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

Lea Caduff Technician Tel. +41 58 765 5714 Send Mail
Dr. Sema Karakurt-Fischer Tel. +41 58 765 5980 Send Mail
Takahashi Kohei Guest Ph.D Student Tel. +41 58 765 6875 Send Mail
Dr. Chujin Ruan Postdoctoral fellow Tel. +41 58 765 5537 Send Mail
Gaétane Sallard Bachelor Student Tel. +41 58 765 5920 Send Mail
Anna Sassara Tel. Send Mail
Philipp Tandler Tel. +41 58 765 5920 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

Spatial organization in microbial range expansion emerges from trophic dependencies and successful lineages

Evidence suggests that bacterial community spatial organization affects their ecological function, yet details of the mechanisms that promote spatial patterns remain difficult to resolve experimentally. In contrast to bacterial communities in liquid cultures, surface-attached range expansion fosters genetic segregation of the growing population with preferential access to nutrients and reduced mechanical restrictions for cells at the expanding periphery. Here we elucidate how localized conditions in cross-feeding bacterial communities shape community spatial organization. We combine experiments with an individual based mathematical model to resolve how trophic dependencies affect localized growth rates and nucleate successful cell lineages. The model tracks individual cell lineages and attributes these with trophic dependencies that promote counterintuitive reproductive advantages and result in lasting influences on the community structure, and potentially, on its functioning. We examine persistence of lucky lineages in structured habitats where expansion is interrupted by physical obstacles to gain insights into patterns in porous domains.
Borer, B.; Ciccarese, D.; Johnson, D.; Or, D. (2020) Spatial organization in microbial range expansion emerges from trophic dependencies and successful lineages, Communications Biology, 3(1), 685 (10 pp.), doi:10.1038/s42003-020-01409-y, Institutional Repository

A brief guide for the measurement and interpretation of microbial functional diversity

The importance of functional diversity for the functioning and behaviour of microbial communities is clear, yet the widespread incorporation of functional diversity measurements into environmental microbiology study designs remains surprisingly limited. This may, at least to some extent, be a consequence of the unique conceptual and methodological challenges to measuring functional diversity in microbial communities. To facilitate the increased incorporation of functional diversity measurements into environmental microbiology study designs, we review here the process and some key caveats for measuring functional diversity and provide specific examples. We highlight three main decision points and provide guidance to making these decisions based on the underlying mechanisms for how functional diversity relates to an ecosystem process or property of interest. We discuss the selection of an appropriate type of functional trait, selection of the specificity at which functional diversity will be measured, and selection of an appropriate metric for estimating functional diversity from quantitative measures of those traits. We further discuss decisions regarding the use of one- or multi-dimensional measures of functional diversity and how advances in the field of trait-based community ecology could be applied or adapted to address questions in environmental microbiology.
Johnson, D. R.; Pomati, F. (2020) A brief guide for the measurement and interpretation of microbial functional diversity, Environmental Microbiology, 22(8), 3039-3048, doi:10.1111/1462-2920.15147, Institutional Repository

Interaction-dependent effects of surface structure on microbial spatial self-organization

Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization. Using pairs of isogenic strains of Pseudomonas stutzeri, we performed range expansion experiments in the absence or presence of physical objects and quantified the effects on spatial self-organization. We demonstrate that physical objects create local deformities along the expansion frontier, and these deformities increase in magnitude during range expansion. The deformities affect the densities of interspecific boundaries and diversity along the expansion frontier, and thus affect spatial self-organization, but the effects are interaction-dependent. For competitive interactions that promote sectorized patterns of spatial self-organization, physical objects increase the density of interspecific boundaries and diversity. By contrast, for cross-feeding interactions that promote dendritic patterns, they decrease the density of interspecific boundaries and diversity. These qualitatively different outcomes are probably caused by fundamental differences in the orientations of the interspecific boundaries. Thus, in order to predict the effects of physical objects on spatial self-organization, information is needed regarding the interactions present within a community and the general geometric shapes of spatial self-organization that emerge from those interactions.
This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
Ciccarese, D.; Zuidema, A.; Merlo, V.; Johnson, D. R. (2020) Interaction-dependent effects of surface structure on microbial spatial self-organization, Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1798), 20190246 (11 pp.), doi:10.1098/rstb.2019.0246, Institutional Repository

Relating metatranscriptomic profiles to the micropollutant biotransformation potential of complex microbial communities

Biotransformation of chemical contaminants is of importance in various natural and engineered systems. However, in complex microbial communities and with chemical contaminants at low concentrations, our current understanding of biotransformation at the level of enzyme-chemical interactions is limited. Here, we explored an approach to identify associations between micropollutant biotransformation and specific gene products in complex microbial communities, using association mining between chemical and metatranscriptomic data obtained from experiments with activated sludge grown at different solid retention times. We successfully demonstrate proportional relationships between the measured rate constants and associated gene transcripts for nitrification as a major community function, but also for the biotransformation of two nitrile-containing micropollutants (bromoxynil and acetamiprid) and transcripts of nitrile hydratases, a class of enzymes that we experimentally confirmed to produce the detected amide transformation products. As these results suggest that metatranscriptomic information can indeed be quantitatively correlated with low abundant community functions such as micropollutant biotransformation in complex microbial communities, we proceeded to explore the potential of association mining to highlight enzymes likely involved in catalyzing less well-understood micropollutant biotransformation reactions. Specifically, we use the cases of nitrile hydration and oxidative biotransformation reactions to show that the consideration of additional experimental evidence (such as information on biotransformation pathways) increases the likelihood of detecting plausible novel enzyme-chemical relationships. Finally, we identify a cluster of mono- and dioxygenase fourth-level enzyme classes that most strongly correlate with oxidative micropollutant biotransformation reactions in activated sludge.
Achermann, S.; Mansfeldt, C. B.; Müller, M.; Johnson, D. R.; Fenner, K. (2020) Relating metatranscriptomic profiles to the micropollutant biotransformation potential of complex microbial communities, Environmental Science and Technology, 54(1), 235-244, doi:10.1021/acs.est.9b05421, Institutional Repository

Projects

Fate of antibiotic resistance during microbial range expansion

Antibiotic resistance during range expansion
A general barcoding approach to monitor invasive populations

Microbial invasion demographics
Microbial interactions determine the production of nitrous oxide

Causes of nitrous oxide production