Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship.

The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.

A Stochastic Mobility-Driven Spatially Explicit SEIQRD covid-19 Model with VOCs, Seasonality, and Vaccines.

In this work, we extend our previously developed compartmental SEIQRD model for sars-cov-2 in Belgium. We introduce sars-cov-2 variants of concern, vaccines, and seasonality in our model, as their addition has proven necessary for modelling sars-cov-2 transmission dynamics during the 2020-2021 covid-19 pandemic in Belgium. The model is geographically stratified into eleven spatial patches (provinces), and a telecommunication dataset provided by Belgium's biggest operator is used to incorporate interprovincial mobility. We calibrate the model using the daily number of hospitalisations in each province and serological data. We find the model adequately describes these data, but the addition of interprovincial mobility was not necessary to obtain an accurate description of the 2020-2021 sars-cov-2 pandemic in Belgium. We further demonstrate how our model can be used to help policymakers decide on the optimal timing of the release of social restrictions.We find that adding spatial heterogeneity by geographically stratifying the model results in more uncertain model projections as compared to an equivalent nation-level model, which has both communicative advantages and disadvantages. We finally discuss the impact of imposing local mobility or social contact restrictions to contain an epidemic in a given province and find that lowering social contact is a more effective strategy than lowering mobility.

Interspecies Interactions of the 2,6-Dichlorobenzamide Degrading Aminobacter sp. MSH1 with Resident Sand Filter Bacteria: Indications for Mutual Cooperative Interactions That Improve BAM Mineralization Activity.

Bioaugmentation often involves an invasion process requiring the establishment and activity of a foreign microbe in the resident community of the target environment. Interactions with resident micro-organisms, either antagonistic or cooperative, are believed to impact invasion. However, few studies have examined the variability of interactions between an invader and resident species of its target environment, and none of them considered a bioremediation context. Aminobacter sp. MSH1 mineralizing the groundwater micropollutant 2,6-dichlorobenzamide (BAM), is proposed for bioaugmentation of sand filters used in drinking water production to avert BAM contamination. We examined the nature of the interactions between MSH1 and 13 sand filter resident bacteria in dual and triple species assemblies in sand microcosms. The residents affected MSH1-mediated BAM mineralization without always impacting MSH1 cell densities, indicating effects on cell physiology rather than on cell number. Exploitative competition explained most of the effects (70%), but indications of interference competition were also found. Two residents improved BAM mineralization in dual species assemblies, apparently in a mutual cooperation, and overruled negative effects by others in triple species systems. The results suggest that sand filter communities contain species that increase MSH1 fitness. This opens doors for assisting bioaugmentation through co-inoculation with "helper" bacteria originating from and adapted to the target environment.

Guiding Mineralization Co-Culture Discovery Using Bayesian Optimization.

Many disciplines rely on testing combinations of compounds, materials, proteins, or bacterial species to drive scientific discovery. It is time-consuming and expensive to determine experimentally, via trial-and-error or random selection approaches, which of the many possible combinations will lead to desirable outcomes. Hence, there is a pressing need for more rational and efficient experimental design approaches to reduce experimental effort. In this work, we demonstrate the potential of machine learning methods for the in silico selection of promising co-culture combinations in the application of bioaugmentation. We use the example of pollutant removal in drinking water treatment plants, which can be achieved using co-cultures of a specialized pollutant degrader with combinations of bacterial isolates. To reduce the experimental effort needed to discover high-performing combinations, we propose a data-driven experimental design. Based on a dataset of mineralization performance for all pairs of 13 bacterial species co-cultured with MSH1, we built a Gaussian process regression model to predict the Gompertz mineralization parameters of the co-cultures of two and three species, based on the single-strain parameters. We subsequently used this model in a Bayesian optimization scheme to suggest potentially high-performing combinations of bacteria. We achieved good performance with this approach, both for predicting mineralization parameters and for selecting effective co-cultures, despite the limited dataset. As a novel application of Bayesian optimization in bioremediation, this experimental design approach has promising applications for highlighting co-culture combinations for in vitro testing in various settings, to lessen the experimental burden and perform more targeted screenings.

Three-species competition with non-deterministic outcomes.

Theoretical and experimental research studies have shown that ecosystems governed by non-transitive competition networks tend to maintain high levels of biodiversity. The theoretical body of work, however, has mainly focused on competition networks in which the outcomes of competition events are predetermined and hence deterministic, and where all species are identical up to their competitive relationships, an assumption that may limit the applicability of theoretical results to real-life situations. In this paper, we aim to probe the robustness of the link between biodiversity and non-transitive competition by introducing a three-dimensional winning probability parameter space, making the outcomes of competition events in a three-species in silico ecosystem uncertain. While two degenerate points in this parameter space have been the subject of previous studies, we investigate the remaining settings, which equip the species with distinct competitive abilities. We find that the impact of this modification depends on the spatial dimension of the system. When the system is well mixed, it collapses to monoculture, as is also the case in the non-transitive deterministic setting. In one dimension, chaotic patterns emerge, which tend to maintain biodiversity, and a power law relates the time that species manage to coexist to the degree of uncertainty regarding competition event outcomes. In two dimensions, the formation of spiral wave patterns ensures that biodiversity is maintained for moderate degrees of uncertainty, while considerable deviations from the non-transitive deterministic setting have strong negative effects on species coexistence. It can hence be concluded that non-transitive competition can still produce coexistence when the assumption of deterministic competition is abandoned. When the system collapses to monoculture, one observes a "survival of the strongest" law, as the species that has the highest probability of defeating its competitors has the best odds to become the sole survivor.

The impact of resource dependence of the mechanisms of life on the spatial population dynamics of an in silico microbial community.

Biodiversity has a critical impact on ecosystem functionality and stability, and thus the current biodiversity crisis has motivated many studies of the mechanisms that sustain biodiversity, a notable example being non-transitive or cyclic competition. We therefore extend existing microscopic models of communities with cyclic competition by incorporating resource dependence in demographic processes, characteristics of natural systems often oversimplified or overlooked by modellers. The spatially explicit nature of our individual-based model of three interacting species results in the formation of stable spatial structures, which have significant effects on community functioning, in agreement with experimental observations of pattern formation in microbial communities.

The impact of initial evenness on biodiversity maintenance for a four-species in silico bacterial community.

Initial community evenness has been shown to be a key factor in preserving the functional stability of an ecosystem, but has not been accounted for in previous modelling studies. We formulate a model that allows the initial evenness of the community to be varied in order to investigate the consequent impact on system diversity. We consider a community of four interacting bacterial species, and present a stochastic, spatial individual-based model simulating the ecosystem dynamics. Interactions take place on a two-dimensional lattice. The model incorporates three processes: reproduction, competition and mobility. In addition to variable initial evenness, multiple competition schemes are implemented, modelling various possible communities, which results in diverse coexistence and extinction scenarios. Simulations show that long-term system behaviour is strongly dependent on initial evenness and competition structure. The system is generally unstable; higher initial evenness has a small stabilizing effect on ecosystem dynamics by extending the time until the first extinction.

Temperature-driven dynamics: unraveling the impact of climate change on cryptic species interactions within the Litoditis marina complex.

Anthropogenic climate change and the associated increase in sea temperatures are projected to greatly impact marine ecosystems. Temperature variation can influence the interactions between species, leading to cascading effects on the abundance, diversity and composition of communities. Such changes in community structure can have consequences on ecosystem stability, processes and the services it provides. Therefore, it is important to better understand the role of species interactions in the development of communities and how they are influenced by environmental factors like temperature. The coexistence of closely related cryptic species, with significant biological and ecological differences, makes this even more complex. This study investigated the effect of temperature on species growth and both intra- and interspecific interactions of three species within the free-living nematode Litoditis marina complex. To achieve this, closed microcosm experiments were conducted on the L. marina species Pm I, Pm III and Pm IV in monoculture and combined cultures at two temperature treatments of 15 °C and 20 °C. A population model was constructed to elucidate and quantify the effects of intra- and interspecific interactions on nematode populations. The relative competitive abilities of the investigated species were quantified using the Modern Coexistence Theory (MCT) framework. Temperature had strong and disparate effects on the population growth of the distinct L. marina species. This indicates temperature could play an important role in the distribution of these cryptic species. Both competitive and facilitative interactions were observed in the experiments. Temperature affected both the type and the strength of the species interactions, suggesting a change in temperature could impact the coexistence of these closely related species, alter community dynamics and consequently affect ecosystem processes and services.

Response of phytoplankton functional types to Hurricane Fabian (2003) in the Sargasso Sea.

Understanding how tropical cyclones affect phytoplankton communities is important for studies on ecological variability. Most studies assessing the post-storm phytoplankton response rely on satellite observations of chlorophyll a concentration, which inform on the ocean surface conditions and the whole phytoplankton community. In this work, we assess the potential of the Massachusetts Institute of Technology marine ecosystem model to account for the response of individual phytoplankton functional types (PFTs, coccolithophores, diatoms, diazotrophs, mixotrophic dinoflagellates, picoeukaryotes, Prochlorococcus and Synechococcus) in the euphotic zone to the passage of Hurricane Fabian (2003) across the tropical and subtropical Sargasso Sea. Fabian induced a significant mean concentration increase (t-test, p < 0.05) of all PFTs in the tropical waters (except for Prochlorococcus), which was driven by the mean nutrient concentration increase and by a limited zooplankton grazing pressure. More specifically, the post-storm nutrient enrichment increased the contribution of fast-growing PFTs (e.g. diatoms and coccolithophores) to the total phytoplankton concentration and decreased the contribution of slow-growing dominant groups (e.g. picoeukaryotes, Prochlorococcus and Synechococcus), which lead to a significant increase (t-test, p < 0.05) of the Shannon diversity index values. Overall, the model captured the causal relationship between nutrient and PFT concentration increases in the tropical waters, although it only reproduced the most pronounced PFT responses such as those in the deep euphotic zone. In contrast, the model did not capture the oceanic perturbations induced by Fabian as observed in satellite imagery in the subtropical waters, probably due to its limited performance in this complex oceanographic area.

No bacterial-mediated alleviation of thermal stress in a brown seaweed suggests the absence of ecological bacterial rescue effects.

While microbiome alterations are increasingly proposed as a rapid mechanism to buffer organisms under changing environmental conditions, studies of these processes in the marine realm are lagging far behind their terrestrial counterparts. Here, we used a controlled laboratory experiment to examine whether the thermal tolerance of the brown seaweed Dictyota dichotoma, a common species in European coastal ecosystems, could be enhanced by the repeated addition of bacteria from its natural environment. Juvenile algae from three genotypes were subjected for two weeks to a temperature gradient, spanning almost the entire thermal range that can be tolerated by the species (11-30 °C). At the start of the experiment and again in the middle of the experiment, the algae were inoculated with bacteria from their natural environment or left untouched as a control. Relative growth rate was measured over the two-week period, and we assessed bacterial community composition prior to and at the end of the experiment. Since the growth of D. dichotoma over the full thermal gradient was not affected by supplementing bacteria, our results indicate no scope for bacterial-mediated stress alleviation. The minimal changes in the bacterial communities linked to bacterial addition, particularly at temperatures above the thermal optimum (22-23 °C), suggest the existence of a barrier to bacterial recruitment. These findings indicate that ecological bacterial rescue is unlikely to play a role in mitigating the effects of ocean warming on this brown seaweed.

Mobility and the spatial spread of sars-cov-2 in Belgium.

We analyse and mutually compare time series of covid-19-related data and mobility data across Belgium's 43 arrondissements (NUTS 3). In this way, we reach three conclusions. First, we could detect a decrease in mobility during high-incidence stages of the pandemic. This is expressed as a sizeable change in the average amount of time spent outside one's home arrondissement, investigated over five distinct periods, and in more detail using an inter-arrondissement "connectivity index" (CI). Second, we analyse spatio-temporal covid-19-related hospitalisation time series, after smoothing them using a generalise additive mixed model (GAMM). We confirm that some arrondissements are ahead of others and morphologically dissimilar to others, in terms of epidemiological progression. The tools used to quantify this are time-lagged cross-correlation (TLCC) and dynamic time warping (DTW), respectively. Third, we demonstrate that an arrondissement's CI with one of the three identified first-outbreak arrondissements is correlated to a substantial local excess mortality some five to six weeks after the first outbreak. More generally, we couple results leading to the first and second conclusion, in order to demonstrate an overall correlation between CI values on the one hand, and TLCC and DTW values on the other. We conclude that there is a strong correlation between physical movement of people and viral spread in the early stage of the sars-cov-2 epidemic in Belgium, though its strength weakens as the virus spreads.

The Potential of Surveillance Data for Dengue Risk Mapping: An Evaluation of Different Approaches in Cuba.

To better guide dengue prevention and control efforts, the use of routinely collected data to develop risk maps is proposed. For this purpose, dengue experts identified indicators representative of entomological, epidemiological and demographic risks, hereafter called components, by using surveillance data aggregated at the level of Consejos Populares (CPs) in two municipalities of Cuba (Santiago de Cuba and Cienfuegos) in the period of 2010-2015. Two vulnerability models (one with equally weighted components and one with data-derived weights using Principal Component Analysis), and three incidence-based risk models were built to construct risk maps. The correlation between the two vulnerability models was high (tau > 0.89). The single-component and multicomponent incidence-based models were also highly correlated (tau ≥ 0.9). However, the agreement between the vulnerability- and the incidence-based risk maps was below 0.6 in the setting with a prolonged history of dengue transmission. This may suggest that an incidence-based approach does not fully reflect the complexity of vulnerability for future transmission. The small difference between single- and multicomponent incidence maps indicates that in a setting with a narrow availability of data, simpler models can be used. Nevertheless, the generalized linear mixed multicomponent model provides information of covariate-adjusted and spatially smoothed relative risks of disease transmission, which can be important for the prospective evaluation of an intervention strategy. In conclusion, caution is needed when interpreting risk maps, as the results vary depending on the importance given to the components involved in disease transmission. The multicomponent vulnerability mapping needs to be prospectively validated based on an intervention trial targeting high-risk areas.

Improved wood species identification based on multi-view imagery of the three anatomical planes.

BACKGROUND: The identification of tropical African wood species based on microscopic imagery is a challenging problem due to the heterogeneous nature of the composition of wood combined with the vast number of candidate species. Image classification methods that rely on machine learning can facilitate this identification, provided that sufficient training material is available. Despite the fact that the three main anatomical sections contain information that is relevant for species identification, current methods only rely on transverse sections. Additionally, commonly used procedures for evaluating the performance of these methods neglect the fact that multiple images often originate from the same tree, leading to an overly optimistic estimate of the performance. RESULTS: We introduce a new image dataset containing microscopic images of the three main anatomical sections of 77 Congolese wood species. A dedicated multi-view image classification method is developed and obtains an accuracy (computed using the naive but common approach) of 95%, outperforming the single-view methods by a large margin. An in-depth analysis shows that naive accuracy estimates can lead to a dramatic over-prediction, of up to 60%, of the accuracy. CONCLUSIONS: Additional images from non-transverse sections can boost the performance of machine-learning-based wood species identification methods. Additionally, care should be taken when evaluating the performance of machine-learning-based wood species identification methods to avoid an overestimation of the performance.

Moisture Dynamics of Wood-Based Panels and Wood Fibre Insulation Materials.

Moisture performance is an important factor determining the resistance of wood-based building materials against fungal decay. Understanding how material porosity and chemistry affect moisture performance is necessary for their efficient use, as well as for product optimisation. In this study, three complementary techniques (X-ray computed tomography, infrared and low-field NMR spectroscopy) are applied to elucidate the influence of additives, manufacturing process and material structure on the liquid water absorption and desorption behaviour of a selection of wood-based panels, thermally modified wood and wood fibre insulation materials. Hydrophobic properties achieved by thermal treatment or hydrophobic additives such as paraffin and bitumen, had a major influence on water absorption and desorption rates. When hydrophobic additives did not play a role, pore distributions and manufacturing process had a decisive influence on the amount and rate of absorption and desorption. In that case, a higher porosity resulted in a higher water absorption rate. Our results show that there is a clear potential for tailoring materials towards specific moisture performance by better understanding the influence of different material characteristics. This is useful both for achieving desired moisture buffering as well as to increase service life of wood-based materials. From a sustainability perspective, fit-for-purpose moisture performance is often easier to achieve and preferred than wood protection by biocide preservative treatments.

Design and parameterization of a stochastic cellular automaton describing a chemical reaction.

Although most of the work concerned with reaction kinetics concentrates on empirical findings, stochastic models, and differential equations, a growing number of researchers is exploring other methods to elucidate reaction kinetics. In this work, the parameterization of an utter discrete spatio-temporal model, more specifically, a cellular automaton (CA), describing the reaction of HCl with CaCO(3) , is suggested. Furthermore, a system of partial differential equations (PDE), deduced from a set of CA rules, is implemented to compare both modeling paradigms. In this article, the experimental setup to acquire time series of data is explained, a stochastic CA-based model and a continuous PDE-based model capable of describing the reaction are proposed, the models are parameterized using the experimental data and, finally, the relationship between a discrete time step of the CA-based model and the physical time is studied. Essentially, the parameterization of both models can be traced back to the quest for a solution of the inverse problem in which a (set of) rule(s), respectively a system of PDE, is deduced starting from the observed data. It is demonstrated that the proposed CA- and PDE-based models are capable of describing the considered chemical reaction with a high accuracy, which is confirmed by a root mean squared error between the simulated and observed data of 0.388 and 0.869 g CO(2) , respectively. Further, it is shown that an exponential or linear relationship can be used to link the physical time to a discrete time step of the CA-based model.

On the topological sensitivity of cellular automata.

Ever since the conceptualization of cellular automata (CA), much attention has been paid to the dynamical properties of these discrete dynamical systems, and, more in particular, to their sensitivity to the initial condition from which they are evolved. Yet, the sensitivity of CA to the topology upon which they are based has received only minor attention, such that a clear insight in this dependence is still lacking and, furthermore, a quantification of this so-called topological sensitivity has not yet been proposed. The lack of attention for this issue is rather surprising since CA are spatially explicit, which means that their dynamics is directly affected by their topology. To overcome these shortcomings, we propose topological Lyapunov exponents that measure the divergence of two close trajectories in phase space originating from a topological perturbation, and we relate them to a measure grasping the sensitivity of CA to their topology that relies on the concept of topological derivatives, which is introduced in this paper. The validity of the proposed methodology is illustrated for the 256 elementary CA and for a family of two-state irregular totalistic CA.

Assessing the effects of non-pharmaceutical interventions on SARS-CoV-2 transmission in Belgium by means of an extended SEIQRD model and public mobility data.

We present a compartmental extended SEIQRD metapopulation model for SARS-CoV-2 spread in Belgium. We demonstrate the robustness of the calibration procedure by calibrating the model using incrementally larger datasets and dissect the model results by computing the effective reproduction number at home, in workplaces, in schools, and during leisure activities. We find that schools and home contacts are important transmission pathways for SARS-CoV-2 under lockdown measures. School reopening has the potential to increase the effective reproduction number from Re=0.66±0.04 (95 % CI) to Re=1.09±0.05 (95 % CI) under lockdown measures. The model accounts for the main characteristics of SARS-CoV-2 transmission and COVID-19 disease and features a detailed representation of hospitals with parameters derived from a dataset consisting of 22 136 hospitalized patients. Social contact during the pandemic is modeled by scaling pre-pandemic contact matrices with Google Community Mobility data and with effectivity-of-contact parameters inferred from hospitalization data. The calibrated social contact model with its publically available mobility data, although coarse-grained, is a cheap and readily available alternative to social-epidemiological contact studies under lockdown measures, which were not available at the start of the pandemic.

Phenomenological study of irregular cellular automata based on Lyapunov exponents and Jacobians.

Originally, cellular automata (CA) have been defined upon regular tessellations of the n-dimensional Euclidean space, while CA on irregular tessellations have received only little attention from the scientific community, notwithstanding serious shortcomings are associated with the former manner of subdividing Rn. In this paper we present a profound phenomenological study of two-state, two-dimensional irregular CA from a dynamical systems viewpoint. We opted to exploit properly defined quantitative measures instead of resorting to qualitative methods for discriminating between behavioral classes. As such, we employ Lyapunov exponents, measuring the divergence rate of close trajectories in phase space, and Jacobians, formulated using Boolean derivatives and expressing the sensitivity of a cellular automaton to its inputs. Both are stated for two-state CA on irregular tessellations, enabling us to characterize these discrete dynamical systems, and advancing us to propose a classification scheme for this CA family. In addition, a relationship between these quantitative measures is established in extension of the insights already developed for the classical CA paradigm. Finally, we discuss the repercussions on the CA dynamics that arise when the geometric variability of the spatial entities is taken into account during the CA simulation.

Identification of Cellular Automata Based on Incomplete Observations With Bounded Time Gaps.

In this paper, the problem of identifying the cellular automata (CAs) is considered. We frame and solve this problem in the context of incomplete observations, i.e., prerecorded, incomplete configurations of the system at certain, and unknown time stamps. We consider 1-D, deterministic, two-state CAs only. An identification method based on a genetic algorithm with individuals of variable length is proposed. The experimental results show that the proposed method is highly effective. In addition, connections between the dynamical properties of CAs (Lyapunov exponents and behavioral classes) and the performance of the identification algorithm are established and analyzed.