http://lod.bco-dmo.org/id/dataset/997806 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 2026-04-30 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Depth profiles of quantitative PCR of ammonia-oxidizing archaea and bacteria from R/V Kilo Moana KM1314 in the North Pacific Ocean 2026-04-30 publication 2026-04-30 revision BCO-DMO Linked Data URI 2026-04-30 creation http://lod.bco-dmo.org/id/dataset/997806 Wei Qin University of Illinois Urbana-Champaign principalInvestigator Hui Shen University of Illinois Urbana-Champaign 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: Shen, H., Qin, W. (2026) Depth profiles of quantitative PCR of ammonia-oxidizing archaea and bacteria from R/V Kilo Moana KM1314 in the North Pacific Ocean. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-04-30 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/997806 [access date] Depth profiles of quantitative PCR of ammonia-oxidizing archaea and bacteria Dataset Description: Methods and Sampling: &lt;p&gt;At Stations 5, 8, and 13, one liter of seawater from each depth was collected by Niskin bottles attached at CTD, then filtered onto 0.22 μm Sterivex filters (GP-type, Millipore) and stored at −80 °C.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1046017 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1046017 onGoing Wei Qin University of Illinois Urbana-Champaign 601 S Goodwin Ave Room C205 CLSL Urbana IL 61801 USA weiqin@illinois.edu pointOfContact Hui Shen University of Illinois Urbana-Champaign hui666@illinois.edu pointOfContact asNeeded Dataset Version: 1 Unknown Datetime_of_sampling Latitude Longitude Station_ID Depth_m AOA_amoA_Calculated_Abundance stdev_AOA AOB_amoA_Calculated_Abundance stdev_AOB LightCycler system (Roche) theme None, User defined ISO_DateTime_UTC latitude longitude station depth abundance standard deviation featureType BCO-DMO Standard Parameters CTD - profiler Niskin bottle qPCR Thermal Cycler instrument BCO-DMO Standard Instruments KM1314 service Deployment Activity The North Pacific Ocean (Cruise from Seattle to Honolulu, including Line P, Station ALOHA) place Locations 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. Dimensions of Biodiversity http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446 Dimensions of Biodiversity (adapted from the NSF Synopsis of Program) Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program.  [MORE from NSF] The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes. Dimensions of Biodiversity largerWorkCitation program Significance of nitrification in shaping planktonic biodiversity in the ocean https://osprey.bco-dmo.org/project/2228 Significance of nitrification in shaping planktonic biodiversity in the ocean <p>Microorganisms sustain the biogeochemical cycling of nitrogen, one of the most important nutrient cycles on earth. A key step in this cycle, the oxidation of ammonia to nitrite by autotrophic microorganisms, was for a century thought mediated by a few restricted bacterial genera. Significant ammonia oxidation, perhaps most, is now attributed to a previously enigmatic group of Archaea - the ammonia-oxidizing archaea (AOA) - of high abundance in both marine and terrestrial environments. The investigators prior physiological and environmental analyses, the foundation for this proposal, have shown that AOA are active within the marine photic zone and that their competitive fitness in the marine environment is at least in part attributable to an extremely high affinity for ammonia, growing at near maximum growth rates at concentrations of ammonia that would not sustain known bacterial ammonia oxidizers, and an unusual copper-based respiratory system that may render them more competitive in iron limited environments. The compelling inference from these prior analyses is that AOA alter and possibly control the forms of fixed nitrogen available to other microbial assemblages within the photic zone by converting ammonia, a nearly universally available form of nitrogen, into nitrite, a form only available to nitrite oxidizing bacteria and some phytoplankton. If correct, this has a significant impact on biodiversity.</p> <p>The PIs will use the most recent technological advances in protein and high throughput sequencing to evaluate the significance of nitrification in shaping biodiversity (genomic and metagenomics), activity (transcriptome, proteome and stable isotope probing), and in controlling availability of an important trace element (copper). In turn, by resolving the environmental and biotic variables that influence the diversity, distribution and activity of AOA, they will advance general understanding of their taxonomy. More directly, functional knowledge of the contribution of AOA to regenerated nitrate will improve estimates of new ocean production ("biological pump") based on nitrate assimilation, which in the past has mostly neglected the importance of nitrification as a major source of nitrate. Together these studies will transform understanding of the marine nitrogen cycle, estimates of new production, and will ultimately provide a better understanding of the impact of human activity on this critical nutrient cycle.</p> <p>The nitrogen cycle has been profoundly affected by anthropogenic inputs of reactive nitrogen into terrestrial, marine, and atmospheric systems having, or predicted to have, major impacts on marine biological production, increased N20 emissions, nitrogen pollution, and eutrophication. Likewise, there is a poor understanding of the relationship between nitrogen cycling and productivity in marine ecosystems. Marine systems are increasingly affected by ocean acidification and by atmospheric inputs of reactive nitrogen. Since both changes greatly alter nitrogen available to microorganisms, the characterization of the response of these environmentally relevant AOA is of tremendous relevance to understanding the affect of acidification and anthropogenic nitrogen inputs on major ocean processes.</p> <p>The proposed project encompasses and integrates the three dimensions (functional genetic, and taxonomic) of biodiversity. First, the project is framed by function: microbial control of one of the most important nutrient cycles on earth, the nitrogen-cycle. Second, it is motivated by recent genetic analyses that associate activities of a novel clade of Archaea (provisionally assigned to a new kingdom within the Archaea, the Thaumarchaeota) with control of ammonia oxidation in the ocean. Third, it is built upon a compelling synthesis of physiological and environmental data that lead to its central hypothesis that by altering and possibly controlling the form of nitrogen, the AOA also alter biodiversity and ecological function in one of the most productive environments on earth. It identifies a specific taxonomic imperative. The tremendous genetic diversity among the globally abundant AOA catalogued almost exclusively by gene sequencing surveys and therefore lacking formal description makes it essential to resolve membership into ecologically relevant groups or clades as a prelude to developing a formal taxonomy. The investigators have assembled a group of researchers with specific expertise in each of dimension and uniquely qualified to address the research objectives outlined in an integrative way.</p> Nitrification and Marine Planktonic Biodiversity largerWorkCitation project eng; USA oceans The North Pacific Ocean (Cruise from Seattle to Honolulu, including Line P, Station ALOHA) -150 -134.6803444 30 50 2013-08-14 2013-08-29 0 BCO-DMO catalogue of parameters from Depth profiles of quantitative PCR of ammonia-oxidizing archaea and bacteria from R/V Kilo Moana KM1314 in the North Pacific Ocean 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/1000178.rdf Name: Datetime_of_sampling Units: unitless Description: <p>Date and time of sampling in UTC time zone</p> http://lod.bco-dmo.org/id/dataset-parameter/1000179.rdf Name: Latitude Units: decimal degrees Description: <p>Latitude of sampling location</p> http://lod.bco-dmo.org/id/dataset-parameter/1000181.rdf Name: Longitude Units: decimal degrees Description: <p>Longitude of sampling location</p> http://lod.bco-dmo.org/id/dataset-parameter/1000183.rdf Name: Station_ID Units: unitless Description: <p>Station identification</p> http://lod.bco-dmo.org/id/dataset-parameter/1000184.rdf Name: Depth_m Units: meters (m) Description: <p>Depth of sampling</p> http://lod.bco-dmo.org/id/dataset-parameter/1000185.rdf Name: AOA_amoA_Calculated_Abundance Units: copies per milliliter (copies/mL) Description: <p>abundance of amoA genes of Ammonia Oxidizing Archaea (AOA)</p> http://lod.bco-dmo.org/id/dataset-parameter/1000186.rdf Name: stdev_AOA Units: copies per milliliter (copies/mL) Description: <p>Standard deviation of abundance of amoA genes of AOA</p> http://lod.bco-dmo.org/id/dataset-parameter/1000187.rdf Name: AOB_amoA_Calculated_Abundance Units: copies per milliliter (copies/mL) Description: <p>abundance of amoA genes of Ammonia Oxidizing Bacteria (AOB)</p> http://lod.bco-dmo.org/id/dataset-parameter/1000188.rdf Name: stdev_AOB Units: copies per milliliter (copies/mL) Description: <p>Standard deviation of abundance of amoA genes of AOB</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/997806/data/download download onLine dataset &lt;p&gt;At Stations 5, 8, and 13, one liter of seawater from each depth was collected by Niskin bottles attached at CTD, then filtered onto 0.22 μm Sterivex filters (GP-type, Millipore) and stored at −80 °C.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;DNA was extracted using a modified manual extraction protocol as previously described (Urakawa et al. 2010). Archaeal and β-proteobacterial amoA genes were quantified by qPCR using primer sets CrenAmoAQ-F/CrenAmoAModR (Mincer et al. 2007) and AmoA1-F/AmoA2-R (Rotthauwe et al. 1997), respectively, on a LightCycler system (Roche), following previously described methods (Horak et al. 2013). Standard curve construction, amplification procedures, melting curves, and gel electrophoresis tests were carried out as previously described (Horak et al. 2013)&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 PI Supplied Instrument Name: Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast. This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/ PI Supplied Instrument Name: Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/ LightCycler system (Roche) LightCycler system (Roche) PI Supplied Instrument Name: LightCycler system (Roche) Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR). Cruise: KM1314 KM1314 R/V Kilo Moana Community Standard Description International Council for the Exploration of the Sea R/V Kilo Moana vessel KM1314 Anitra E. Ingalls University of Washington R/V Kilo Moana Community Standard Description International Council for the Exploration of the Sea R/V Kilo Moana vessel