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: www.mca-johnson.com

Group Leader

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

Team

Jelena Bitterli BSc Student Tel. Send Mail
Lea Caduff Technician Tel. +41 58 765 5714 Send Mail
Miao Han Guest PhD Student Tel. +41 58 765 6479 Send Mail
Sahil Oza BSc Student Tel. Send Mail
Helena Moser BSc student Tel. Send Mail
Dr. Chujin Ruan Postdoctoral fellow Tel. +41 58 765 5537 Send Mail
Janis Steiner BSc Student Tel. 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

Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion

Plasmids are the main vector by which antibiotic resistance is transferred between bacterial cells within surface-associated communities. In this study, we ask whether there is an optimal time to administer antibiotics to minimize plasmid spread in new bacterial genotypes during community expansion across surfaces. We address this question using consortia of Pseudomonas stutzeri strains, where one is an antibiotic resistance-encoding plasmid donor and the other a potential recipient. We allowed the strains to co-expand across a surface and administered antibiotics at different times. We find that plasmid transfer and transconjugant proliferation have unimodal relationships with the timing of antibiotic administration, where they reach maxima at intermediate times. These unimodal relationships result from the interplay between the probabilities of plasmid transfer and loss. Our study provides mechanistic insights into the transfer and proliferation of antibiotic resistance-encoding plasmids within microbial communities and identifies the timing of antibiotic administration as an important determinant.
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

Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion

The amount of bacterial diversity present on many surfaces is enormous; however, how these levels of diversity persist in the face of the purifying processes that occur as bacterial communities expand across space (referred to here as range expansion) remains enigmatic. We shed light on this apparent paradox by providing mechanistic evidence for a strong role of fungal hyphae-mediated dispersal on regulating bacterial diversity during range expansion. Using pairs of fluorescently labeled bacterial strains and a hyphae-forming fungal strain that expand together across a nutrient-amended surface, we show that a hyphal network increases the spatial intermixing and extent of range expansion of the bacterial strains. This is true regardless of the type of interaction (competition or resource cross-feeding) imposed between the bacterial strains. We further show that the underlying cause is that flagellar motility drives bacterial dispersal along the hyphal network, which counteracts the purifying effects of ecological drift at the expansion frontier. We finally demonstrate that hyphae-mediated spatial intermixing increases the conjugation-mediated spread of plasmid-encoded antibiotic resistance. In conclusion, fungal hyphae are important regulators of bacterial diversity and promote plasmid-mediated functional novelty during range expansion in an interaction-independent manner.
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

Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment

Spatial self-organization is a hallmark of surface-associated microbial communities that is governed by local environmental conditions and further modified by interspecific interactions. Here, we hypothesize that spatial patterns of microbial cell-types can stabilize the composition of cross-feeding microbial communities under fluctuating environmental conditions. We tested this hypothesis by studying the growth and spatial self-organization of microbial co-cultures consisting of two metabolically interacting strains of the bacterium Pseudomonas stutzeri. We inoculated the co-cultures onto agar surfaces and allowed them to expand (i.e. range expansion) while fluctuating environmental conditions that alter the dependency between the two strains. We alternated between anoxic conditions that induce a mutualistic interaction and oxic conditions that induce a competitive interaction. We observed co-occurrence of both strains in rare and highly localized clusters (referred to as “spatial jackpot events”) that persist during environmental fluctuations. To resolve the underlying mechanisms for the emergence of spatial jackpot events, we used a mechanistic agent-based mathematical model that resolves growth and dispersal at the scale relevant to individual cells. While co-culture composition varied with the strength of the mutualistic interaction and across environmental fluctuations, the model provides insights into the formation of spatially resolved substrate landscapes with localized niches that support the co-occurrence of the two strains and secure co-culture function. This study highlights that in addition to spatial patterns that emerge in response to environmental fluctuations, localized spatial jackpot events ensure persistence of strains across dynamic conditions.
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

Projects

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.

Antibiotic resistance during range expansion
Why do toxic cyanobacteria bloom? A gene to ecosystem approach...

Cyano Bloom
Microbial interactions determine the production of nitrous oxide

Causes of nitrous oxide production