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


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…)

Fellow Travelers

Observations suggest diazotrophs like Crocosphaera and Trichodesmium pay for their ability to fix nitrogen with a very low growth rate, yet diatom-diazotroph associations or DDAs exhibit high growth rates. CBIOMES...

3 Questions: Greg Britten on how marine life can recover by 2050

Committing to aggressive conservation efforts could rebuild ocean habitats and species populations in a few decades. (more…)

April 2020 CBIOMES e-meeting – Mick Follows (MIT)

"A model of macro-molecular allocation and elemental composition in steady-state cultures of phytoplankton" Please note access to this page is restricted to CBIOMES associates. (more…)

CBIOMES Welcomes Enrico Ser-Giacomi

A warm welcome to postdoc Enrico Ser-Giacomi who joins the MIT CBIOMES Group this month. (more…)

Seen at Ocean Sciences: CBIOMES Posters

Several CBIOMES members shared posters at this year’s Ocean Sciences conference which took place in San Diego in February. Please note access to this page is restricted to CBIOMES associates....

Seeding Oceans With Iron May Not Impact Climate Change

Study involving members of MIT-CBIOMES finds Earth’s oceans contain just the right amount of iron; adding more may not improve their ability to absorb carbon dioxide. (more…)

Exploring Phytoplankton Diversity

In a new paper, MIT-CBIOMES investigator Stephanie Dutkiewicz and collaborators use the Darwin ecosystem model to develop theories seeking to explain and predict phytoplankton biogeography. (more…)

February 2020 CBIOMES e-meeting – Zhen Wu (MIT)

'Modeling Photosynthesis and Exudation of DOM in Subtropical Oceans.' Please note access to this page is restricted to CBIOMES associates. (more…)

CBIOMES Goes to Ocean Sciences 2020

Look out for members of the CBIOMES team, sharing their work at this year’s Ocean Sciences conference taking place February 16-21 in San Diego, California. (more…)


Keisuke Inomura, Curtis Deutsch, Samuel T. Wilson, Takako Masuda, Evelyn Lawrenz, Bučinská Lenka, Roman Sobotka, Julia M. Gauglitz, Mak A. Saito, Ondřej Prášil, Michael J. Follows (2019), Quantifying Oxygen Management and Temperature and...


Svetlana N. Losa, Stephanie Dutkiewicz, Martin Losch, Julia Oelker, Mariana A. Soppa, Scarlett Trimborn, Hongyan Xi, and Astrid Bracher (2019), On modeling the Southern Ocean Phytoplankton Functional Types, Biogeosciences Discussions, doi: 10.5194/bg-2019-289 Get the PDF...

Fall 2019 SCOPE Gradients Workshop

Twelve from CBIOMES attended the 2019 Gradients Workshop held at the Alexis Hotel in Seattle WA October 15 through 17. Please note access to this page is restricted to CBIOMES...


Jann Paul Mattern, Christopher A. Edwards, Christopher N. Hill (2019), Dual number-based variational data assimilation: Constructing exact tangent linear and adjoint code from nonlinear model evaluations, PLoS One, doi: 10.1371/journal.pone.0223131 Get the PDF [Requires...


Emily J. Zakem, Amala Mahadevan, Jonathan M. Lauderdale, and Michael J. Follows (2019), Stable aerobic and anaerobic coexistence in anoxic marine zones, The ISME Journal, doi: 10.1038/s41396-019-0523-8 Get the PDF [Requires login]

CBIOMES Welcomes Zhen Wu

by Helen Hill for CBIOMES A warm welcome to incoming postdoc Zhen Wu who joins MIT-CBIOMES this month. (more…)

Fourth Annual Traits Workshop

Reporting by Helen Hill for CBIOMES The fourth Workshop on Trait-Based Approaches to Ocean Life, held August 18-21, 2019 at Chicheley Hall in Buckinghamshire in the UK was a wonderful opportunity for...

CBIOMES Welcomes Deepa Rao

by Helen Hill for CBIOMES A warm welcome to graduate student Deepa Rao, who joins the MIT-CBIOMES Group this month. (more…)


David Talmy, Stephen J. Beckett, Darcy A.A. Taniguchi, Corina P.D. Brussard, Joshua S. Weitz, and Michael J. Follows (2019), An empirical model of carbon flow through marine viruses and microzooplankton grazers, Environmental Microbiology, doi:...

When Phytoplankton Go Hungry

Story by Helen Hill | CBIOMES News The Redfield ratio, the atomic ratio of carbon, nitrogen, and phosphorus (C:N:P) in phytoplankton and deep ocean waters, has often been treated as a...

A Model for Nitrogen Fixation in the Presence of Ammonium

Former MIT Darwin Group member Keisuke Inomura, working with MIT CBIOMES investigator Mick Follows, presents a new quantitative model of nitrogen fixation in the presence of ammonium. (more…)

Study: Much of the surface ocean will shift in color by end of 21st century

Climate-driven changes in phytoplankton communities will intensify the blue and green regions of the world’s oceans. New work from CBIOMES researchers Stephanie Dutkiewicz and Oliver Jahn.  (more…)

Lab Notes: Britten visits Dalhousie

Greg Britten from the MIT CBIOMES Group travels to Dalhousie University in Halifax, Canada (more…)

CBIOMES Welcomes Greg Britten

A warm welcome to incoming postdoc Dr Greg Britten who joins the MIT CBIOMES Group. (more…)

Past Annual Reporting

2019 | 2018 [login required]