System efficiency of microbial consortia

Jakob Pernthaler

Alizée Le Moigne

Owen Petchey

Samuel Abivan


The carbon utilization efficiency (CUE) of microbial systems is related to microbial biomass production, respiration, and the transfer losses between trophic levels. CUE has gained importance in understanding global microbial CO2 emissions, and related concepts, such as substrate degradation efficiency, play a role in environmental engineering. The project will explore the hypothesis that CUE is also related to the specific interactions between microbial taxa, and that identical growth conditions may, therefore, result in assemblages with vastly different CUEs. It is suggested that functional redundancy and stochastic community assembly processes will allow for multiple self-stabilizing interaction networks.


The above questions will be studied in experimental consortia generated from freshwater microbial inocula. Knowledge about aquatic habitats will guide the design of microcosms with defined non-trivial growth conditions. Initially, the project will investigate the context that maximizes the functional differences between sets of microbial consortia with respect to biomass production and degradation of a recalcitrant substrate the above response variables: It will be tested if particular environmental settings (albeit within the overall design limits of the experimental microcosms) select for a higher intrinsic variation of community efficiency than others. The impact of the composition of the original community for the efficiency properties of the derived assemblages will be assessed by using inocula from different vertical zones of a single lake (epi-, hypolimnion), from different seasons, and potentially from a variety of other freshwater systems. Moreover, a labile substrate source will be offered at various flux rates in order to simulate different levels of primary productivity, thereby pushing the community assembly process towards stochasticity. Another set of treatments will investigate the effect of stable vs. pulsed availability of the labile substrate source on the variability of system efficiency. Finally, the presence or absence of predators on the variance of community assembly will be compared by selective pre-filtration of the inocula.

Subsequent focus will be put on a single growth scenario that leads to the stochastic establishment of experimental assemblages with greatly varying system efficiency and presumably genotypic composition. Only a subset of the so produced consortia will be further studied, i.e., those assemblages that represent the highest/lowest percentiles of the system efficiency distribution. A set of ‘biotic’ manipulations will be performed on the experimental assemblages with the aim of elucidating, altering or disrupting the interactions networks that underly the observed system efficiency. In the simplest case, the diversity of consortia will be rarefied by dilution to assess the role of rare community members. The ‘breeding’ of consortia with high and low efficiency will allow to investigate the resistance, resilience or ‘reshuffling’ of interaction networks. In a similar fashion, consortia will be exposed to invasion by isolates from other consortia, to a model predator, or to the removal of predation via filtration. A second set of treatments will manipulate the growth conditions in terms of substrate flux and stability, in order to assess the resilience and resistance of more or less efficient microbial assemblages and their possible transformation to a different system state. In addition, isolates will be collected from these consortia. Experiments with defined co-cultures of these isolates will be performed to address specific hypotheses about functional interaction networks that arise during the investigation of the consortia. It will also be tested if the overall system efficiency of whole consortia can be reproduced or even enhanced by co-cultivating a limited number of strains from these consortia.