aquaticmicrobes

Aquatic microbial ecology · Biophysics

Johannes Keegstra

I study how bacteria live, move, and cooperate at the scale of a single cell — in the water of lakes and seas.

Newton Research Fellow, Queen Mary University of London — becoming a Lecturer and starting my own group in 2028. Previously a senior researcher at ETH Zurich.

I'm an experimental biophysicist and computational microbiologist. My work sits at the border between microbial ecology and microbial physiology: I want to understand why individual bacteria behave the way they do, and how those decisions — made cell by cell — add up to the structure and function of whole aquatic communities.

To watch this happen I use microfluidics and live single-cell microscopy, following bacteria one at a time as they swim, sense their surroundings, feed, and interact. It's a way of seeing behaviour that averaged, population-level measurements tend to hide.

What I work on

Research

01 — Behaviour

How a single cell decides to move

Swimming is powerful but costly. I study the motility, chemotaxis, and foraging of aquatic bacteria — how they navigate toward food and when it's worth the energy to do so. This led to a risk–reward trade-off that splits marine bacteria into distinct search strategies, and, more broadly, to a quantitative movement ecology of micro-organisms.

02 — Communities

How microbes interact and assemble

Bacteria rarely live alone. In my new work at Queen Mary I'm studying the interactions between a freshwater cyanobacterium and the heterotrophic bacteria that live alongside it — who feeds whom, who survives starvation, and how communities assemble from these encounters across lakes and seas.

03 — Methods

Watching cells one at a time

Much of my work is about building the right instrument. I develop microfluidic "on-a-chip" devices and single-cell FRET imaging to observe living communities directly, and I use the physics of signalling networks — including near-critical cooperativity in the bacterial chemosensory array — to understand what cells can and can't sense.

Selected work

Publications

  1. 2025

    Risk–reward trade-off in motility endurance generates dichotomy in search strategies among copiotrophic marine bacteria J. M. Keegstra, Z. C. Landry, S. Zweifel, B. Roller, D. Baumgartner, F. Carrara, C. Martínez-Pérez, E. Clerc, M. Ackermann, R. Stocker. Nature Microbiology 10, 1393–1403. Behind the paper: To swim or not to swim

  2. 2026

    Spontaneous switching in a protein signalling array reveals near-critical cooperativity J. M. Keegstra, F. Avgidis, E. Usher, Y. Mullah, J. S. Parkinson, T. S. Shimizu. Nature Physics 22, 452–460. Behind the paper: A critical sense of smell

  3. 2022

    The ecological roles of bacterial chemotaxis J. M. Keegstra, F. Carrara, R. Stocker. Nature Reviews Microbiology 20, 491–504.Review

  4. 2023

    Interspecies interactions determine growth dynamics of biopolymer-degrading populations in microbial communities G. D'Souza, J. Schwartzman, J. M. Keegstra, J. E. Schreier, M. Daniels, O. Cordero, R. Stocker, M. Ackermann. PNAS 120(44), e2305198120.

  5. 2026

    Stochastic resilience enables particle foraging in oligotrophic environments V. I. Fernandez, N. Blitvic, J. M. Keegstra, R. Stocker. PNAS 123(11), e2508238123.

  6. 2017

    Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET J. M. Keegstra, F. Anquez, M. D. Lazova, K. Kamino, T. Emonet, T. S. Shimizu. eLife 6, e27455.

Path here

About

I trained as a physicist at Delft University of Technology before moving into biophysics for my PhD at the AMOLF institute in Amsterdam, where I built single-cell FRET methods to watch signalling inside individual bacteria.

As a postdoc and then senior researcher in Roman Stocker's Environmental Microfluidics group at ETH Zurich, I turned to the sea — using microfluidics to follow how marine bacteria find, colonise, and break down sinking particles, and how their motility shapes the communities that form. In August 2026 I joined Queen Mary University of London as a Newton Research Fellow, where my questions have broadened from the ocean to aquatic systems more generally, freshwater lakes included. From 2028 I'll continue there as a Lecturer, building my own group.

Microfluidics Live single-cell microscopy In vivo FRET Image analysis Stochastic simulation Python · MATLAB

Away from the bench

Favourite waters

Most of the world's population lives along a coast or close to a lake — we have always settled near water. These are my favourite water bodies, and each one connects back to the science.

Waves on the sandy North Sea coast under a bright sky
North Sea · Dutch coast

The North Sea

I grew up a few kilometres from the North Sea, and what I miss most is its everlasting wind — and the herring, the one thing I still crave from the Netherlands. Almost everything else you notice on that coast is really microbes at work: the briny smell of the sea is mostly dimethyl sulfide, a gas made by marine microorganisms, and the foam whipped up in the surf is organic matter released by blooms of algae and bacteria.

Narrowboats moored on the leafy Regent's Canal in London
Regent's Canal · London

Regent's Canal

The canal runs beside Queen Mary's Mile End campus and threads across the city, from Little Venice to the Thames at Limehouse. It's a favourite of runners and cyclists, a fine place to walk, and the commute route of a lucky few. I love it as an everyday piece of urban freshwater — a reminder that aquatic microbial life belongs to cities as much as to oceans.

A jetty on Lake Zürich with the city and hills beyond
Lake Zürich · Switzerland

Lake Zürich

Lake Zürich is an optimistic story. Through the twentieth century, phosphorus from the city's sewage and detergents tipped it into eutrophication — the deep water losing oxygen, and the cyanobacterium Planktothrix rubescens tinting autumn blooms a burgundy red. Switzerland's response — wastewater treatment across the whole catchment and cutting phosphate at the source — turned it around. Today it is clean enough to supply drinking water to hundreds of thousands of people, and clear enough to swim in from the middle of the city.

Photographs © Johannes Keegstra.

Get in touch

Contact

I'm always glad to talk about aquatic microbes and the questions behind this work. If your research touches on any of it, or you'd simply like to get in touch, do send a note.

Queen Mary University of London · School of Biological and Behavioural Sciences