Discovering data‐driven microbial growth models with symbolic regression

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Evolution induced state shifts in a long-term microbial community experiment | PNAS

Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain p...

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Universal bacterial clade dynamics dominate under predation despite altered phenotypes and mutation targets

Abstract. Recent studies have revealed bacterial genome-wide evolution to be complex and dynamic even in a constant environment, characterized by the emerg

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Ecological tristability driven by total carbon availability over resource complexity in a synthetic microbial community

Even though complex microbial communities are ubiquitous and provide essential services for natural and human-associated ecosystems, our knowledge about their assembly and dynamics is incomplete. There is an ongoing debate whether the behavior of complex communities can be predicted from the outcome of pairwise competition of species, and whether communities reach alternative stable states depending on the level and complexity of resource provided for growth. To estimate the effect of two resource gradients, total carbon availability and resource complexity, on the compositional dynamics of a complex microbial community, we conducted a 16-day serial passage experiment, transferring a 16-species synthetic community in 96 different resource environments. We observed that although both resource dimensions influenced community composition, total carbon exerted a considerably larger effect. Additionally, we saw the emergence of a tristable pattern along the total carbon gradient, a feature not observed for the resource complexity gradient. Using monoculture assays, we identified lag phase duration as the dominant predictor of competitive success at carbon extremes, with maximum growth rate increasing in importance as lag times converged. Total carbon availability thus structured community state transitions and regulated which growth trait governed competitive sorting. These results suggest the importance of total carbon level over resource complexity and identifying dominant species for the quest to successfully manage, maintain and manipulate complex microbial communities. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, https://ror.org/00yjd3n13, P500PB_214345 Knut and Alice Wallenberg Foundation, KAW 2024.0159 Jenny ja Antti Wihurin Rahasto, 00250005 Finnish Cultural Foundation, 85241664 Research Council of Finland, 346126, 364232

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Environmental heterogeneity determines evolutionary pathways to species coexistence

A cornerstone of biology is that species interactions drive evolution of niche divergence, thereby maintaining biodiversity. Yet controlled experiments consistently find evolution of competitive-abili...

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Normative assembly rule reveals fairness in microbial communities

Understanding and predicting how communities assemble is a paramount challenge in ecology. Here we address these questions normatively by comparing the ecological distribution of growth surplus to a g...

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Evolution induced state shifts in a long-term microbial community experiment

Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evoluti...

biorxiv.org

Professor or Assistant / Associate (tenure track) Professor in Plant Ecology

The Faculty of Science is looking for a full professor or assistant/associate professor (tenure track) in Plant Ecology. The aim of the professorship is to strengthen scientific research and education...

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Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto - Työpaikat - Duunitori

Avoin työpaikka: Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto, Turku. Duunitorilla lisäksi yli 30 000 muuta avointa työpaikkaa. Lue lisää nyt!

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Doctoral Researcher / Project researcher in Experimental Evolution of Host–Microbiota Interactions

The Faculty of Science at the University of Turku invites applications for a doctoral researcher / project researcher position at the Department of Biology. The position is fully funded 4-years. Emplo...

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Doctoral Researcher / Project researcher in Experimental Evolution of Host–Microbiota Interactions

The Faculty of Science at the University of Turku invites applications for a doctoral researcher / project researcher position at the Department of Biology. The position is fully funded 4-years. Emplo...

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Universal bacterial clade dynamics dominate under predation despite altered phenotypes and mutation targets

Recent studies have revealed bacterial genome-wide evolution to be complex and dynamic even in a constant environment. The evolution is characterized by the emergence of new clades competing or tempor...

biorxiv.org

Pre-exposure to disturbance enhances species resilience and protects from change - Nature Ecology & Evolution

In a serial passage experiment with a 23-species model microbial community, we found that higher dispersal led to stronger spread of the effects of antibiotic disturbance across a metacommunity. This ...

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Pre-exposure of abundant species to disturbance improves resilience in microbial metacommunities

Nature Ecology & Evolution - Community resilience to stress is affected by factors such as pre-exposure to the same stress and intercommunity dispersal. The authors show that pre-exposing the...

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Temporal Changes in the Role of Species Sorting and Evolution Determine Community Dynamics

Evolutionary change within community members and shifts in species composition contribute to community and trait dynamics. To integrate when and how both processes structure communities, we estimated...

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