Award Abstract # 2129823
Collaborative Research: Microdiversity drives ecosystem function: SAR11 bacteria as models for oceanic nitrogen loss

NSF Org: OCE
Division Of Ocean Sciences
Recipient: GEORGIA TECH RESEARCH CORP
Initial Amendment Date: November 18, 2021
Latest Amendment Date: November 18, 2021
Award Number: 2129823
Award Instrument: Standard Grant
Program Manager: Jayne Gardiner
jgardine@nsf.gov
 (703)292-4828
OCE
 Division Of Ocean Sciences
GEO
 Directorate for Geosciences
Start Date: December 1, 2021
End Date: November 30, 2025 (Estimated)
Total Intended Award Amount: $436,628.00
Total Awarded Amount to Date: $436,628.00
Funds Obligated to Date: FY 2022 = $436,628.00
History of Investigator:
  • Konstantinos Konstantinidis (Principal Investigator)
    kostas@ce.gatech.edu
Recipient Sponsored Research Office: Georgia Tech Research Corporation
926 DALNEY ST NW
ATLANTA
GA  US  30318-6395
(404)894-4819
Sponsor Congressional District: 05
Primary Place of Performance: Georgia Institute of Technology
225 North Avenue, NW
Atlanta
GA  US  30332-0002
Primary Place of Performance
Congressional District:
05
Unique Entity Identifier (UEI): EMW9FC8J3HN4
Parent UEI: EMW9FC8J3HN4
NSF Program(s): BIOLOGICAL OCEANOGRAPHY
Primary Program Source: 01002223DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 8242, 9250, 8811, 1097, 9117
Program Element Code(s): 165000
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.050

ABSTRACT

This project studies how low oxygen availability influences the biodiversity and ecological role of SAR11 bacteria, one of the most abundant microbial groups in the ocean. The work involves oceanographic sampling across a range of oxygen and nutrient levels in the Eastern Tropical North Pacific Ocean. Using a combination of genomic, microbiological, and biogeochemical methods, the study identifies the mechanisms by which SAR11 strains diversify into separate niches and species and contribute biochemically to the ecosystem, likely through removing nitrogen from seawater. The project equips the next generation of researchers and educators, notably those from underrepresented minority groups, to use oceanographic, genomic, and microbiological concepts to meet contemporary scientific challenges. This goal is met through a combination of bioinformatic workshops that target undergraduate students from the University System of Puerto Rico, middle school teacher-training workshops, and middle or high school teacher internships in the investigator?s labs. This multifaceted research and educational agenda fills a gap in our understanding of marine biological diversity, identifies the contribution of SAR11 bacteria to nutrient and carbon cycles in low oxygen oceans, and provides lessons and analytical tools to study microbial processes in other ecosystems.

This project has two aims. Aim 1 employs comparative metagenomic and single-cell genomic analyses to identify metabolic properties that distinguish SAR11 clades from low oxygen regions and processes of selection or gene flow operating across the clades. Aim 2 combines microbial transcriptomics, incubation experiments with isotope tracers, and culturing to delimit the oxygen and nutrient conditions that define the niche space of each SAR11 clade and to correlate SAR11 gene transcription with community biochemical outcomes, including nitrogen loss through denitrification. The results of these aims and the informatic methods used to probe microbial microdiversity are disseminated through genomics-focused undergraduate workshops, and new teacher-training educational modules, including lab-based modules focused on the importance of microorganisms under environmental change in the oceans. Data, manuscripts, and informatics workflows from this project are made publicly available. The results are critical for resolving the processes that create and sustain microbial diversity in the oceans and informing biogeochemical models that predict how diversity influences ecosystem processes.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 12)
Viver, Tomeu and Conrad, Roth E. and Lucio, Marianna and Harir, Mourad and Urdiain, Mercedes and Gago, Juan F. and Suárez-Suárez, Ana and Bustos-Caparros, Esteban and Sanchez-Martinez, Rodrigo and Mayol, Eva and Fassetta, Federico and Pang, Jinfeng and M "Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., S" Systematic and Applied Microbiology , v.46 , 2023 https://doi.org/10.1016/j.syapm.2023.126416 Citation Details
Zhao, Jianshu and Both, Jean_Pierre and Rodriguez-R, Luis M. and Konstantinidis, Konstantinos T. "GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs" Nucleic Acids Research , v.52 , 2024 https://doi.org/10.1093/nar/gkae609 Citation Details
Viver, Tomeu and Conrad, Roth E. and Rodriguez-R, Luis M. and Ramírez, Ana S. and Venter, Stephanus N. and Rocha-Cárdenas, Jairo and Llabrés, Mercè and Amann, Rudolf and Konstantinidis, Konstantinos T. and Rossello-Mora, Ramon "Towards estimating the number of strains that make up a natural bacterial population" Nature Communications , v.15 , 2024 https://doi.org/10.1038/s41467-023-44622-z Citation Details
Aldeguer-Riquelme, Borja and Conrad, Roth E and Antón, Josefa and Rossello-Mora, Ramon and Konstantinidis, Konstantinos T "A natural ANI gap that can define intra-species units of bacteriophages and other viruses" mBio , v.15 , 2024 https://doi.org/10.1128/mbio.01536-24 Citation Details
Blake G. Lindner a, 1 "A users guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection" International journal of food microbiology , 2023 Citation Details
Conrad, Roth E and Brink, Catherine E and Viver, Tomeu and Rodriguez-R, Luis M and Aldeguer-Riquelme, Borja and Hatt, Janet K and Venter, Stephanus N and Rossello-Mora, Ramon and Amann, Rudolf and Konstantinidis, Konstantinos T "Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination" Nature Communications , v.15 , 2024 https://doi.org/10.1038/s41467-024-53787-0 Citation Details
Gerhardt, Kenji and Ruiz-Perez, Carlos A. and Rodriguez-R, Luis M. and Conrad, Roth E. and Konstantinidis, Konstantinos T. "RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity" Frontiers in Bioinformatics , v.1 , 2022 https://doi.org/10.3389/fbinf.2021.826701 Citation Details
Konstantinidis, Konstantinos T "Sequencediscrete species for prokaryotes and other microbes: A historical perspective and pending issues" mLife , v.2 , 2023 https://doi.org/10.1002/mlf2.12088 Citation Details
Konstantinos T. Konstantinidis "Sequencediscrete species for Prokaryotes and other microbes: A historical perspective and pending issues" mLife , 2023 Citation Details
Lindner, Blake G and Gerhardt, Kenji and Feistel, Dorian J and Rodriguez-R, Luis M and Hatt, Janet K and Konstantinidis, Konstantinos T "A users guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection" International Journal of Food Microbiology , v.410 , 2024 https://doi.org/10.1016/j.ijfoodmicro.2023.110488 Citation Details
Luis M. Rodriguez-R, 1 Roth "An ANI gap within bacterial species that advances the definitionsdefinitionsof intra-species units" MBio , 2023 Citation Details
(Showing: 1 - 10 of 12)

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