Biology subjects

Ratzke, C.

Publications and source records attributed to Ratzke, C..

8 recordsLinked to original sources

bioRxiv2025

Emergent loss of microbial biodiversity with increasing resource diversity

The origin of biodiversity is arguably the most fundamental question in ecology -- especially how countless microbial species coexist within a single community. A prevailing hypothesis holds that microbial species coexist by specializing on different resources, thereby reducing competition. Accordingly, increasing resource diversity is expected to promote species coexistence and boost biodiversity. Surprisingly, we observe the opposite: microbial biodiversity often declines as resource diversity increases. This unexpected result emerges from a widespread physiological response across diverse microbial taxa, in which more complex environments trigger higher overall resource uptake. This intensifies competition and drives biodiversity loss. Updating a central ecological model to include this physiological trait accurately reproduces the observed decline. Our findings demonstrate that physiological changes at the individual level can overturn classical ecological principles and scale up to restructure entire ecosystems.

microbiology↗

bioRxiv2024

Biotic resistance predictably shifts microbial invasion regimes

Invading new territory is a central aspect of the microbial lifestyle, allowing microbes to expand to remote locations and pathogens to spread and infect their hosts. However, invading microbes rarely find novel territories uninhabited. In such a scenario, resident microbes can interact with the newcomers and, in many cases, impede their invasion - an effect known as biotic resistance. Accordingly, invasions are shaped by the interplay between dispersal and resistance. However, these two factors are difficult to disentangle or manipulate in natural systems, making their interplay difficult to understand. To address this challenge, we tracked microbial invasions in the lab over space and time - first in a model system of two interacting microbes, then in a multi-strain system involving a pathogen invading resident communities. In the presence of biotic resistance, we observed three qualitatively different invasion regimes: consistent, pulsed, and pinned, where, in the third regime, strong biotic resistance stalled the invasion entirely despite ongoing invader dispersal. Surprisingly, these rich invasion dynamics could be qualitatively predicted with a simple, parameter-free framework that ignores individual species interactions, even for rather complex communities. Moreover, we showed that this simple framework could accurately predict simulated invasions from different mechanistic models, indicating its broad applicability. Our work offers a thorough understanding of how biotic resistance impacts invasions and introduces a predictive tool to identify invasion-resistant communities.

systems biology↗

bioRxiv2024

Environment-mediated interactions cause an externalized and collective memory in microbes

Microbes usually live in complex communities interacting with many other microbial species. These interactions determine who can persist in a community and how the overall community forms and functions. Microbes often exert interactions by chemically changing the environment, like taking up nutrients or producing toxins. These environmental changes can persist over time. We show here that such lasting environmental changes can cause a memory effect where current growth conditions alter interaction outcomes in the future. Importantly, this memory is only stored in the environment and not inside the bacterial cells. Only the collective effort of many bacteria can build up this memory, making it an emergent property of bacterial populations. This "population memory" can also impact the assembly of more complex communities and lead to different final communities depending on the systems past. Overall, we show that to understand interaction outcomes fully, we not only have to consider the interacting species and abiotic conditions but also the systems history.

systems biology↗

bioRxiv2022

A taste for numbers: Caenorhabditis elegans foraging follows a low-dimensional rule of thumb

Rules of thumb are behavioral algorithms that approximate optimal behavior while lowering cognitive and sensory costs. One way to reduce these costs is by reducing dimensionality: While the theoretically optimal behavior may depend on many environmental variables, a rule of thumb may use a low-dimensional combination of variables that performs reasonably well. Experimental proof of a dimensionality reduction requires an exhaustive mapping of all relevant combinations of several environmental parameters, which we performed for Caenorhabditis elegans foraging by covering all combinations of food density (across 4 orders of magnitude) and food type (across 12 bacterial strains). We found a one-dimensional rule: Worms respond to food density measured as number of bacteria per unit surface, disregarding other factors such as biomass content or bacterial strain. We also measured fitness experimentally, determining that the rule is near-optimal and therefore constitutes a rule of thumb that leverages the most informative environmental variable.

animal behavior and cognition↗

bioRxiv2019

Strength of species interactions determines biodiversity and stability in microbial communities

Organisms - especially microbes - tend to live in complex communities. While some of these ecosystems are very bio-diverse, others arent1-3, and while some are very stable over time others undergo strong temporal fluctuations4,5. Despite a long history of research and a plethora of data it is not fully understood what sets biodiversity and stability of ecosystems6,7. Theory as well as experiments suggest a connection between species interaction, biodiversity, and stability of ecosystems8-13, where an increase of ecosystem stability with biodiversity could be observed in several cases7,9,14. However, what causes these connections remains unclear. Here we show in microbial ecosystems in the lab that the concentrations of available nutrients can set the strength of interactions between bacteria. At high nutrient concentrations, extensive microbial growth leads to strong chemical modifications of the environment, causing more negative interactions between species. These stronger interactions exclude more species from the community - resulting in a loss of biodiversity. At the same time, these stronger interactions also decrease the stability of the microbial communities, providing a mechanistic link between species interaction, biodiversity and stability.

ecology↗

bioRxiv2019

Transient invaders can induce shifts between alternative stable states of microbial communities

Microbial dispersal often leads to the arrival of outsider organisms into ecosystems. When their arrival give rise to successful invasions, outsider species establish within the resident community, which can dramatically alter the ecosystem. Seemingly less influential, the potential impact of unsuccessful invaders that interact only transiently with the community has remained largely ignored. Here, we experimentally demonstrate that such transient invasions can perturb the stability of microbial ecosystems and induce a lasting transition to an alternative stable state, even when the invader species itself does not survive the transition. First, we develop a mechanistic understanding of how environmental changes caused by such transient invaders can drive a community shift in a simple, bistable model system. Beyond this, we show that transient invaders can also induce switches between stable states in more complex communities isolated from natural soil samples. Our results demonstrate that short-term interactions with an invader species can induce lasting shifts in community composition and function.\n\nOne Sentence SummaryTransient invaders can cause lasting shifts in community composition and function.

ecology↗

bioRxiv2017

Ecological suicide in microbes

The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment, such as the cooperative breakdown of complex nutrients in microbes [1]-[3] or the construction of elaborate architectures in social insects [4]. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them, eg by resource depletion or the production of toxic byproducts [5]. Here we find an extreme type of negative interactions, in which bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon we call ecological suicide. Modification of the pH is more pronounced at higher population densities, and thus ecological suicide is more likely with increasing bacterial density. Correspondingly, promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances - like antibiotics - can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We find ecological suicide in a wide variety of microbes, suggesting that it could play a significant role in microbial ecology and evolution.

systems biology↗

bioRxiv2017

Modifying And Reacting To The Environmental pH Drives Bacterial Interactions

Microbes usually exist in communities consisting of myriad different but interacting species. These interactions are typically mediated through environmental modifications; microbes change the environment by taking up resources and excreting metabolites, which affects the growth of both themselves and also other microbes. A very common environmental modification is a change of the environmental pH. Here we show that changing and reacting to the pH leads to a feedback loop that can determine the fate of bacterial populations. We find experimentally that these pH changes can decide the fate of bacterial populations; they can either facilitate or inhibit growth, and in extreme cases will cause extinction of the bacterial population. Moreover, modifying the pH can determine the interactions between different species. Understanding how single species change the pH and react to it allowed us to estimate their pairwise interaction outcomes. Those interactions lead to a set of generic interaction motifs--bistability, succession, murder suicide, and mutualism--that may be independent of which environmental parameter is modified and thus reoccur in different microbial systems.

microbiology↗