Competition between microbes is extremely common, with many investing in mechanisms to harm other strains and species. Yet positive interactions between species have also been documented. What makes species help or harm each other is currently unclear. Here, we studied the interactions between 4 bacterial species capable of degrading metal working fluids (MWF), an industrial coolant and lubricant, which contains growth substrates as well as toxic biocides. We were surprised to find only positive or neutral interactions between the 4 species. Using mathematical modeling and further experiments, we show that positive interactions in this community were likely due to the toxicity of MWF, whereby each species’ detoxification benefited the others by facilitating their survival, such that they could grow and degrade MWF better when together. The addition of nutrients, the reduction of toxicity, or the addition of more species instead resulted in competitive behavior. Our work provides support to the stress gradient hypothesis by showing how harsh, toxic environments can strongly favor facilitation between microbial species and mask underlying competitive interactions.

Natural microbial communities perform many functions that are crucial for human well-being. Yet we have very little control over them, and we do not know how to optimize their functioning. One idea is to breed microbial communities as we breed dogs: by comparing a set of microbiomes and allowing the best-performing ones to generate new communities, and so on. Although this idea seems simple, designing such a selection experiment brings with it many decisions with surprising outcomes. Xie and colleagues developed a computational model that reveals this complexity and shows how different experimental design decisions can impact the success of such an experiment.

1 Competition between microbes is extremely common, with 2 many investing in a wide range of mechanisms to harm 3 other strains and species. Yet positive interactions between 4 species have also been documented. What makes species 5 help or harm each other is currently unclear. Here, we stud-6 ied the interactions between four bacterial species capa-7 ble of degrading Metal-Working Fluids (MWF), an industrial 8 coolant and lubricant, which contains growth substrates as 9 well as toxic biocides. We were surprised to find only posi-10 tive or neutral interactions between the four species. Using 11 mathematical modeling and further experiments, we show 12 that positive interactions in this community are likely due 13 to the toxicity of MWF, whereby each species' detoxification 14 benefited the others by facilitating their survival, such that 15 they could grow and degrade MWF better when together. 16 The addition of nutrients, the reduction of toxicity or the 17 addition of more species instead resulted in competitive 18 behavior. Our work provides support to the stress gradi-19 ent hypothesis by showing how harsh, toxic environments 20 can strongly favor facilitation between microbial species and 21 mask underlying competitive interactions. 22 Cooperation | Competition | Mutualism | Metal Working Fluid | Stress Gradient 23 Hypothesis | Species diversity | Community function | Bacterial community 24 Correspondence: sara.mitri@unil.ch 25 82 resents a tractable model system for exploring how abiotic 83 and biotic interactions shape the ecological dynamics of mi-84 crobial communities. By quantifying MWF degradation effi-85 ciency and mapping it to species composition and their inter-86 actions, this model system can also help answer another key 87 question in microbial ecology: how do inter-species interac-88 tions affect ecosystem functioning? 89 Below, we show that when growing in MWF, facilitation 90 dominates interactions between these four species, and that 91 this is likely due to the toxicity of MWF. By making the 92 Piccardi et al. | bioRχiv | April 11, 2019 | 1-9 93 tions become competitive, in a pattern that is consistent with 94 the SGH. In turn, degradation efficiency only improves with 95 community size when the environment is toxic and interac-96 tions are positive. Our experiments shed light on how nutrient 97 and toxicity gradients modulate interactions between species 98 and community functioning. 99 Results 100 Facilitation dominates the community in MWF. We first 101 characterized the effect of each species in the MWF com-102 munity on the others. The four species were incubated alone 103 (mono-culture) or in combination with a second species (pair-104 wise co-culture) in shaken flasks containing MWF medium 105 over 12 days (see Methods). The inoculum volume for each 106 species was held constant across all conditions, i.e. the total 107 was higher in co-cultures. In mono-culture, C. testosteroni 108 was able to survive and grow in MWF, while A. tumefaciens 109 survived in some replicates, and M. sa...

There is increasing interest in artificially selecting or breeding microbial communities, but experiments have reported modest success and it remains unclear how to best design such a selection experiment. Here, we develop computational models to simulate two previously known selection methods and compare them to a new "disassembly" method that we have developed. Our method relies on repeatedly competing different communities of known species combinations against one another, and sometimes changing the species combinations. Our approach significantly outperformed previous methods that could not maintain enough between-community diversity for selection to act on. Instead, the disassembly method allowed many species combinations to be explored throughout a single selection experiment. Nevertheless, selection at the community level in our simulations did not counteract selection at the individual level. Species in our model can mutate, and we found that they evolved to invest less into community function and more into growth. Increased growth compensated for reduced investment, however, and overall community performance was barely affected by within-species evolution. Our work provides important insights that will help design community selection experiments.

The dynamics of many microbial ecosystems are driven by cross-feeding interactions, in which metabolites excreted by some species are metabolised further by others. The population dynamics of such ecosystems are governed by frequency-dependent selection, which allows for stable coexistence of two or more species. We have analysed a model of cross-feeding based on the replicator equation, with the aim of establishing criteria for coexistence in ecosystems containing three species, given the information of the three species' ability to coexist in their three separate pairs, i.e. the long term dynamics in the three two-species component systems. The triple-system is studied statistically and the probability of coexistence in the species triplet is computed for two models of species interactions. The interaction parameters are modelled either as stochastically independent or organised in a hierarchy where any derived metabolite carries less energy than previous nutrients in the metabolic chain. We differentiate between different modes of coexistence with respect to the pair-wise dynamics of the species, and find that the probability of coexistence is close to 1 2 for triplet systems with three pairwise coexistent pairs and for so-called intransitive systems. Systems with two and one pair-wise coexistent pairs are more likely to exist for random interaction parameters, but are on the other hand much less likely to exhibit triplet coexistence. Hence we conclude that certain species triplets are, from a statistical point of view, rare, but if allowed to interact are likely to coexist. This knowledge might be helpful when constructing synthetic microbial communities for industrial purposes.