Skip to content


Coupled Model Intercomparison Project Phase 6 (CMIP6): Projected trends in bacterial carbon biomass under future emission scenarios

Marine heterotrophic bacteria respire a large fraction of organic carbon into CO2 and regenerate nutrients, playing an important biogeochemical role in global climate. This project aims to examine the global and regional trends in bacterial carbon biomass under future emission scenarios over the 21st century (2015-2100) using the results from a three-dimensional Earth System Model with an explicit bacterial treatment (CMCC-ESM2) as a part of the Coupled Model Intercomparison Project Phase 6 (CMIP6). This project provides a first critical step toward better quantification and projection of the ocean's microbial feedback on global climate.

Funding source: WHOI Independent Research & Development Award ′20

Kim, H. H., Laufkötter, C., Lovato, T., Doney, S. C., Ducklow, H. W. Projected 21st-Century Changes in Marine Heterotrophic Bacteria Under Climate Change, Under Review, Global Change Biology

Predicting coupled ice-ocean-microbial interactions along the warming West Antarctic Peninsula

The marginal ice zone along the West Antarctic Peninsula is an important region with potentially strong feedbacks between sea ice, ocean physics, biogeochemistry, and air-sea CO2 fluxes. This project aims to investigate the influence of winds and ocean subsurface heat on seasonal sea-ice dynamics, microbial system processes, and their impacts on air-sea CO2 fluxes in the West Antarctic Peninsula, using a one-dimensional prognostic ice-ocean-biogeochemical model (the KPP-Ecosystem-Ice model).

Funding source: WHOI Independent Research & Development Award ′21

Developing a multi-scale modeling framework to reconcile the carbon budget in the ocean's mesopelagic zone

Photosynthesis produces ~100 gigatons of organic carbon per year in the surface ocean, but only a small fraction of this carbon settles into the mesopelagic zone because of strong respiration by heterotrophic bacteria and zooplankton. Many studies have demonstrated significant imbalances between carbon supply and demand in the mesopelagic zone, in particular particle flux attenuation that is up to two orders of magnitude lower than heterotrophic respiration. This suggests that particle export alone is insufficient to meet the carbon demand of mesopelagic biota, and that additional, unaccounted for, sources of organic carbon to the mesopelagic ocean exist. This project aims to reassess the current carbon budget in the mesopelagic zone by developing a novel, multi-scale modeling framework linking a one-dimensional variational assimilation model and the three-dimensional Community Earth System Model (CESM).

Funding source: WHOI Independent Study Award ′21

Quantifying microbial control of carbon and biogeochemical cycling in the West Antarctic Peninsula 

This project aims to develop and evaluate a one-dimensional numerical marine biogeochemical model for the West Antarctic Peninsula region (WAP-1D-VAR v1.0). The WAP-1D-VAR v1.0 model is equipped with a built-in data assimilation scheme via a variational adjoint method. This project is the first to apply a mechanistic model to the coastal West Antarctic Peninsula region that simulates the time-evolving dynamics of carbon, nitrogen, and phosphorus driven by biogeochemical processes. The model is utilized to investigate the microbial, ecosystem, and biogeochemical responses to climate change and variability along the West Antarctic Peninsula.

Kim, H. H., Luo, Y.-W., Ducklow, H. W., Schofield, O. M., Steinberg, D. K., and Doney, S. C (2021). WAP-1D-VAR v1.0: Development and Evaluation of a One-Dimensional Variational Data Assimilation Model for the Marine Ecosystem Along the West Antarctic Peninsula, Geoscientific Model Development, 14, 4939-4975,

Predicting ecosystem functions using bacterial taxonomic and physiological traits in the West Antarctic Peninsula 

This project aims to develop a trait-based biogeochemical model (WAP-1D-VAR v2.0) in order to link individual cell-based and ecosystem scales in heterotrophic marine bacterial dynamics. The WAP-1D-VAR v2.0 model assimilates 16S rRNA gene amplicon and flow cytometry data as a part of Palmer Long-Term Ecological Research and differently parameterizes the physiology, biogeochemistry, and trophic dynamics of high nucleic acid and low nucleic acid bacterial groups. The model simulates the microbially-mediated carbon, nitrogen, and phosphorus stocks and flows of a distinct bacterial mode, a dimension reduction product of the bacterial community structure associated with its specific genomic and functional traits. The model is also utilized to examine the predictability of bacterial traits in ecosystem functions.

Kim, H. H., Bowman, J. S., Luo, Y.-W., Ducklow, H. W., Schofield, O. M., Steinberg, D. K., and Doney, S. C (2022). Modeling polar marine ecosystem functions guided by bacterial physiological and taxonomic traits, Biogeosciences, 19, 117-136,