1b:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1c:T11de,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. 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. 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. 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.6:["$","$L1b",null,{"dataset":{"_id":"997800","description":"","problem":"","acquisition":"

Samples were collected onboard the R/V Kilo Moana between 8/7 and 9/5 2013. At Stations 5, 8, and 13, seawater samples (1 L per depth) were collected by Niskin bottles attached at CTD ,and then filtered onto 0.22 μm Durapore membrane filters (Millipore Co.) for archaeal lipid extraction.

\n","processing":"

Isoprenoidal GDGTs (glycerol dibiphytanyl glycerol tetraethers) were subsequently extracted from the filters. Lipid extracts were analyzed by atmospheric pressure chemical ionization on an Agilent 1100 Series liquid chromatograph coupled to an Agilent ion trap mass spectrometer. Detailed methodologies for archaeal lipid extraction and analysis are described in Qin et al. (2015). TEX₈₆ values were calculated based on the relative abundances of GDGT-1, GDGT-2, GDGT-3, and crenarchaeol regioisomer (Cren’), using their respective peak areas according to the following equation in Qin et al. 2015.

\n","bcodmoProcessing":"- Converted Latitude column from degrees-minutes-seconds format (with N/S directional) to decimal degrees\r\n- Converted Longitude column from degrees-minutes-seconds format (with E/W directional) to decimal degrees\r\n- Rounded Latitude and Longitude to 8 decimal places\r\n- Renamed the following columns to remove special characters and spaces: \"Station ID\" to Station_ID, \"Depth (m)\" to Depth_m, \"insitu T(℃)\" to insitu_T_degC, \"TEX86-derived temperature(℃)\" to TEX86_derived_temperature_degC, \"Isoprenoid (ng/L)\" to Isoprenoid_ng_per_L","title":"Depth profiles of lipid biomarkers from R/V Kilo Moana KM1314 in the North Pacific Ocean (Seattle to Honolulu, Line P, Station ALOHA), Aug-Sept 2013","nickname":"Depth profiles of lipid biomarkers KM1314","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"1","version_date":"2026-07-23T04:00:00.000Z","abstract":"This dataset contains in situ temperature (°C), TEX86-derived temperature (°C), and isoprenoid concentrations (ng L−1) measured from 0 to 300 m depth at Stations 5, 8, and 13 in the Northeastern Pacific Ocean during the R/V Kilo Moana cruise KM1314 in August 2013. Samples were collected to characterize vertical variations in archaeal lipid biomarkers and evaluate the relationship between TEX86 paleotemperature estimates and ambient water column temperature. In situ temperatures were obtained from CTD measurements, TEX86 values were calculated from the relative abundances of GDGT-1, GDGT-2, GDGT-3, and the crenarchaeol regioisomer, and TEX86-derived temperatures were reconstructed using a published calibration equation. These data were generated to assess how environmental gradients influence archaeal lipid distributions and the accuracy of TEX86 temperature reconstructions in the upper ocean.","citation":"Shen, H., Qin, W. (2026) Depth profiles of lipid biomarkers from R/V Kilo Moana KM1314 in the North Pacific Ocean (Seattle to Honolulu, Line P, Station ALOHA), Aug-Sept 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-07-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.997800.1 [access date]","citationParts":{"identifier":"doi:10.26008/1912/bco-dmo.997800.1","versionDate":"2026-07-23","versionId":"1","year":"2026","title":"Depth profiles of lipid biomarkers from R/V Kilo Moana KM1314 in the North Pacific Ocean (Seattle to Honolulu, Line P, Station ALOHA), Aug-Sept 2013","authors":"Shen, H., Qin, W.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"10.26008/1912/bco-dmo.997800.1","release_date":null,"field_dataset_location":"","temporal_extent":{"start":"2013-08-14T04:00:00.000Z","end":"2013-08-29T04:00:00.000Z"},"temporal":{"resolution":"time:unitDay","type":"time:Interval","start":{"value":"1376452800","label":"2013-08-14"},"end":{"value":"1377748800","label":"2013-08-29"}},"spatial_extent":{"shape":"polygon","center":{"latitude":40,"longitude":-142.34017222},"wkt":"POLYGON ((-150 30, -134.68034444 30, -134.68034444 50, -150 50, -150 30))","north":50,"east":-134.68034444,"south":30,"west":-150},"dataset_type":["Other Field Results"],"keywords":["oceans"],"data_files":[{"id":"1002892","title":"997800_v1_lipidbiomarkers.csv","url":"https://datadocs.bco-dmo.org/dataset/997800/file/N7z8wk6sVmO6z5/997800_v1_lipidbiomarkers.csv","showTableUrl":"https://www.bco-dmo.org/dataset/997800/data/view/1002892","description":"Primary data file for dataset ID 997800, version 1","filename":"997800_v1_lipidbiomarkers.csv","bytesize":1782,"checksum":{"value":"aae291cd9524b3ea67a7035719e0c0e2","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"bcodmo_dataset_997800_v1","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false}],"supplemental_files":[],"roles":[{"role":{"_id":"138","name":"Principal Investigator"},"performedBy":{"_id":"921941","name":"Wei Qin"},"performedAtOrganization":{"_id":"997859","name":"University of Illinois Urbana-Champaign"}},{"role":{"_id":"133","name":"Contact"},"performedBy":{"_id":"998786","name":"Hui Shen"},"performedAtOrganization":{"_id":"997859","name":"University of Illinois Urbana-Champaign"}},{"role":{"_id":"135","name":"Technician"},"performedBy":{"_id":"998786","name":"Hui Shen"},"performedAtOrganization":{"_id":"997859","name":"University of Illinois Urbana-Champaign"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"748773","name":"Karen Soenen"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[{"_id":"536050","name":"KM1314","synonyms":[],"dates":{"start":"2013-08-07T00:00:00.000Z","end":"2013-09-05T00:00:00.000Z"},"platform":{"_id":"54009","name":"R/V Kilo Moana"},"chiefScientists":[{"id":"50741","name":"Anitra E. Ingalls","role":"Chief Scientist"}]}],"funding":[{"_id":"536043","name":"OCE-1046017","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1046017"}],"instruments":[{"_id":"998793","name":"CTD SBE 911plus","description":"","type_id":"591","type_name":"CTD Sea-Bird SBE 911plus","type_desc":"The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics","type_acronym":"CTD SBE 911plus"},{"_id":"998795","name":"Agilent 1100 Series liquid chromatograph","description":"Agilent 1100 Series liquid chromatograph coupled to an Agilent ion trap mass spectrometer","type_id":"506","type_name":"High-Performance Liquid Chromatograph","type_desc":"A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase.","type_acronym":"HPLC"},{"_id":"998796","name":"Agilent ion trap mass spectrometer","description":"Agilent 1100 Series liquid chromatograph coupled to an Agilent ion trap mass spectrometer","type_id":"685","type_name":"Mass Spectrometer","type_desc":"General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.","type_acronym":"Mass Spec"},{"_id":"998794","name":"Niskin Bottle","description":"","type_id":"413","type_name":"Niskin bottle","type_desc":"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.","type_acronym":"Niskin bottle"}],"parameters":[{"_id":"998829","name":"Datetime_of_sampling","format":"%Y-%m-%dT%H:%M:%S","frictionlessType":"datetime","description":"

Date and time of sampling in UTC time zone

","units":{"_id":"","name":"unitless"},"type":{"_id":"1908","name":"ISO_DateTime_UTC","description":"

Date/Time (UTC) ISO formatted
\nThis standard is based on ISO 8601:2004(E) and takes on any of the following forms:
\n2009-08-30T09:05:00[.xx] (local time)
\n2009-08-30T14:05:00[.xx]Z (UTC time)
\n2009-08-30T14:05:00[.xx]-05:00
\nThe dashes and the colons can be dropped.
\nThe T can also be dropped \"by mutual agreement\", but one needs the trailing Z if the time is UTC.

Sample ISO_datetime_utc:
\n2009-08-30T14:05:00[.xx]Z (UTC time)

Format: YYYY-mm-ddTHH:MM:SS[.xx]Z (UTC time)

"}},{"_id":"998830","name":"Latitude","format":"","frictionlessType":"number","description":"

Latitude of sampling location

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"998831","name":"Longitude","format":"","frictionlessType":"number","description":"

Longitude of sampling location

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"998832","name":"Station_ID","format":"","frictionlessType":"integer","description":"

Station identification

","units":{"_id":"","name":"unitless"},"type":{"_id":"1120","name":"sta_id","description":"

station identification; file dependent; specific definition will vary from file to file

"}},{"_id":"998833","name":"Depth_m","format":"","frictionlessType":"integer","description":"

Depth of sampling

","units":{"_id":"","name":"meters (m)"},"type":{"_id":"808","name":"depth","description":"

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

\nWhen used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

"}},{"_id":"998834","name":"insitu_T_degC","format":"","frictionlessType":"number","description":"

in situ temperature at depth of sampling

","units":{"_id":"","name":"degrees Celsius (°C)"},"type":{"_id":"733","name":"temperature","description":"

water temperature at measurement depth

"}},{"_id":"998835","name":"TEX86_derived_temperature_degC","format":"","frictionlessType":"number","description":"

TEX86 values were calculated based on the relative abundances of GDGT-1, GDGT-2, GDGT-3, and the crenarchaeol regioisomer. TEX₈₆-derived temperatures were reconstructed using the calibration equation in https://doi.org/10.1073/pnas.1501568112.

","units":{"_id":"","name":"degrees Celsius (°C)"},"type":{"_id":"733","name":"temperature","description":"

water temperature at measurement depth

"}},{"_id":"998836","name":"Isoprenoid_ng_per_L","format":"","frictionlessType":"number","description":"

Concentration of Isoprenoid

","units":{"_id":"","name":"nano gram per liter (ng/L)"},"type":{"_id":"771412","name":"Sed_Lipids","description":"

Sediment lipid concentrations. Lipids are defined as small water-insoluble biomolecules including fats, fatty acids, esters, sterols, isoprenoid compounds, etc.. Sediment is defined as material collected by a corer (including fluff).

"}}],"related_publications":[{"id":"998801","citation":"Qin, W., Carlson, L. T., Armbrust, E. V., Devol, A. H., Moffett, J. W., Stahl, D. A., & Ingalls, A. E. (2015). Confounding effects of oxygen and temperature on the TEX signature of marine Thaumarchaeota. Proceedings of the National Academy of Sciences, 112(35), 10979–10984. https://doi.org/10.1073/pnas.1501568112\r\n","relation_type":["Methods"],"relation_desc":""}],"related_datasets":[],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/997800/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"ERDDAP","items":[{"name":"SUBSET DATA","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_997800_v1.html","contentType":"text/html","actionType":"tool"},{"name":"VIEW TABLE","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_997800_v1.htmlTable","contentType":"text/html","actionType":"view"},{"name":"CSV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_997800_v1.csv","contentType":"text/csv","actionType":"download"},{"name":"TSV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_997800_v1.tsv","contentType":"text/tsv","actionType":"download"},{"name":"GeoJSON","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_997800_v1.geoJson","contentType":"application/geo+json","actionType":"download"},{"name":"MATLAB","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_997800_v1.mat","contentType":"text/x-matlab","actionType":"download"},{"name":"netCDF","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_997800_v1.nc","contentType":"application/x-netcdf","actionType":"download"},{"name":"ODV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_997800_v1.odvTxt","contentType":"text/plain","actionType":"download"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/997800/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/997800/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/997800/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[{"_id":"2031","name":"Dimensions of Biodiversity","acronym":"Dimensions of Biodiversity"}],"projects":[{"_id":"2228","name":"Significance of nitrification in shaping planktonic biodiversity in the ocean","acronym":"Nitrification and Marine Planktonic Biodiversity","description":"$1c"}],"archives":[{"id_value":"10.26008/1912/bco-dmo.997800.1","url":"https://doi.org/10.26008/1912/bco-dmo.997800.1","date_assigned":"2026-07-23","version_date":"2026-07-23","archiver":"Woods Hole Oceanographic Institution (WHOI BCO-DMO)","archiver_id":"191"}],"license":{"name":"Creative Commons Attribution 4.0","id":"CC-BY-4.0","uri":"https://creativecommons.org/licenses/by/4.0/","spdxUri":"https://spdx.org/licenses/CC-BY-4.0"},"metrics":{"views":{"count":24},"downloads":{"count":82}}},"fileId":"1002892"}]