NSF Org:	OCE Division Of Ocean Sciences
Recipient:	J. CRAIG VENTER INSTITUTE, INC.
Initial Amendment Date:	September 22, 2011
Latest Amendment Date:	September 22, 2011
Award Number:	1136477
Award Instrument:	Standard Grant
Program Manager:	David Garrison OCE  Division Of Ocean Sciences GEO  Directorate For Geosciences
Start Date:	January 1, 2012
End Date:	December 31, 2014 (Estimated)
Total Intended Award Amount:	$599,967.00
Total Awarded Amount to Date:	$599,967.00
Funds Obligated to Date:	FY 2011 = $599,967.00
History of Investigator:	Andrew Allen (Principal Investigator) aallen@jcvi.org
Recipient Sponsored Research Office:	J. Craig Venter Institute, Inc. 4120 CAPRICORN LN LA JOLLA CA  US  92037-3498 (858)200-1864
Sponsor Congressional District:	50
Primary Place of Performance:	J. Craig Venter Institute, Inc. 10355 Science Center Drive San Diego CA  US  92121-1118
Primary Place of Performance Congressional District:	50
Unique Entity Identifier (UEI):	FL8UNYTG72D1
Parent UEI:
NSF Program(s):	BIOLOGICAL OCEANOGRAPHY
Primary Program Source:	01001112DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s):	1650, 7968, 9117, 9169, EGCH
Program Element Code(s):	165000
Award Agency Code:	4900
Fund Agency Code:	4900
Assistance Listing Number(s):	47.050

ABSTRACT

Intellectual Merit: Phytoplankton form the basis of the marine food web and thus are a crucial element in the biological pump whereby CO2 from the atmosphere is sequestered in the deep ocean. For decades, biological oceanography focused on the eukaryotic phytoplankton. In the 1970-80s, it was discovered that the single celled picocyanobacteria are numerically dominant in the oceans and are responsible for a large fraction of ocean photosynthesis. What ensued was the growth of a new paradigm in which the picocyanobacteria dominate upper ocean biology and biogeochemistry. In fact, new data support the classic view that the eukaryotic phytoplankton are disproportionately important in both N and C cycling, even in regions where very small cells dominate the biomass and where the eukaryotes themselves are in the "pico" size fraction. In oligotrophic environments, where very small cells dominate, in situ recycling appears to supply most of the nitrogen (i.e., ammonium) required for primary production. New nitrate supply must balance N loss from the system, however, and new data suggest that this nitrate is an important contribution to phytoplankton N, even in the oceanic deserts. It is not known whether the nitrate supply in these systems is used by the entire assemblage or predominantly by larger phytoplankton (essentially entirely eukaryotic). On the basis of still quite limited molecular surveys, we now recognize that the diversity of both large and small eukaryotic phytoplankton is greater than previously thought and that the most abundant and widespread eukaryotes are probably not in culture and may not be closely related to known cultivated organisms. This project will investigate the taxonomic, genetic and functional diversity of eukaryotic phytoplankton at two North Atlantic sites (subarctic and subtropical) in two seasons.
The PIs will use diagnostic microarrays for community analysis based on functional genes (both DNA and RNA) and next generation sequencing (i.e., transcriptomics using 454 technology) to identify the players, both in terms of community composition and activity, and to explore the functional diversity of the natural assemblage. In order to identify which groups are active in C and N assimilation and which N source is being utilized by the different size and functional groups, both filter-separated and flow cytometry-sorted samples will be used to 1) measure 13C primary production and 15N assimilation by incubations with isotope tracers, 2) measure the natural stable N isotope signatures of different taxonomic groups and 3) link the molecular diversity to the functional diversity in C and N transformations. Using flow cytometry linked to mass spectrometry, these investigators have found an unexpectedly strong differentiation in the form of N assimilated by prokaryotes and eukaryotes, with eukaryotes being more dynamic.

Integration: This project will investigate the taxonomic, genetic and functional diversity of eukaryotic phytoplankton and to link this diversity and assemblage composition to the carbon and nitrogen biogeochemistry of the surface ocean. Taxonomic diversity will be investigated by identifying the components of the phytoplankton assemblages using molecular, chemical and microscope methods. Genetic diversity will be explored at several levels, including direct sequencing of clone libraries of key functional genes and metatranscriptomic sequencing and microarray analysis of size fractionated/sorted phytoplankton assemblages. Using natural abundance and tracer stable isotope methods, genetic and taxonomic diversity will be linked to functional diversity in C and N assimilation in size- fractionated and taxon-sorted populations.

Broader Impacts: The broader impacts of this project include contributions to fundamental research and education: 1) continued development of new advanced methods of isotope analysis in environmental samples, with increasing breadth of applications in biogeochemistry and biodiversity; 2) undergraduate teaching in foundation courses on climate and environmental science to recruit freshmen and sophomore students into the science majors; 3) undergraduate research experience through internships and senior thesis research (a requirement at Princeton) for upper level undergraduates; 4) training the next generation of microbial ecology/ biogeochemistry researchers through classroom and research experience at the graduate level. In addition, a new module will be created (The Forests and Deserts of the Ocean) for the Princeton outreach program for middle school teachers (QUEST, Questioning Underlies Effective Science Teaching).

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

This research examined functional, genetic and taxonomic diversity of eukaryotic phytoplankton in the surface ocean. Marine phytoplankton account for about half the annual global primary production.  As the basis of the marine food web, phytoplankton are a crucial element in the biological pump whereby CO₂ from the atmosphere is eventually sequestered in the deep ocean.  Many factors contribute to the diversity of phytoplankton and their roles in primary production, the local food web and global export production.  In addition to variations in size, different groups of phytoplankton exhibit different physiological and biochemical capabilities, “preferences” for nutrient utilization and growth form.  For example, small cells, whether prokaryotic or eukaryotic, have the advantage of large surface to volume ratios and generally grow faster than their larger congeners or functional parallels at lower nutrient concentrations.  With their simplified genomes, the most abundant picophytoplankton, Prochlorococcus, is generally unable to utilize nitrate, and apparently achieves its high cell abundance in the oligotrophic ocean by exploiting regenerated nitrogen. In contrast, diatoms, generally larger cells with larger more complex genomes, can grow nearly as fast and they achieve their highest growth rates on nitrate.  Although stochastic factors – essentially, being in the right place at the right time – may determine which species dominates a bloom, similarities in some fundamental properties may be selective in defining a winning life form.  For example, species able to  escape microzooplankton predation because of their size (large cells) or protection (chemical or mechanical) consistently dominate the biomass in blooms .

 

Size and functional diversity are important parameters in biogeochemical models, which are used to investigate the fate of carbon and nitrogen in the ocean.   Differences in the physical regime of, e.g., the central gyres vs. the subpolar oceans, are reflected in differences in phytoplankton community composition in terms of size and taxonomy.  Therefore we expect that global change that includes perturbation of the temperature and nutrient structure of the ocean will lead to changes in the phytoplankton community and the rest of the food web. Climate change and nitrogen fertilization of the open ocean are potential new drivers of phytoplankton biodiversity.  Understanding the current structure and function of phytoplankton assemblages is thus essential to the effectiveness of models for predicting response of ocean productivity to global changes.

 

Here we assign specific functions to major groups of phytoplankton that dominate the oceans largest biomes. Three major groups, the mamiellales, pyrmnesiophytes, and pelagophytes, dominate these ecosystems. Through comparative ecological genomics we contrast the evolution and ecology of these groups to the large phytoplankton cells that dominate coastal regions.

Last Modified: 04/14/2015
Modified by: Andrew E Allen

Addendum # 1

This project has been registered at BCO-DMO:

http://www.bco-dmo.org/project/544343

Molecular and diversity/genomic data has been deposited at BCO-DMO under: http://www.bco-dmo.org/dataset/565717 and linked to the project page above. This BCO-DMO entry includes results broken down by bacteria, archaea, eukaryotic chloroplast, and eukaryote. As noted in BCO-DMO, processed sequences from this data set can be found at http://scripps.ucsd.edy/labs/aallen/data/ under microbi...

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