Particulate vitamin B12 profiles from R/V Kilo Moana KM1314 in the N Pacific Ocean (Seattle to Honolulu, Line P, Station ALOHA), Aug-Sept 2013 (Nitrification and Planktonic Biodiversity project)

Data Type: Cruise Results
Version Date: 2017-01-04

» Significance of nitrification in shaping planktonic biodiversity in the ocean (Nitrification and Marine Planktonic Biodiversity)

» Dimensions of Biodiversity (Dimensions of Biodiversity)
Stahl, David A.University of Washington (UW)Principal Investigator
Armbrust, E. VirginiaUniversity of Washington (UW)Co-Principal Investigator
Devol, AllanUniversity of Washington (UW)Co-Principal Investigator
Ingalls, Anitra E.University of Washington (UW)Co-Principal Investigator
Moffett, James W.University of Southern California (USC)Co-Principal Investigator
Copley, NancyWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Dataset Description

Particulate vitamin B12 data from R/V Kilo Moana KM1314 in the North Pacific Ocean. These data are published in Heal et al (2016), Supplemental Table 2.

Related Datasets: 
Ammonia oxidation rate profiles
Amplicon sequencing of ammonia oxidizing archaea amoA gene

Related Reference:
Katherine R. Heal, Wei Qin, Francois Ribalet, Anthony D. Bertagnolli, Willow Coyote-Maestas, Laura R. Hmelo, James W. Moffett Allan H. Devol, E. Virginia Armbrust, David A. Stahl, and Anitra E. Ingalls. Two distinct pools of B12 analogs reveal community interdependencies in the ocean. (2016) PNAS.
Supplemental Information

Acquisition Description

Environmental samples (particulate material > 0.2 µm) were analyzed for cobalamins and pseudocobalamins using an organic solvent extraction paired with LC-MS as described in Heal et al. 2014.

Heal, K.R., Carlson, L.T., Devol, A.H., Armbrust, E.V., Moffett, J.W., Stahl, D.A., et al., 2014. Determination of four forms of vitamin B12 and other B vitamins in seawater by liquid chromatography/tandem mass spectrometry. Rapid Commun. Mass Spectrom. 28, 2398–2404. DOI: 10.1002/rcm.7040

Processing Description

BCO-DMO Data Processing Notes:

- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standards

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cruise_idcruise identifier unitless
stastation number unitless
depthsampling depth meters
latlatitude; north is positive decimal degrees
lonlongitude; east is positive decimal degrees
OH_PseudoHydroxopseudocobalamin concentration; dl=below detection limit picomole (pM)
Me_PseudoMethylpseudocobalamin concentration; dl=below detection limit picomole (pM)
OH_CobalaminHydroxocobalamin concentration; dl=below detection limit picomole (pM)
Me_CobalaminMethylcobalamin concentration; dl=below detection limit picomole (pM)
Ado_CobalaminAdenosylcobalamin concentration; dl=below detection limit picomole (pM)

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Dataset-specific Instrument Name
HPLC (Agilent 1100) and UPLC Waters Acquity
Generic Instrument Name
High Performance Liquid Chromatograph
Generic Instrument Description
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.

Dataset-specific Instrument Name
a quadrupole time-of-flight mass spectrometer (Waters Xevo G2-S QTOF)
Generic Instrument Name
Mass Spectrometer
Generic Instrument Description
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.

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R/V Kilo Moana
Start Date
End Date

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Project Information

Significance of nitrification in shaping planktonic biodiversity in the ocean (Nitrification and Marine Planktonic Biodiversity)

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.

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Program Information

Dimensions of Biodiversity (Dimensions of Biodiversity)

Coverage: global

(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.

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Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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