Department Environmental Microbiology

Microbial Community Assembly

Research areas

Our research is inspired by the extraordinary levels of biodiversity that are typically present within microbial communities. For example, a single liter from a lake, a river, or the aeration basin of a wastewater treatment plant is estimated to contain many thousands of microbial strains and express tremendous numbers of functional traits. These extraordinary levels of biodiversity underscore two of the most profound and enigmatic questions in the discipline of microbial ecology.

  • Why are microbial communities so biodiverse? In other words, what are the mechanisms that promote these levels of biodiversity and enable the apparent co-existence of many thousands of microbial strains?
  • Is biodiversity important for the provision of a particular ecosystem service? If so, can we predict how differences or changes in biodiversity are likely to affect the provision of that ecosystem service?

We investigate the mechanisms that promote biodiversity using experimental systems. The central hypothesis is that particular metabolic processes are in biochemical conflict with each other, thus causing those processes to be more effectively performed by different microbial strains than by the same strain. One possible consequence of a biochemical conflict is the emergence of biodiversity. To test this hypothesis, we experimentally measure biochemical conflicts between different metabolic processes and track their cellular fate over evolutionary time. The ultimate goal is to improve our general understanding about how biodiversity is promoted and maintained within the natural environment.

We investigate the relationship between biodiversity and the provision of ecosystem services using environmental systems. The central hypothesis is that biodiversity is more important for the provision of specialist ecosystem services (i.e. services that are performed by only a few strains) than for generalist ecosystem services (i.e. services that are performed by many strains). To test this hypothesis, we measure the provision of many different ecosystem services in parallel and quantify their relationships with biodiversity. We then test whether the shapes of the relationships depend on the degree of specialization of each ecosystem service. The ultimate goal is to improve our general understanding about why biodiversity is more important for the provision of some ecosystem services than for others.

For more information click here:

Group Leader

Dr. David Johnson Group Leader Tel. +41 58 765 5520 Send Mail


Lea Caduff Technician Tel. +41 58 765 5714 Send Mail
Miao Han Guest PhD Student Tel. +41 58 765 6479 Send Mail
Dr. Chujin Ruan Postdoctoral fellow Tel. +41 58 765 5537 Send Mail
Deepthi Vinod PhD Student Tel. +41 58 765 6441 Send Mail
Agustina Ziliani PhD Student Tel. +41 58 765 5446 Send Mail

Selected Publications

Ma, Y.; Ramoneda, J.; Johnson, D. R. (2023) Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion, Nature Communications, 14(1), 3530 (12 pp.), doi:10.1038/s41467-023-39354-z, Institutional Repository
Ruan, C.; Ramoneda, J.; Gogia, G.; Wang, G.; Johnson, D. R. (2022) Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion, Current Biology, 32(24), 5285-5294, doi:10.1016/j.cub.2022.11.009, Institutional Repository
Ciccarese, D.; Micali, G.; Borer, B.; Ruan, C.; Or, D.; Johnson, D. R. (2022) Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment, ISME Journal, 16, 1453-1463, doi:10.1038/s41396-022-01189-9, Institutional Repository


The plasmid-mediated spread of antibiotic resistance (AR) within and between microbial communities is one of the most pressing problems facing our society, yet the causes and potential mitigation measures remain unclear.
Why do toxic cyanobacteria bloom? A gene to ecosystem approach...
Microbial interactions determine the production of nitrous oxide