Biology subjects

Scheuring, I.

Publications and source records attributed to Scheuring, I..

9 recordsLinked to original sources

bioRxiv2025

Multi-omics time-series analysis in microbiome research: a systematic review

Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and characterizing temporal variation simultaneously across multiple scales, from specific molecular interactions to entire ecosystems, is crucial for uncovering biological mechanisms and understanding the emergence of complex phenotypes. With the increasing number of studies incorporating multi-omics data sampled over time, it has become clear that integrated approaches are pivotal for these efforts. However, standard data analytical practices in longitudinal multi-omics are still shaping up and many of the available methods have not yet been widely evaluated and adopted. Thus, we performed a systematic literature review on data science methods for longitudinal multi-omics, with a particular focus on microbiome research.

bioinformatics↗

bioRxiv2025

Invaders' trophic position and their direct and indirect relationship influence on resident food webs

Many ecosystems are undergoing simultaneous colonization and spread of multiple alien species. Invaders often negatively affect communities by reducing population sizes of resident species or even decreasing community diversity through extinctions. Direct and indirect interactions between them can amplify or mitigate their impacts on native communities. In this study, we compare the effects of two invaders on the resident model food webs under two scenarios: separate versus simultaneous invasion. We examined the resident food webs response from two perspectives: the number of extinct species as a measure of diversity loss, and the net change in total biomass of the food web. Using dynamic simulations based on the Allometric Bioenergetic Model, we tracked these changes in silico and compared the results of the two scenarios. We examined how the invaders trophic positions relative to each other and their direct/indirect interactions influence the additive or non-additive nature of the outcomes of their co-invasion. Our results have corroborated previous field and experimental observations, showing that when co-occurring invaders occupy different trophic levels, their combined effects may be dampened if one invader preys on the other. Further, we have shown that the probability of synergistic effect increases when invaders form a trophic cascade or share a common predator. However, we have also shown that all of these relationships are influenced by i) the metric used to track changes in the resident community, ii) the trophic level at which the invasion occurs, and iii) whether the invader has a predator (either resident or another invader). HighlightsO_LIThe impact of a joint invasion on the resident community depends on the used metric C_LIO_LIAdditivity of the co-invasions impact is influenced by the invaders trophic position C_LIO_LIThe effects of the invaders direct/indirect interactions depend on the trophic level C_LIO_LIInvaders in top position have stronger effects than those of intermediate position C_LI

ecology↗

bioRxiv2024

Effects of joint invasion: how co-invaders affect each other's success in model food webs?

While there is considerable research on interactions between invasive and native species, as well as on the impact of invasive species on the resident community, less focus has been placed on exploring the relationship and interactions among invasive species themselves. Nevertheless, it is widely acknowledged that invasive species can have either positive or negative effects on one anothers success, in addition to neutral outcomes. In the present theoretical study, we compared the success of two invasive non-native species in two scenarios: when they invaded the resident food web separately and simultaneously. We investigated the correlations between their direct and indirect ecological relationships and the topological positions of them in the food web, with the varying outcomes of joint invasion. Using the allometric bioenergetic model (ABM) for dynamical simulations, we detected the success of invasion (presence or absence of invaders) and the direction of their biomass change comparing separated and simultaneous invasion scenarios. We studied the relationships among these variables after detailed numerical simulations with variable key parameters of the model. We found that direct and indirect ecological relationships between the two invaders are significantly modifies the invasion scenarios: the predator-prey relationship increases the probability of invasion success for both invaders, but the equilibrium biomass of at least one of them is more likely to be reduced than in separate invasions. The trophic cascade or competitive relationship between them during simultaneous invasion also affects their success rate, with the former having a positive effect and the latter a negative one. Further, we found that higher trophic level and lower betweenness centralities of the invaders reduces the likelihood of invasion success regardless of the presence or absence of another invasive species. The results of the study can be tested experimentally in micro- and mesocosms. HIGHLIGHTSO_LIIn a joint invasion, invaders can influence each others success C_LIO_LIPredator-prey relationships between invaders increase the joint invasion success C_LIO_LICompetition increases the failure of at least one invader C_LIO_LIThe trophic cascade between invaders increases the joint invasion success C_LIO_LIHigher trophic levels or lower betweenness centralities of the invaders increase the probability of unsuccessful joint invasion C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/573872v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1b3638eorg.highwire.dtl.DTLVardef@4d1f47org.highwire.dtl.DTLVardef@1409573org.highwire.dtl.DTLVardef@113dfd2_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2023

Threshold public goods game in well mixed populations: Cooperation in density independent and density dependent cases

The threshold public goods game is one of the best-known models of nonlinear public goods dilemmas. Cooperators and defectors typically coexist in this game when the population is assumed to follow the so-called structured deme model. In this paper we develop a dynamical model of a general N-player game in which there is no deme structure: individuals interact with randomly chosen neighbours and selection occurs between randomly chosen pairs of individuals. We show that in the deterministic limit the dynamics in this model leads to the same replicator dynamics as in the structured deme model, i.e. coexistence of cooperators and defectors is typical in threshold public goods game even when the population is completely well-mixed. We extend the model to study the effect of density dependence and density fluctuation on the dynamics. We show analytically and numerically that decreasing population density increases the equilibrium frequency of cooperators till the fixation of this strategy, but below a critical density cooperators abruptly disappear from the population. Our numerical investigations show that weak density fluctuations enhance cooperation, while strong fluctuations suppress it. HighlightsO_LIThe dynamics of threshold dilemma game in a well-mixed population. C_LIO_LIFluctuation of density can help or suppress cooperation. C_LIO_LICooperation is more pronounced at lower density. C_LIO_LICooperation abruptly disappears below a critical density level. C_LI

evolutionary biology↗

bioRxiv2023

Cue-driven microbial cooperation and communication: evolving quorum sensing with honest signalling.

BackgroundQuorum sensing (QS) is the ability of microorganisms to assess local clonal density by measuring the extracellular concentration of signal molecules that they produce and excrete. QS is also the only known way of bacterial communication that supports the coordination of within-clone cooperative actions requiring a certain threshold density of cooperating cells. Cooperation aided by QS communication is sensitive to cheating in two different ways: laggards may benefit from not investing in cooperation but enjoying the benefit provided by their cooperating neighbors, whereas Liars explicitly promise cooperation but fail to do so, thereby convincing potential cooperating neighbors to help them, for almost free. Given this double vulnerability to cheats, it is not trivial why QS-supported cooperation is so widespread among prokaryotes. ResultsWe investigated the evolutionary dynamics of QS in populations of cooperators for whom the QS signal is an inevitable side effect of producing the public good itself (cue-based QS). Using spatially explicit agent-based lattice simulations of QS-aided threshold cooperation (whereby cooperation is effective only above a critical cumulative level of contributions) and three different (analytical and numerical) approximations of the lattice model we explored the dynamics of QS-aided threshold cooperation under a feasible range of parameter values. We demonstrate three major advantages of cue-driven cooperation. First, laggards cannot wipe out cooperation under a wide range of reasonable environmental conditions, in spite of an unconstrained possibility to mutate to cheating; in fact, cooperators may even exclude laggards at high cooperation thresholds. Second, lying almost never pays off, if the signal is an inevitable byproduct (i.e., the cue) of cooperation; even very cheap fake signals are selected against. And thirdly, QS is most useful if local cooperator densities are the least predictable, i.e., if their lattice-wise mean is close to the cooperation threshold with a substantial variance. ConclusionsComparing the results of the four different modelling approaches indicates that cue-driven threshold cooperation may be a viable evolutionary strategy for microbes that cannot keep track of past behavior of their potential cooperating partners, in spatially viscous and in well-mixed environments alike.

ecology↗

bioRxiv2020

Density-dependent private benefit leads to bacterial mutualism

Microorganisms produce materials leaked from the cell which are beneficial for themselves and their neighbors. We modeled the situation when cells can produce different costly secretions which increase the carrying capacity of the population. Strains that lose the function of producing one or more secretions avoid the cost of production and can exhaust the producers. However, secreting substances provides a private benefit for the producers in a density-dependent way. We developed a model to examine the outcome of the selection among different type of producer strains from the non-producer strain to the partial producers, to the full producer one. We were particularly interested in circumstances under which selection maintains partners that produce complementary secreted materials thus forming an interdependent mutualistic interaction. We show that interdependent mutualism is selected under broad range of conditions if private benefit decreases with density. Selection frequently causes the coexistence of more and less generalist cooperative strains, thus cooperation and exploitation co-occur. Interdependent mutual-ism is evolved under more specific circumstances if private benefit increases with density and these general observations are valid in a well-mixed and in a structured deme model. We show that the applied population structure supports cooperation in general, which, depending on the level of private benefit and intensity of mixing helps either the specialist or the generalist cooperators.

evolutionary biology↗

bioRxiv2019

Dispersal behaviour as the outcome and trigger of multilevel selection in a social spider

The facultatively social spider Anelosimus studiosus offers a unique opportunity for understanding how multilevel selection acts in natural populations. However, the importance of previous empirical studies are shaded by a conceptual debate about whether colony-level selection is truly present in these populations or not. Here we introduce a detailed individual based model, where practically all assumptions are supported by empirical data. The only element of the female A. studiosus life cycle missing from the literature is how maturing female spiders decide whether to disperse. This behavioural component we estimate with evolutionary simulations. This model is able to recapitulate the characteristic size and composition distributions of natural populations in different environments. The evolutionary simulations revealed that the optimal dispersal behaviour of a maturing female varies both with her ecological environment and behavioural phenotype. This finding is open for straightforward empirical testing. In agreement with empirical findings we have established parameter ranges where the population is prone to extinction without multiple-female nests. We propose that the dispersal behaviour of individuals is both the result and the prerequisite of multilevel selection in this species.

evolutionary biology↗

bioRxiv2018

Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability

Understanding the mechanisms promoting the assembly and maintenance of host-beneficial microbiomes is an open problem. An increasing amount of evidence supports the idea that animal and plant hosts can use private resources and the ecological phenomenon known as community bistability to favour some microbial strains over others. We briefly review empirical evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotic compounds to suppress non-beneficial, competitor strains, and (iii) provide resources (for a limited time) that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. By explicitly modelling localized microbial interactions and diffusion dynamics, we further show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that that there is a wide range of conditions under which hosts can promote the assembly of a self-sustaining defensive microbiome. This, in turn, supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes.

microbiology↗

bioRxiv2018

Experimental demonstration that screening can enable the environmental recruitment of a defensive microbiome

Many animals and plants recruit beneficial microbes from the environment, enhancing their defence against pathogens. However, we have only a limited understanding of the assembly mechanisms involved. A game-theoretical concept from economics, screening, potentially explains how a host selectively recruits mutualistic microbes from the environment by fomenting and biasing competition among potential symbionts in such a way that the more likely winners are antibiotic producers. The cuticular microbiomes of Acromyrmex leaf-cutting ants inspired one of the first applications of screening theory, and here we simulate this system in vitro to test screening. On agar infused with antibacterial metabolites from Acromyrmexs vertically transmitted Pseudonocardia bacteria, we show that antibiotic-producing Streptomyces bacteria exhibit higher growth rates than do non-antibiotic-producer strains and are more likely to win in direct competition. Our results demonstrate how game-theoretical concepts can provide powerful insight into host-microbiome coevolution.

evolutionary biology↗