Multi-species Model Research Articles

Spatial and temporal niche overlap of aardwolves and aardvarks in Serengeti National Park, Tanzania.

Species interactions can influence species distributions, but mechanisms mitigating competition or facilitating positive interactions between ecologically similar species are often poorly understood. Aardwolves (Proteles cristata) and aardvarks (Orycteropus afer) are nocturnal, insectivorous mammals that co-occur in eastern and southern Africa, and knowledge of these species is largely limited to their nutritional biology. We used aardwolf and aardvark detections from 105 remote cameras during 2016-2018 to assess their spatial and temporal niche overlap in the grasslands of Serengeti National Park, Tanzania. Using a multispecies occupancy model, we identified a positive interaction between occupancy probabilities for aardwolves and aardvarks. Slope, proportion of grassland and termite mound density did not affect the occupancy probabilities of either species. The probability of aardwolf, but not aardvark, occupancy increased with distance to permanent water sources, which may relate to predation risk avoidance. Diel activity overlap between aardwolves and aardvarks was high during wet and dry seasons, with both species being largely nocturnal. Aardwolves and aardvarks have an important ecological role as termite consumers, and aardvarks are suggested to be ecosystem engineers. Our results contribute to a better understanding of the spatial and temporal niche of insectivores like aardwolves and aardvarks, suggesting high spatial and temporal niche overlap in which commensalism occurs, whereby aardwolves benefit from aardvark presence through increased food accessibility.

Tropical forest mammal occupancy and functional diversity increase with microhabitat surface area.

Many animal-environment interactions are mediated by the physical forms of the environment, especially in tropical forests, where habitats are structurally complex and highly diverse. Higher structural complexity, measured as habitat surface area, may provide increased resource availability for animals, leading to higher animal diversity. Greater habitat surface area supports increased animal diversity in other systems, such as coral reefs and forest canopies, but it is uncertain how this relationship translates to communities of highly mobile, terrestrial mammal species inhabiting forest floors. We tested the relative importance of forest floor habitat structure, encompassing vegetation and topographic structure, in determining species occupancy and functional diversity of medium to large mammals using data from a tropical forest in the Udzungwa Mountains of Tanzania. We related species occupancies and diversity obtained from a multispecies occupancy model with ground-level habitat structure measurements obtained from a novel head-mounted active remote sensing device, the Microsoft HoloLens. We found that habitat surface area was a significant predictor of mean species occupancy and had a significant positive relationship with functional dispersion. The positive relationships indicate that surface area of tropical forest floors may play an important role in promoting mammal occupancy and functional diversity at the microhabitat scale. In particular, habitat surface area had higher mean effects on occupancy for carnivorous and social species. These results support a habitat surface area-diversity relationship on tropical forest floors for mammals.

Assessing trends in population size of three unmarked species: A comparison of a multi-species N-mixture model and random encounter models.

Estimation of changes in abundances and densities is essential for the research, management, and conservation of animal populations. Recently, technological advances have facilitated the surveillance of animal populations through the adoption of passive sensors, such as camera traps (CT). Several methods, including the random encounter model (REM), have been developed for estimating densities of unmarked populations but require additional information. Hierarchical abundance models, such as the N-mixture model (NMM), can estimate abundances without performing additional fieldwork but do not explicitly estimate the area effectively sampled. This obscures the interpretation of its densities and requires its users to focus on relative measures of abundance instead. Hence, the main objective of our study is to evaluate if REM and NMM yield consistent results qualitatively. Therefore, we compare relative trends: (i) between species, (ii) between years and (iii) across years obtained from annual density/abundance estimates of three species (fox, wild boar and red deer) in central Spain monitored by a camera trapping network for five consecutive winter periods. We reveal that NMM and REM provided density estimates in the same order of magnitude for wild boar, but not for foxes and red deer. Assuming a Poisson detection process in the NMM was important to control for inflation of abundance estimates for frequently detected species. Both methods consistently ranked density/abundance across species (between species trend), but did not always agree on relative ranks of yearly estimates within a single population (between years trend), nor on its linear population trends across years (across years trend). Our results suggest that relative trends are generally consistent when the range of variability is large, but can become inconsistent when the range of variability is smaller.

Dynamic interactions between Candida albicans and different streptococcal species in a multispecies oral biofilm.

The oral cavity is colonized by a plethora of bacteria, fungi, and archaea, including streptococci of the mitis group (MSG) and the yeast Candida albicans. This study aims to investigate the role of streptococcal species in the development of oral biofilm and the cross-kingdom interactions between some of the members of the commensal MSG and the pathogen yeast C. albicans using a multispecies supragingival biofilm model. A total of nine different in vitro biofilms were grown, quantified with culture analyses, and visually examined with confocal laser scanning microscopy (CLSM). A four-species biofilm without any streptococcal species was used as a basic biofilm. In each subsequent inoculum, one species of MSG was added and afterward combined with Streptococcus mutans. The eight-species biofilm contained all eight strains used in this study. Culture analyses showed that the presence of S. mutans in a four-species biofilm with Streptococcus oralis or S. oralis subsp. tigurinus did not differ significantly in C. albicans colony-forming unit (CFU) counts compared to biofilms without S. mutans. However, compared to other mitis species, Streptococcus gordonii combined with S. mutans resulted in the lowest CFUs of C. albicans. Visual observation by CLSM showed that biofilms containing both S. mutans and one species of MSG seemed to induce the formation of filamentous form of C. albicans. However, when several species of MSG were combined with S. mutans, C. albicans was again found in its yeast form.

Integrating existing data to assess the risk of an expanding land use change on mammals

ContextLand-use change, including agricultural expansion, is one of the major drivers of biodiversity loss globally. Given the rapid pace of land-use change, data-driven, strategic, and dynamic conservation planning is imperative.ObjectivesWe present an exemplar application of using existing data to inform conservation planning. Specifically, we developed a systematic approach for identifying areas of conservation concern due to cannabis cultivation in California, USA.MethodsWe used three existing datasets: (1) camera trap data from ten projects (n = 1186); (2) the locations of cannabis cultivation sites eradicated by law enforcement (n = 834); and (3) the locations of cultivation licenses (n = 4366). We analyzed this data using multi-species occupancy models to estimate the occupancy and richness of 30 species, and maximum entropy models to estimate the risk of unlicensed and trespass cultivation. We then identified areas of overlap and determined the percent of suitable habitat potentially impacted by cannabis cultivation.ResultsCannabis cultivation was estimated to overlap 39–74% of suitable habitat for special status species. Private land cultivation tended to have a larger influence on generalist species whereas trespass cultivation had the largest potential influence on fisher (Pekania pennanti), a special status species.ConclusionsOur results can be used to prioritize eradication, restoration, and remediation activities; to target mitigation efforts; and to guide the placement of new, licensed cultivation. Our approach demonstrates the utility of aggregating existing biological and socioeconomic data to inform conservation planning and is broadly applicable to other data sources and ecological stressors.

Spatiotemporal monitoring of a periodontal multispecies biofilm model: demonstration of prebiotic treatment responses.

Biofilms are complex polymicrobial communities which are often associated with human infections such as the oral disease periodontitis. Studying these complex communities under controlled conditions requires in vitro biofilm model systems that mimic the natural environment as close as possible. This study established a multispecies periodontal model in the drip flow biofilm reactor in order to mimic the continuous flow of nutrients at the air-liquid interface in the oral cavity. The design is engineered to enable real-time characterization. A community of five bacteria, Streptococcus gordonii-GFPmut3*, Streptococcus oralis-GFPmut3*, Streptococcus sanguinis-pVMCherry, Fusobacterium nucleatum, and Porphyromonas gingivalis-SNAP26 is visualized using two distinct fluorescent proteins and the SNAP-tag. The biofilm in the reactor develops into a heterogeneous, spatially uniform, dense, and metabolically active biofilm with relative cell abundances similar to those in a healthy individual. Metabolic activity, structural features, and bacterial composition of the biofilm remain stable from 3 to 6 days. As a proof of concept for our periodontal model, the 3 days developed biofilm is exposed to a prebiotic treatment with L-arginine. Multifaceted effects of L-arginine on the oral biofilm were validated by this model setup. L-arginine showed to inhibit growth and incorporation of the pathogenic species and to reduce biofilm thickness and volume. Additionally, L-arginine is metabolized by Streptococcus gordonii-GFPmut3* and Streptococcus sanguinis-pVMCherry, producing high levels of ornithine and ammonium in the biofilm. In conclusion, our drip flow reactor setup is promising in studying spatiotemporal behavior of a multispecies periodontal community. IMPORTANCE Periodontitis is a multifactorial chronic inflammatory disease in the oral cavity associated with the accumulation of microorganisms in a biofilm. Not the presence of the biofilm as such, but changes in the microbiota (i.e., dysbiosis) drive the development of periodontitis, resulting in the destruction of tooth-supporting tissues. In this respect, novel treatment approaches focus on maintaining the health-associated homeostasis of the resident oral microbiota. To get insight in dynamic biofilm responses, our research presents the establishment of a periodontal biofilm model including Streptococcus gordonii, Streptococcus oralis, Streptococcus sanguinis, Fusobacterium nucleatum, and Porphyromonas gingivalis. The added value of the model setup is the combination of simulating continuously changing natural mouth conditions with spatiotemporal biofilm profiling using non-destructive characterization tools. These applications are limited for periodontal biofilm research and would contribute in understanding treatment mechanisms, short- or long-term exposure effects, the adaptation potential of the biofilm and thus treatment strategies.

Electrochemical transport modelling and open-source simulation of pore-scale solid–liquid systems

The modelling of electrokinetic flows is a critical aspect spanning many industrial applications and research fields. This has introduced great demand in flexible numerical solvers to describe these flows. The underlying phenomena are microscopic, non-linear, and often involving multiple domains. Therefore often model assumptions and several numerical approximations are introduced to simplify the solution. In this work we present a multi-domain multi-species electrokinetic flow model including complex interface and bulk reactions. After a dimensional analysis and an overview of some limiting regimes, we present a set of general-purpose finite-volume solvers, based on OpenFOAM® , capable of describing an arbitrary number of electrochemical species over multiple interacting (solid or fluid) domains (Icardi and Barnett in F Municchi spnpFoam, 2021. https://doi.org/10.5281/zenodo.4973896). We provide a verification of the computational approach for several cases involving electrokinetic flows, reactions between species, and complex geometries. We first present three one-dimensional verification test-cases, and then show the capability of the solver to tackle two- and three-dimensional electrically driven flows and ionic transport in random porous structures. The purpose of this work is to lay the foundation of a general-purpose open-source flexible modelling tool for problems in electrochemistry and electrokinetics at different scales.

Research on the Impact of Drought Environment on Plant Community Diversity Based on Differential Equation Models

Plants play a crucial role in the influence of ecological environment. In order to predict the changes of plant communities in dry weather, this paper firstly collected monitoring data from a sample of grassland ecological stations from the China Biological Research Network (CERN), and constructed a linear model for the changes of plant communities under different climatic conditions, and since the linear correlation of this model was not strong, this paper then constructed a new non-linear correlation model. Firstly, the interspecific competition model of vegetation community was constructed from the interspecific competition model, and then the functional relationship between drought rate and plant growth rate was obtained using the logistic function, and the multi-species competition model was improved. Finally, data from ecological stations were used to visualise vegetation competition and development.

Biofilm formation by heat-resistant dairy bacteria: multispecies biofilm model under static and dynamic conditions.

In the food industry, especially dairy, biofilms can be formed by heat-resistant spoilage and pathogenic bacteria from the farm. Such biofilms may persist throughout the processing chain and contaminate milk and dairy products continuously, increasing equipment cleaning, maintenance costs, and product recalls. Most biofilms are multispecies, yet most studies focus on single-species models. A multispecies model of dairy biofilm was developed under static and dynamic conditions using heat-resistant Bacillus licheniformis, Pseudomonas aeruginosa, Clostridium tyrobutyricum, Enterococcus faecalis, Streptococcus thermophilus, and Rothia kristinae isolated from dairies. C. tyrobutiricum and R. kristinae were weak producers of biofilm, whereas the other four were moderate to strong producers. Based on cross-streaking on agar, P. aeruginosa was found to inhibit B. licheniformis and E. faecalis. In multispecies biofilm formed on stainless steel in a CDC reactor fed microfiltered milk, the strong biofilm producers were dominant while the weak producers were barely detectable. All biofilm matrices were dispersed easily by proteinase K treatment but were less sensitive to DNase or carbohydrases. Further studies are needed to deepen our understanding of multispecies biofilms and interactions within to develop improved preventive strategies to control the proliferation of spoilage and pathogenic bacteria in dairies and other food processing environments. IMPORTANCE A model of multispecies biofilm was created to study biofilm formation by heat-resistant bacteria in the dairy industry. The biofilm formation potential was evaluated under static conditions. A continuous flow version was then developed to study multispecies biofilm formed on stainless steel in microfiltered milk under dynamic conditions encountered in dairy processing equipment. The study of biofilm composition and bacterial interactions therein will lead to more effective means of suppressing bacterial growth on food processing equipment and contamination of products with spoilage and pathogenic bacteria, which represent considerable economic loss.

A coupled flow and transport model for simulation of multi-species reactive transport in unconfined aquifer using meshless local Petrov Galerkin (MLPG) method.

An understanding of natural degradation of multiple reactive contaminants in the aquifers is essential before designing the monitoring or remediation programs for polluted aquifers. Since such reactive contaminants are ubiquitous, a number of research works has been performed in the past three decades for the modelling of multi-species reactive transport (MSRT) phenomenon. The widely used finite difference method (FDM) and finite element method (FEM)-based models suffer a drawback of relying on a grid/mesh, which makes the solution unstable. Addressing such difficulties, the latest research on the MSRT models is directed towards the meshless methods. In this study, the meshless local Petrov Galerkin (MLPG) method-based multi-species reactive transport model (MLPG-MSRT) is presented, with an objective to create a robust simulation tool for the prediction of fate of multiple contaminants of the first-order reaction network. The developed model is validated for reversible as well as irreversible reaction networks with the available analytical solutions. Also, the MLPG model for unconfined aquifer flow (UF) is developed, validated, and coupled with the MLPG-MSRT model. The MLPG-UF-MSRT model results are further compared with the established FDM-based MODFLOW-RT3D model solutions for a rectangular and a real field type study. The results showed that the proposed model can simulate MSRT as accurately as the FDM-based models with an additional advantage of simplicity and stability, and thus, is more efficient for complex field problems.

ATMOSPHERIX: II- Characterizing exoplanet atmospheres through transmission spectroscopy with SPIRou

ABSTRACT In a companion paper, we introduced a publicly available pipeline to characterize exoplanet atmospheres through high-resolution spectroscopy. In this paper, we use this pipeline to study the biases and degeneracies that arise in atmospheric characterization of exoplanets in near-infrared ground-based transmission spectroscopy. We inject synthetic planetary transits into sequences of SPIRou spectra of the well known M dwarf star Gl 15 A, and study the effects of different assumptions on the retrieval. We focus on (i) mass and radius uncertainties, (ii) non-isothermal vertical profiles, and (iii) identification and retrieval of multiple species. We show that the uncertainties on mass and radius should be accounted for in retrievals and that depth-dependent temperature information can be derived from high-resolution transmission spectroscopy data. Finally, we discuss the impact of selecting wavelength orders in the retrieval and the issues that arise when trying to identify a single species in a multispecies atmospheric model. This analysis allows us to understand better the results obtained through transmission spectroscopy and their limitations in preparation to the analysis of actual SPIRou data.

Species specific and multi-species allometric models for estimating aboveground biomass of native perennial plant species grown in the agricultural landscape of Central Ethiopia

Species specific and multi-species allometric models for estimating aboveground biomass of native perennial plant species grown in the agricultural landscape of Central Ethiopia

Habitat modification destabilizes spatial associations and persistence of Neotropical carnivores

Spatial relationships between sympatric species underpin biotic interactions, structure ecological communities, and maintain ecosystem health. However, the resilience of interspecific spatial associations to human habitat modification remains largely unknown, particularly in tropical regions where anthropogenic impacts are often greatest. We applied multi-state multi-species occurrence models to camera trap data across nine tropical landscapes in Colombia to understand how prominent threats to forest ecosystems influence Neotropical carnivore occurrence and interspecific spatial associations, with implications for biotic interactions. We show that carnivore occurrence represents a delicate balance between local environmental conditions and interspecific interactions that can be compromised in areas of extensive habitat modification. The stability of carnivore spatial associations depends on forest cover to mediate antagonistic encounters with apex predators and structurally intact forests to facilitate coexistence between competing mesocarnivores. Notably, we demonstrate that jaguars play an irreplaceable role in spatially structuring mesocarnivore communities, providing novel evidence on their role as keystone species. With increasing global change, conserving both the extent and quality of tropical forests is imperative to support carnivores and preserve the spatial associations that underpin ecosystem stability and resilience.

Projecting fish community responses to dam removal – Data-limited modeling

Modeling fish community responses to dam removal is an emerging field of study as dam removals become more common, but uncertainties concerning recovery time and community stability remain. In Europe, an EU-wide biodiversity strategy plans to restore around 25,000 km of rivers to free-flowing status, which emphasizes the importance of being able to predict fish community responses after dam removal. We developed a multi-species size spectrum model for a fish community in the Mörrum River in Sweden to identify possible outcomes after a dam was removed in 2020. Electrofishing monitoring before the dam removal was used to calibrate the model. We projected multiple scenarios into the future to explore patterns of community stability, individual species responses, and recovery time while varying parameters related to dam removal mortality, base resource rate change, and maximum recruitment change. We created 30 hypothetical scenarios using an abrupt change perspective (parameters are step-based) and 30 scenarios using a gradual change perspective (parameters are smooth). In both perspectives, dam removal mortality and a decreasing resource rate reduced community biomass and delayed recovery time compared to pre-dam removal conditions. Our results demonstrate that recovery from a dam removal scenario is not necessarily a benefit for all species. In scenarios where dam removal practices or dam failures cause high mortality events and sustained impacts on base trophic level resources, recovery of pre-removal biomass may take decades, while community stability may be unstable for twice that time-period. Our study shows that size spectrum models can be applied to dam removal scenarios to explore potential recovery outcomes, particularly from a risk avoidance perspective. A benefit of using such an approach is the relatively low data requirements needed to perform projections (e.g., present species, fish growth rates, relative fish abundance). Implementing this model in other river systems, particularly at the reach scale, can help river restoration and management assess tradeoffs associated with different habitat restoration approaches prior to committing to a dam removal plan.

Enhancement of a multi-species reactive transport model for cement-based materials under cyclic wetting and drying conditions

To understand the underlying phenomena that drive concrete deterioration under cyclic environmental conditions in the marine environment, a reactive transport model (RTM) for unsaturated cement-based materials has been established in this study, including multi-ionic and moisture transport coupled with a chemical equilibrium computation. The two-phase moisture transport model, which considers pore structure changes, is introduced with capillary pressure as the primary variable parameter. The modified Poisson-Nernst-Planck (PNP) equations were illustrated for multi-ionic transport through pore solution under unsaturated conditions. A modelling approach for moisture conductivity based on the pore structure and moisture storage was presented to account for pore structure changes on the mass transports. The consideration of boundary conditions and moisture flux through the exposed surface is demonstrated for wetting and drying conditions, separately. Numerical results for mortar samples subjected to NaCl solutions under various cyclic wetting and drying conditions were in good agreement with experimentally measured moisture gain and total chloride content. Under more prolonged wetting conditions, the deeper influence depth and a wider range of moisture fluctuation lead to an increase in concrete deterioration. For all cyclic wetting conditions, the precipitation of Friedel's salt is predicted, which subsequently limits the transport of chloride ions to deeper depths from the exposed surface. A peak in the chloride profile is observed near the exposed surface. Meanwhile, the peak region continuously expands and moves deeper into the specimens with increasing wetting time duration and exposure times, consistent with Friedel's salt precipitation. In contrast, the chloride content near the exposure surface shows a significant decrease due to the decomposition of the C–S–H phase caused by ion leaching and carbonation of the exposed surface.

Global injustice and animals: towards a multispecies social connection model

In this article I argue for and sketch the outlines of a multispecies social connection model, based on the work of Iris Marion Young. This multispecies social connection model responds to shortcomings in existing approaches to multispecies global justice in animal philosophy and IR. Because the model focuses on concrete structures of injustice, it allows for taking into account relations without categorizing other animals beforehand and for being attentive to nonhuman animal agency, and it recognizes the entanglement of political and economic forces in perpetuating injustice towards animals. The multispecies model also brings to light problems with anthropocentrism in theorizing structural injustice and responsibility. Analyzing multispecies structures of injustice shows how different forms of oppression are connected globally, which offers a better view of animal and human oppression than anthropocentric theorizing. This is important for determining the responsibilities of different kinds of social, political, and economic actors in working toward social change, and for knowing what to work toward. This model can either complement existing political models, or function as the starting point for new multispecies politics.

Dynamics of consumer-resource reaction-diffusion models: single and multiple consumer species.

A consumer-resource reaction-diffusion model with a single consumer species was proposed and experimentally studied by Zhang et al.(Ecol Lett 20:1118-1128, 2017). Analytical study on its dynamics was further performed by He et al.(J Math Biol 78:1605-1636, 2019). In this work, we completely settle the conjecture proposed by He et al.(J Math Biol 78:1605-1636, 2019) about the global dynamics of the consumer-resource model for small yield rate. We then study a multi-species consumer-resource model where all the consumer species compete with each other through depression of the limited resources by consumption and there is no direct competition between them. We show that in this case, all consumer species persist uniformly, which implies that "competition exclusion" phenomenon will never happen. We also clarify its dynamics in both homogeneous and heterogeneous environments under various circumstances.

Multifactorial Diffusion of Chloride Ions in Concrete considering the Non-linear Voltage Distortion of Other Species

AbstractOne of the most relevant deterioration mechanisms of reinforced concrete (RC) structures is the corrosion of steel bars by chloride ions. The service life of structures could be extended by monitoring this process. The lack of correlation data between chloride ion diffusion and the electrical field has meant that alternative methods have been developed in this paper. One such method considers diffusivity and the electrical field as non-constant, although they are usually assumed constant, that is, without there being any variability of the involved factors. Therefore, a multi-factorial diffusivity that accounts for the material characteristics and environmental variations is adopted. In addition, an innovative stochastic approach to evaluate the variation of the electrical field while accounting for the non-linear voltage distortion, which considers a multispecies model, has been proposed. More complete 1D/2D electro-mechanical models that are solved by advanced numerical and analytical solutions for electro-mechanical diffusion have been developed. Results show that spatiotemporal numerical models estimate the chloride concentration well, estimating more reliable scenarios to provide information on the safety situation of the structure and make it more sustainable by employing successful preventive treatments.

Uncoupling Techniques for Multispecies Diffusion–Reaction Model

We consider the multispecies model described by a coupled system of diffusion–reaction equations, where the coupling and nonlinearity are given in the reaction part. We construct a semi-discrete form using a finite volume approximation by space. The fully implicit scheme is used for approximation by time, which leads to solving the coupled nonlinear system of equations at each time step. This paper presents two uncoupling techniques based on the explicit–implicit scheme and the operator-splitting method. In the explicit–implicit scheme, we take the concentration of one species in coupling term from the previous time layer to obtain a linear uncoupled system of equations. The second approach is based on the operator-splitting technique, where we first solve uncoupled equations with the diffusion operator and then solve the equations with the local reaction operator. The stability estimates are derived for both proposed uncoupling schemes. We present a numerical investigation for the uncoupling techniques with varying time step sizes and different scales of the diffusion coefficient.

Estimating the effects of land abandonment on mammal communities in the Karoo region of South Africa

Small livestock production has significantly transformed natural land within South Africa, but the extent and nature of the impacts of this land use on wildlife remains poorly understood. The establishment of a formal protected area (PA) within a well-established small livestock farming area in the Karoo provided a unique opportunity to investigate the response of mammal communities to both sustained farming impacts and how the cessation of farming activities across a large area may impact the persistence and colonisation of highly mobile species. Through extensive camera trapping and a dynamic multi-species occurrence model within a (Before-After-Control-Intervention) BACI design, we investigated the community diversity and structure of medium and large mammals in addition to changes in their persistence and colonisation following this land use change. Camera traps detected 25 species, from 14 families, within the combined study area. Community-level and species-specific probability of colonisation and persistence did not differ significantly between land that remained in use for commercial livestock farming and that which was abandoned to form a new protected area. Farmer concerns that predators would leave the PA and colonise their farms were not supported. Long term monitoring of these sites will prove important to our understanding of the potential of land, subject to prolonged livestock farming, to recover and support higher levels of species richness and wildlife abundance.