Award Abstract # 1739144
Collaborative Research: Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea

NSF Org: OCE
Division Of Ocean Sciences
Recipient: UNIVERSITY OF CALIFORNIA, SANTA BARBARA
Initial Amendment Date: April 10, 2017
Latest Amendment Date: April 10, 2017
Award Number: 1739144
Award Instrument: Standard Grant
Program Manager: David Garrison
OCE
 Division Of Ocean Sciences
GEO
 Directorate For Geosciences
Start Date: July 1, 2016
End Date: March 31, 2018 (Estimated)
Total Intended Award Amount: $10,313.00
Total Awarded Amount to Date: $10,313.00
Funds Obligated to Date: FY 2013 = $10,313.00
History of Investigator:
  • Alyson Santoro (Principal Investigator)
    asantoro@ucsb.edu
Recipient Sponsored Research Office: University of California-Santa Barbara
3227 CHEADLE HALL
SANTA BARBARA
CA  US  93106-0001
(805)893-4188
Sponsor Congressional District: 24
Primary Place of Performance: University of California-Santa Barbara
Marine Science Institute
Santa Barbara
CA  US  93106-6150
Primary Place of Performance
Congressional District:
24
Unique Entity Identifier (UEI): G9QBQDH39DF4
Parent UEI:
NSF Program(s): BIOLOGICAL OCEANOGRAPHY
Primary Program Source: 01001314DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 0000, 9117
Program Element Code(s): 1650
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.050

ABSTRACT

Intellectual Merit. How organisms respond to their physical and chemical and environment is a central question in marine ecology. For microbes living in the mesopelagic - the ocean's "twilight zone" - an efficient response is particularly important to capitalize on the intermittent delivery of organic and inorganic compounds sinking from the surface ocean. These organisms must have a suite of metabolic and regulatory strategies used to cope with environmental variability, but these strategies are largely unknown. Understanding when and why metabolic genes are expressed is critical to our understanding of nutrient remineralization in the ocean. Marine group 1 (MG1) archaea are ubiquitous, abundant microbes in the meso- and bathypelagic and promising model organisms for investigating these questions. MG1 archaea are chemolithoautotrophs that oxidize ammonia for energy and fix carbon for biomass, and as such, play a central role in the ocean's coupled carbon and nitrogen cycles. Though MG1 have historically eluded cultivation, recent efforts have been successful at bringing representative MG1 archaea from the open ocean into culture and demonstrating their importance in the production of the greenhouse gas nitrous oxide. This project takes advantage of unique MG1 cultures and the recently sequenced draft genome of one of the organisms - strain CN25 - to investigate the physiological and transcriptional responses of MG1 archaea to variations in their chemical environment, specifically:
1. Comparative transcriptomics of CN25 cells grown under a range of energy availability and nitrosative stress will identify select genes that can be used to diagnose the physiological state of natural populations
2. Improvements in the genomic and transcriptomic knowledge of MG1 archaea will facilitate a thorough reinterpretation of existing metagenomic and metatranscriptomic datasets, as well as provide a better contextual understanding in future studies
The investigators will conduct comparative transcriptomics of CN25 cells harvested in mid-exponential growth and stationary phase versus starved cells. Transcriptomes of cells grown at high nitrate concentrations and low pO2 with those grown in standard conditions will be characterized. A strand-specific, high-density RNAseq approach will be used to examine the expression of putative ORFs, polycistronic operons, and small RNAs, which, in addition to gene expression profiling, has the ancillary benefit of improving genome annotation. Finally, the investigators will sequence the genomes of two additional MG1 strains isolated from the open ocean, as well as single cells from environmental surveys, and leverage the combination with the CN25 genome to reanalyze available metagenomic and metatranscriptomic datasets. The results will define the transcriptional response of a model mesopelagic microbe to a range of chemical environments, and show how the physicochemical environment induces changes in gene expression and gene content that result in greenhouse gas production. This work will rapidly generate new knowledge of how some of the most ubiquitous, yet heretofore elusive, microorganisms respond to geochemical variability and shape our evolving understanding of the marine nitrogen cycle.

Broader Impacts. The scientific and societal impact of the project will be to elucidate the mechanisms of greenhouse gas production in a model marine organism that is of broad interest to biological and chemical oceanographers. Transcriptome sequencing will improve the assembly of the CN25 genome, the first genome of an MG1 archaeon from the open ocean. Both the genome and transcriptomes will be important references for researchers using metagenomics, metatranscriptomics, and metaproteomics in the ocean, as these techniques are reliant on a knowledgebase composed of both DNA sequence and physiology. Thus, the results add value to both existing and future studies. The proposed research will advance education, teaching, and training for the next generation of marine scientists by providing support for two early-career investigators, one postdoctoral researcher, and a secondary school teacher.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Hurley, S.J., Elling, F.J., Konneke, M., Buchwald, C.*, Wankel, S.D., Santoro, A.E., Lipp, J.S., Hinrichs, K-U., Pearson, A. "Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX86 proxy" Proceedings of the National Academy of Sciences , 2016 10.1073/pnas.1518534113
Santoro, A.E., Saito, M.A., Goepfert, T.J., Lamborg, C.H., Dupont, C.L., and G.R. DiTullio. "Thamarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation" Limnology & Oceanography , 2017 10.1002/lno.10547
Monteiro, M., Seneca, J., Torgo, L., Cleary, D.F.R., Gomes, N.C.M., Santoro, A.E., Magalhaes, C "Environmental controls on estuarine nitrifying communities along a salinity gradient" Aquatic Microbial Ecology , 2017 10.3354/ame01847

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.

Archaea are single-celled organisms that are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. One group, the marine Thaumarchaotaa, was a focus for this project. Thaumarchaea are among the most abundant microbes in the oceans and catalyze the globally relevant process of ammonia oxidation.

The goal of our project was to use unique cultures of thaumarchaea established by our laboratory to understand the ecology, evolution, and gene expression of this abundant group of microbes. We found that open ocean thaumarchaea have some of the smallest genomes of any free-living cell in the microbial world, and that they express nearly every protein encoded by their genome during growth. This information can be used for synthetic biology approaches that aim to construct a minimal cell.  

We also generated several additional high quality genomes for thaumarchaeal enrichment cultures from the open ocean through metagenomic sequencing, assembly, genome binning, genome closure, and subsequent annotation. Recruitment of metagenomics data from global expeditions show that these genomes are more representative of shallow open ocean populations of thaumarchaea, though it was also noted that different lineages are found in deeper waters. Controlled growth experiments with these enrichment cultures were combined with metatranscriptomes from marine ecosystems to compare gene expression in cultures and the lab.

Results from this award were presented at numerous national and international meetings, and incorporated into graduate and undergraduate teaching modules at the University of Maryland and the University of California Santa Barbara. All data generated by the project have been made publically available through NSF's BCO-DMO database. The award trained two postdoctoral researchers, one graduate student, three technicians and multiple undergraduate researchers.

 


Last Modified: 09/27/2018
Modified by: Alyson E Santoro

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