protein Portal to allow oceanographers and the metals in biology community to examine the distribution of proteins and metalloenzymes in the ocean. Undergraduate students will be supported by this project at all three institutions, with an effort to recruit minority students. The proposed research will also be synergistic with the goals of early community-building efforts for a potential global scale microbial biogeochemistry program modeled after the success of the GEOTRACES program, provisionally called "Biogeoscapes: Ocean metabolism and nutrient cycles on a changing planet".</p> <p>The proposed research project will test the following three hypotheses: (1) the microbial metalloenzyme distribution of the mesopelagic is spatially dynamic in response to environmental gradients in oxygen and trace metals, (2) nitrite oxidation in the Eastern Tropical Pacific Ocean can be limited by iron availability in the upper mesopelagic through an inability to complete biosynthesis of the microbial protein nitrite oxidoreductase, and (3) nitrite-oxidizing bacteria increase their metalloenzyme requirements at low oxygen, impacting the distribution of both dissolved and particulate metals within oxygen minimum zones. One of the challenges to characterizing the biogeochemistry of the mesopelagic ocean is an inability to effectively sample it. As a sampling platform, we will use the novel biogeochemical AUV Clio that enables high-resolution vertical profile samples for biochemical and microbial measurements by large volume filtration of microbial particulate material on a research expedition in the Eastern Tropical Pacific Ocean. Specific research activities will be orchestrated to test the hypotheses. Hypothesis 1 will be explored by comparison of hydrographic, microbial distributions, dissolved and particulate metal data, and metaproteomic results with profile samples collected by Clio. Hypothesis 2 will be tested by incubation experiments using 15NO2- oxidation rates on Clio-collected incubation samples. Hypothesis 3 will be tested by dividing targeted nitrite oxidoreductase protein copies by qPCR (quantitative polymerase chain reaction)-based nitrite oxidizing bacteria abundance (NOB) to determine if cellular copy number varies with oxygen distributions, and by metalloproteomic analyses of NOB cultures. The demonstration of trace metal limitation of remineralization processes, not just primary production, would transform our understanding of the role of metals in biogeochemical cycling and provide new ways with which to interpret sectional data of dissolved and particulate trace metal distributions in the ocean. The idea that oxygen may play a previously underappreciated role in controlling trace metals due not just to metals' physical chemistry, but also from changing biological demand, will improve our ability to predict trace metal distributions in the face of decreasing ocean oxygen content.</p> <p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p> CliOMZ largerWorkCitation project eng; USA oceans -119.84912 -119.84912 34.413962 34.413962 2018-03-12 2021-08-20 Eastern Tropical Pacific 0 BCO-DMO catalogue of parameters from Cellular carbon (C) and nitrogen (N) measurements of marine nitrifiers 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/871118.rdf Name: Nitrifier_strain Units: unitless Description: <p>Name of cultured nitrifier</p> http://lod.bco-dmo.org/id/dataset-parameter/871119.rdf Name: Growth_phase Units: unitless Description: <p>Growth phase of the culture when the measurement was taken (EEXP, early exponential growth; LEXP, late exponential growth; STAT, stationary phase)</p> http://lod.bco-dmo.org/id/dataset-parameter/871120.rdf Name: Filtered_volume Units: liters (L) Description: <p>Culture volume filtered onto glass fiber filter</p> http://lod.bco-dmo.org/id/dataset-parameter/871121.rdf Name: Blank_corrected_C Units: microgram carbon (ug C) Description: <p>Amount of organic carbon corrected for blank (culture medium filtered onto glass fiber filter)</p> http://lod.bco-dmo.org/id/dataset-parameter/871122.rdf Name: Blank_corrected_N Units: microgram nitrogen (ug N) Description: <p>Amount of nitrogen corrected for blank (culture medium filtered onto glass fiber filter)</p> http://lod.bco-dmo.org/id/dataset-parameter/871123.rdf Name: C_to_N_molar Units: moles of carbon per mole of nitrogen (mol C/mol N) Description: <p>Molar C:N ratio of biomass</p> http://lod.bco-dmo.org/id/dataset-parameter/871124.rdf Name: Cell_abundance Units: cells per liter (cells/L) Description: <p>Cell numbers of cultured nitrifiers</p> http://lod.bco-dmo.org/id/dataset-parameter/871125.rdf Name: C_content Units: femtogram per cell (fg/cell) Description: <p>Cellular carbon content</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 1324 https://darchive.mblwhoilibrary.org/bitstream/1912/28207/1/dataset-871075_nitrifier-cn__v1.tsv download https://doi.org/10.26008/1912/bco-dmo.871075.1 download onLine dataset &lt;p&gt;100-500 mL of culture was filtered onto combusted (450°C, 4h) glass fiber filters (Advantec, GF-75, 25mm). Filters were acidified with HCl (10% v/v), dried (60°C, 24 h), and packed into tin capsules prior to being analyzed on a CHN elemental analyzer (Exeter Analytical, CEC 440HA). The instrument was calibrated with acetanilide following manufacturer protocols.&lt;/p&gt; &lt;p&gt;A detailed description of materials and methods can be found in Bayer et al. 2022.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;&lt;strong&gt;Data Processing:&lt;/strong&gt;&lt;br /&gt; Cellular carbon (C) content was calculated by dividing total particulate organic C by the number of newly produced cells.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;BCO-DMO Processing:&lt;/strong&gt;&lt;br /&gt; - renamed fields to conform with BCO-DMO naming conventions;&lt;br /&gt; - replaced &quot;NA&quot; with &quot;nd&quot; (no data).&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 CHN elemental analyzer (Exeter Analytical, CEC 440HA) CHN elemental analyzer (Exeter Analytical, CEC 440HA) PI Supplied Instrument Name: CHN elemental analyzer (Exeter Analytical, CEC 440HA) Instrument Name: CHN Elemental Analyzer Instrument Short Name:CHN_EA Instrument Description: A CHN Elemental Analyzer is used for the determination of carbon, hydrogen, and nitrogen content in organic and other types of materials, including solids, liquids, volatile, and viscous samples.