Deciphering bacterial colonization of marine snow

Host laboratory and collaborators




Diazotrophs are prokaryotes capable of reducing atmospheric dinitrogen (N2) to reactive nitrogen, the main nutrient sustaining life in the ocean. The majority of diazotrophs live attached to "marine snow": amorphous aggregations of cell debris, polysaccharides and detritus that form by interaction of dead cells suspended in seawater [1]. Marine snow is rich in nutrients and energy, and hence thought to provide resources for diazotrophs to thrive in the ocean. However, how diazotrophs swim towards and colonize marine snow, and how such colonization stimulates their metabolism has not been studied. This project will combine cell trajectory tracking and analysis on model marine snow [2] with single-cell mass spectrometry [3] to understand how diazotroph colonization dynamics and metabolism differ among i) marine snow types, ii) environmental conditions, and iii) diazotroph species.


Marine bacteria, motility, single-cell metabolism, cell tracking, dynamical inference


The main objective of this project is to understand how diazotrophs colonize marine snow and how colonization may benefit their metabolic performance. To that end we propose the following specific objectives:

Objective 1) Determine  diazotroph trajectories and infer colonization/decolonization dynamics
Objective 2) Determine single-cell N2 fixation rates in diazotrophs attached to marine snow

Proposed approach (experimental / theoretical / computational)

This project combines experimental and computational approaches. First we will set the image acquisition system using model artificial marine snow and time-lapse microscopy, supported by the CENTURI Eng platform. Image data and cell trajectories will be analyzed to quantitatively reconstruct stochastic dynamics models of diazotroph interactions with marine snow [4]. Images and metadata will be stocked in OMERO, ensuring FAIR data. Second, different snow types (%sugar, lipid, protein), treatments (temperature, nutrients) and diazotrophs (Vibrio, Rhodopseudomonas) will be tested. Finally, time-course colonization will be tracked and the 15N-enrichment of diazotrophs measured by nanoscale secondary ion mass spectrometry (nanoSIMS). Isotopic enrichment planes will be drift-corrected and accumulated to infer single-cell nitrogen assimilation rates [5]. This approach will link colonization dynamics to diazotroph nitrogen metabolism at the single-cell level.


The proposed project is interdisciplinary as it combines techniques from multiple fields to decipher particle colonization dynamics: image analysis as well as modern statistical inference methods will be used to analyze the tracks, while single-cell isotope probing will reveal how marine snow colonization impacts the metabolism of diazotrophs. The obtained results will provide unprecedented insights into the behaviour of diazotrophs and their impact on marine snow dynamics in the ocean.

Expected profile

We are looking for a student with a background in data science and microbial ecology. Skills in optical microscopy, programming (Python, R), multivariate statistics and image analysis are highly desired. Cell culturing skills are desirable but not essential.

Is this project the continuation of an existing project or an entirely new one? In the case of an existing project, please explain the links between the two projects

This is a new project and includes the first collaboration between the Benavides (MIO) and Ronceray (CINaM) labs.

2 to 5 references related to the project

1. Boyd PW, Kennedy F. doi: 10.1038/s41564-021-01005-8
2. Smriga S, Fernandez VI, Mitchell JG, Stocker R. doi:10.1073/pnas.1512307113
3. Benavides M, Berthelot H, Duhamel S, Raimbault P, Bonnet S. doi:10.1038/srep41315
4. Frishman A, Ronceray P. doi: 10.1103/PhysRevX.10.021009
5. Polerecky L, Adam B, Milucka J, Musat N, Vagner T, Kuypers MMM. doi:10.1111/j.1462-2920.2011.02681.x.

3 main publications from each PI over the last 5 years

*equal contribution

1. Benavides, M.; Robidart, J. Bridging the Spatiotemporal Gap in Diazotroph Activity and Diversity With High-Resolution Measurements. Frontiers in Marine Science 2020, 7.
2. Benavides, M.; Conradt, L.; Bonnet, S.; Berman-Frank, I.; Barrillon, S.; Petrenko, A.; Doglioli, A. M. Fine scale sampling unveils diazotroph patchiness in the South Pacific Ocean. ISME Communications 2021, 1–6.
3. Benavides, M.; P. H. Moisander, Hugo Berthelot, Thorsten Dittmar, Olivier Grosso, and Sophie Bonnet. 2015. Mesopelagic N2 Fixation Related to Organic Matter Composition in the Solomon and Bismarck Seas (Southwest Pacific). PloS One 10 (12): 1–19.
4. Shunsuke F. Shimobayashi, Pierre Ronceray, David W. Sanders, Mikko P. Haataja, Clifford P. Brangwynne, Nucleation landscape of biomolecular condensates, Nature 599, 503-506 (2021).
5. David Brückner*, Pierre Ronceray* and Chase Broedersz, Inferring the dynamics of underdamped stochastic systeMarine snow, Phys. Rev. Lett. 125 (5), 058103.
6. Yu Long Han*, Pierre Ronceray*, Guoqiang Xu, Andrea Malandrino, Roger Kamm, Martin Lenz, Chase P Broedersz and Ming Guo, Cell contraction induces long-ranged stress stiffening in the extracellular matrix, Proc. Nat. Acad. Sci. USA, 115, 16, 4075-4080 (2018).