Models of Marine Microbial Biogeography and Biogeochemistry

Investigators: Mick Follows and Stephanie Dutkiewicz
Massachusetts Institute of Technology

Microbial communities in the sea mediate the global cycles of elements including climatically significant carbon, sulfur and nitrogen. Photosynthetic microbes in the surface ocean fix carbon and other elements into organic molecules, fueling food webs that sustain fisheries and most other life in the ocean. Sinking and subducted organic matter is remineralized and respired in the dark, sub-surface ocean maintaining a store of carbon about three times the size of the atmospheric inventory of CO2. The communities of microbes that sustain these global-scale cycles are functionally and genetically extremely diverse, non-uniformly distributed and sparsely sampled. Their biogeography reflects selection according to the relative fitness of myriad combinations of traits that govern interactions with the environment and other organisms. Trait-based theory and simulations provide tools with which to interpret biogeography and microbial mediation of biogeochemical cycles. Several outstanding challenges remain: observations to constrain the biogeography of marine microbes are still sparse and based on eclectic sampling methods, theories of the organization of the system have not been quantitatively tested, and the models used to simulate the system still lack sufficiently mechanistic biological foundations that will enable meaningful, dynamic simulations and state estimation.

Our goals are to integrate key new data sets in real time as they are collected at sea to facilitate direct tests of theoretical predictions; to synthesize an atlas of marine microbial biogeography suitable for testing some specific ecological theories and quantifying the skill of numerical simulations; to develop new trait-based models and simulations of regional and global microbial communities bringing to bear the power of metabolic constraints and knowledge of macro-molecular composition; to analyze these data and models using statistical tools to interpolate and extrapolate the sparse data sets, formally quantify the skill of numerical simulations; and employ data assimilation technologies to identify and optimize compatible model frameworks. Together, the results of these efforts will advance new theoretical approaches and lead to improved global ocean-scale predictions and regional state-estimates, constrained by observed biogeography. They will provide a quantification of the associated biogeochemical fluxes.

CBIOMES Collaborators in the MIT Group

News from the MIT Group

May 2022 CBIOMES e-meeting Jonathan Lauderdale (MIT)

"Attribution of space-time variability in global-ocean dissolved inorganic carbon using the ECCO-Darwin data‐assimilative global ocean biogeochemistry model." Please note access to this page is restricted to CBIOMES associates. (more…)

May 2022 CBIOMES e-meeting Enrico Ser-Giacomi (MIT)

“Dilution-driven heterogeneity enhances plankton productivity in Lagrangian ecosystems” Please note access to this page is restricted to CBIOMES associates. (more…)

April 2022 CBIOMES e-meeting Zhen Wu (MIT)

“Significant organic carbon acquisition by Prochlorococcus in the oceans” Please note access to this page is restricted to CBIOMES associates. (more…)


Jann Paul Mattern, Kristof Glauninger, Gregory L. Britten, John R. Casey, Sangwon Hyun, Zhen Wu, E. Virginia Armbrust, Zaid Harchaoui, Francois Ribalet (2022), A Bayesian approach to modeling phytoplankton population...


Dustin Carroll et al (2022), Attribution of space-time variability in global-ocean dissolved inorganic carbon, Global Biogeochemical Cycles, doi: 10.1029/2021GB007162 (Stephanie Dutkiewicz, Jonathan M. Lauderdale, Chris Hill, Oliver Jahn) Get the...

March 2022 CBIOMES e-meeting Mick Follows (MIT)

"Eddy-driven, isopycnal resupply of nutrients and the productivity of the North Pacific Subtropical Gyre" Please note access to this page is restricted to CBIOMES associates. (more…)


Inès Mangolte, Marina Lévy, Stephanie Dutkiewicz, Sophie Clayton, Oliver Jahn (2022), Plankton community response to fronts: winners and losers, Journal of Plankton Research, doi: 10.1093/plankt/fbac010 Get the PDF [Requires login]  

February 2022 CBIOMES All Hands Poster Meeting

A big THANK-YOU to everyone who presented at the February e-meeting!  (more…)


Simona Meiler, Gregory L. Britten, Stephanie Dutkiewicz, Mary Rose Gradoville, Pia H. Moisander, Oliver Jahn, Michael J. Follows (2022), Constraining uncertainties of diazotroph biogeography from nifH gene abundance, Limnology and Oceanography, doi: 10.1002/lno.12036 Get the PDF [Requires...


Vinitha Ebenezer, Yingyu Hu, Olga Carnicer, Andrew J. Irwin, Michael J. Follows, Zoe V. Finkel (2022), Elemental and macromolecular composition of the marine Chloropicophyceae, a major group of oceanic photosynthetic picoeukaryotes, Limnology and Oceanography, doi:...

A Systems Level Approach to Biogeography

Microbial simulations bridge the gap between the molecular and ecosystem scales. A new CBIOMES paper presents, for the first time, an interpretation of observed, strain-level, basin-scale biogeography using genome-scale modeling...

Plankton’s Place

According to CBIOMES researchers predator interactions chiefly determine where Prochlorococcus thrive - a finding that may help researchers hone predictions for where phytoplankton will migrate with climate change. (more…)

CBIOMES Welcomes Barbara Duckworth

by Helen Hill for CBIOMES A warm CBIOMES-welcome to Barbara (Barbie) Duckworth who recently joined the group to work with Chris Follet. (more…)


Bardon, L. R., Ward, B. A., Dutkiewicz, S., & Cael, B. B. (2021), Testing the skill of a species distribution model using a 21st-century virtual ecosystem, Geophysical Research Letters, doi: 10.1029/2021GL093455 Get the PDF [Requires login]  

CBIOMES Welcomes Zoe Aarons

by Helen Hill for CBIOMES A warm welcome to Zoe Aarons who recently joined MIT CBIOMES. (more…)

CBIOMES Welcomes Stephanie Anderson

by Helen Hill for CBIOMES A warm welcome to Stephanie Anderson who recently joined MIT CBIOMES to work with Stephanie Dutkiewicz. (more…)

CBIOMES Welcomes Camila Sera Pompeii

by Helen Hill for CBIOMES A warm welcome to incoming Simons postdoctoral Fellow Camila Serra Pompei, a new member of the MIT CBIOMES Group working. (more…)

CBIOMES Welcomes Junkun Ren

by Helen Hill for CBIOMES A warm welcome to Junkun Ren who recently joined MIT CBIOMES. (more…)


Zhen Wu, Stephanie Dutkiewicz, Oliver Jahn, Daniel Sher, Angelicque White, Michael J. Follows (2021), Modeling Photosynthesis and Exudation in Subtropical Oceans, Global Biogeochemical Cycles, doi: 10.1029/2021GB006941 Get the PDF [Requires login]...


Stephanie A. Henson, B. B. Cael, Stephanie R. Allen and Stephanie Dutkiewicz (2021), Future phytoplankton diversity in a changing climate, Nature Communications, doi: 10.1038/s41467-021-25699-w Get the PDF [Requires login]  

September 2021 CBIOMES e-meeting Anne-Willem Omta (MIT)

“The closure problem revisited: The case for a hyperbolic zooplankton mortality” Please note access to this page is restricted to CBIOMES associates. (more…)

Explaining Diversity Patterns Among Marine Phytoplankton

Scientists extend a concept from network theory to develop a new diagnostic for fluid flows useful in understanding the structuring of marine phytoplankton distributions. (more…)


Subhendu Chakraborty, Ken H. Andersen, André W. Visser, Keisuke Inomura, Michael J. Follows & Lasse Riemann (2021), Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles, Nature Communications, doi:...


Gregory L. Britten, Carlos M. Duarte, Boris Worm (2021), The recovery of global fish stocks remains uncertain, PNAS, doi: 10.1073/pnas.2108532118 Get the PDF [Requires login]  

Recordings and microtalks from the Follows Group. Please note access to this page is restricted to CBIOMES associates. (more…)

2021 Annual Meeting microtalk: Do non-trophic interactions drive micronutrient cycling and microbial community succession in Antarctic coastal seas? – Deepa Rao (MIT)



Christopher P. Kempes,  Michael J. Follows, Hillary Smith, Heather Graham, Christopher H. House, Simon A. Levin (2021), Generalized Stoichiometry and Biogeochemistry for Astrobiological Applications, Bulletin of Mathematical Biology, doi: 10.1007/s11538-021-00877-5 Get the PDF [Requires login]  


Christopher L. Follett, Stephanie Dutkiewicz, Gael Forget, B.B. Cael, Michael J. Follows (2021), Moving ecological and biogeochemical transitions across the North Pacific, Limnology and Oceanography, doi: 10.1002/lno.11763 Get the PDF [Requires...


Gael Forget (2021), IndividualDisplacements.jl: a Julia package to simulate and study particle displacements within the climate system, The Journal of Open Source Software, doi: 10.21105/joss.02813 Get the PDF [Requires login]  


B.B. Cael, Bisson, K., Conte, M., Duret, M. T., Follett, C., Henson, S. A., et al. (2021), Open ocean particle flux variability from surface to seafloor, Geophysical Research Letters, doi: 10.1029/2021GL092895 Get the...


Lauderdale, J. M., & Cael, B. B. (2021), Impact of remineralization profile shape on the air-sea carbon balance,  Geophysical Research Letters, doi: 10.1029/2020GL091746 Get the PDF [Requires login]  


Mohammad D. Ashkezari, Norland R. Hagen, Michael Denholtz, Andrew Neang, Tansy C. Burns, Rhonda L. Morales, Charlotte P. Lee, Christopher N. Hill and Virginia Armbrust (2021), Simons Collaborative Marine Atlas Project (Simons CMAP): an...

March 2021 CBIOMES e-meeting Greg Britten (MIT)

“Seasonal productivity and photoacclimation in the North Pacific Transition Zone” Please note access to this page is restricted to CBIOMES associates. (more…)

CBIOMES Welcomes Four Graduate Students

A warm welcome to Delaney Nolin and Rae Santora from USC, and Lexi Jones and Ari Krinos from MIT as they bring their skills and energy to the CBIOMES collaboration....

February 2021 CBIOMES e-meeting Chris Follett (MIT)

“When should we trust Niche model predictions under Climate Change???” (A case study using the Flombaum model for Prochlorococcus populations.) Please note access to this page is restricted to CBIOMES...


Keisuke Inomura, Curtis Deutsch, Takako Masuda, Ondřej Prášil,  Michael J. Follows (2020), Quantitative models of nitrogen-fixing organisms, Computational and Structural Biotechnology Journal, doi: 10.1016/j.csbj.2020.11.022 Get the PDF [Requires login]


B.B. Cael, Emma L. Cavan, and Gregory L. Britten (2021), Reconciling the size-dependence of marine particle sinking speed, Geophysical Research Letters, doi: 10.1029/2020GL091771 Get the PDF [Requires login]  


Stephanie Dutkiewicz, Philip W. Boyd, Ulf Riebesell (2020), Exploring biogeochemical and ecological redundancy in phytoplankton communities in the global ocean, Global Change Biology, doi: 10.1111/gcb.15493 Get the PDF [Requires login]

December 2020 CBIOMES (Poster) e-Meeting

To provide an opportunity to "pick up the conversation" and chat with colleagues about where work had gone since our Annual Meeting in June, the December gathering was an all-hands...

November 2020 CBIOMES e-meeting – John Casey (MIT)

“Simulating Prochlorococcus growth, metabolism and physiology across a meridional transect of the North and South Atlantic Oceans” Please note access to this page is restricted to CBIOMES associates. (more…)


Emily J. Zakem, Martin F. Polz and Michael J. Follows (2020), Redox-informed models of global biogeochemical cycles, Nature Communications, doi: 10.1038/s41467-020-19454-w Get the PDF [Requires login]

2020 Joint Simons Marine Collaborations Meeting

Please note access to this page is restricted to CBIOMES associates only. Besides CBIOMES, the Simons Foundation supports three other marine collaborations: BIOS-SCOPE, PriME, and SCOPE. A joint meeting, October...

Towards a Better Model for the Microbe Membrane (Revisited)

Postdoc John Casey continues to work closely with MIT-CBIOMES Group PI Mick Follows on research combining quantitative proteomics, flux balance analysis, and molecular modeling of membrane transports to develop a...


Emily Zakem, Jonathan Maitland Lauderdale, Reiner Schlitzer, Michael J. Follows (2020),  A flux-based threshold for anaerobic activity in the ocean, ESSOar (for Geophysical Research Letters), doi: 10.1002/essoar.10504387.1 Get the PDF [Requires login]


John Casey and Michael J. Follows (2020), A steady-state model of microbial acclimation to substrate limitation, PLoS Computational Biology, doi: 10.1371/journal.pcbi.1008140 Get the PDF [Requires login]

August 2020 CBIOMES e-meeting – Enrico Ser-Giacomi (MIT)

“Lagrangian Betweenness and Bottlenecks of the Ocean Circulation” Please note access to this page is restricted to CBIOMES associates. (more…)


A.W. Omta, D. Talmy, K. Inomura, A.J. Irwin, Z.V. Finkel, D. Sher, and M.J. Follows (2020), Quantifying nutrient throughput and DOM production by algae in continuous culture, Journal of Theoretical Biology, doi: 10.1016/j.jtbi.2020.110214 Get the PDF [Requires...

The Follows Group goes to Annual Meeting

The MIT-CBIOMES group is developing new computational frameworks for modeling marine microbial biogeography and biogeochemistry. In this video, Mick presents an overview of their progress and advertises MIT member posters....


Inomura, K. A-W. Omta, D. Talmy, J. Bragg, C. Deutsch, and M.J. Follows (2020), A Mechanistic Model of Macromolecular Allocation, Elemental Stoichiometry, and Growth Rate in Phytoplankton, Frontiers in Microbiology, doi: 10.3389/fmicb.2020.00086 Get the PDF [Requires login]

Machine learning helps map global ocean communities

Technique developed by MIT-CBIOMES investigators could aid in tracking the ocean’s health and productivity. (more…)

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Past Annual Reporting

2019 | 2018 [login required]