The competitive exclusion principle in stochastic environments

Scale dependent niche conservatism in fish communities of the largest freshwater lake in China

Two major theoretical concepts of niche evolution lead to conflicting predictions in ecological studies: the competitive exclusion principle (CEP) predicts that closely-related species should be sufficiently divergent to coexist, whereas niche conservatism (NC) suggests that closely-related species should be more ecologically similar. Here, we test this conundrum by employing stable isotope ratios (δ13C, δ15N) to estimate trophic niches and test niche evolution in fish communities of Poyang Lake, central China. At a broad phylogenetic scale involving 57 species, we examined the relationships between trophic niche differences along genetic distances and tested phylogenetic signals. We found that trophic differences were positively associated with genetic distances when genetic distances were less than 0.24, showing strong phylogenetic signal, but not when larger than 0.24. We then focused on seven Cultrinae species coexisting at a local scale and compared trophic niche differences within and between sister species, closely-related species, and distantly-related species. We found that trophic differences between distantly-related species were significantly larger than those between closely-related species at a broad spatial scale, supporting NC. However, trophic differences between sister species were larger than those between closely-related species at a small local scale (individual sampling sites), suggesting the importance of CEP not NC. Hence, our findings suggest that niche evolution operates in a scale-dependent manner: in a phylogenetic scale (time scale), NC predictions were met well below a certain range, not above that range; at a spatial scale, CEP predictions were met for coexisting sister species, however the other species followed the NC predictions.

Long-term behavior of stochastic SIQRS epidemic models

In this paper we analyze and classify the dynamics of SIQRS epidemiological models with susceptible, infected, quarantined, and recovered classes, where the recovered individuals can become reinfected. We are able to treat general incidence functional responses. Our models are more realistic than what has been studied in the literature since they include two important types of random fluctuations. The first type is due to small fluctuations of the various model parameters and leads to white noise terms. The second type of noise is due to significant environment regime shifts in that can happen at random. The environment switches randomly between a finite number of environmental states, each with a possibly different disease dynamic. We prove that the long-term fate of the disease is fully determined by a real-valued threshold λ . When λ < 0 the disease goes extinct asymptotically at an exponential rate. On the other hand, if λ > 0 the disease will persist indefinitely. We end our analysis by looking at some important examples where λ can be computed explicitly, and by showcasing some simulation results that shed light on real-world situations.

Revisiting the exclusion principle in epidemiology at the limit of a large competitive advantage

The competitive exclusion principle in epidemiology implies that when competing strains of a pathogen provide complete protection for each other, the strain with the largest reproduction number outcompetes the other strains and drives them to extinction. The introduction of various trade-off mechanisms may facilitate the coexistence of competing strains, especially when their respective basic reproduction numbers are close so that the competition between the strains is weak. Yet, one may expect that a substantial competitive advantage of one of the strains will eventually outbalance trade-off mechanisms driving less competitive strains to extinction. The literature, however, lacks a rigorous validation of this statement. In this work, we challenge the validity of the exclusion principle at a limit in which one strain has a vast competitive advantage over the other strains. We show that when one strain is significantly more transmissible than the others, and under broad conditions, an epidemic system with two strains has a stable endemic equilibrium in which both strains coexist with comparable prevalence. Thus, the competitive exclusion principle does not unconditionally hold beyond the established case of complete immunity.

Inter-annual variation in amphibian larval interspecies interactions

The outcomes of species interactions can vary by life stage, year, and surrounding environmental conditions. Amphibian species are expected to compete most strongly during their tadpole stage when they exist in the highest densities. Changes in arrival timing, surrounding aquatic communities, and yearly conditions could all affect the outcome of larval competition. In Long Point, Ontario, the Fowler's toad (Anaxyrus fowleri) is at the northern edge of its range and overlaps with the more common American toad (Anaxyrus americanus). Both species breed in ponds that encounter high inter-annual variation. To determine whether these species compete strongly, and if this effect was replicated across multiple years, we raised both species as tadpoles together and, apart, in mesocosms in 2018 and 2021. We measured survivorship to, weight at, and time to metamorphosis for both species in both years. We determined that the presence of American toad tadpoles consistently had a detrimental effect on Fowler's toad tadpoles, even though this effect presented itself differently across years. Our study suggests that competitive exclusion by American toads could be occurring at the edge of the Fowler's toad's range. This study further demonstrates the importance of studying communities across multiple years to understand the full scope of species interactions.

Deciphering endogenous and exogenous regulations of anammox consortia in responding to lincomycin by multiomics: quorum sensing and CRISPR system

The widespread use of antibiotics has created an antibiotic resistance genes (ARGs)-enriched environment, which causes high risks on human and animal health. Although antibiotics can be partially adsorbed and degraded in wastewater treatment processes, striving for a complete understanding of the microbial adaptive mechanism to antibiotic stress remains urgent. Combined with metagenomics and metabolomics, this study revealed that anammox consortia could adapt to lincomycin by spontaneously changing the preference for metabolite utilization and establishing interactions with eukaryotes, such as Ascomycota and Basidiomycota. Specifically, quorum sensing (QS) based microbial regulation and the ARGs transfer mediated by clustered regularly interspaced short palindromic repeats (CRISPR) system and global regulatory genes were the principal adaptive strategies. Western blotting results validated that Cas9 and TrfA were mainly responsible for the alteration of ARGs transfer pathway. These findings highlight the potential adaptative mechanism of microbes to antibiotic stress and fill gaps in horizontal gene transfer pathways in the anammox process, further facilitating the ARGs control through molecular and synthetic biology techniques.

Exploring Old Data with New Tricks: Long-Term Monitoring Indicates Spatial and Temporal Changes in Populations of Sympatric Prairie Grouse in the Nebraska Sandhills

The contiguous grasslands of the Sandhills region in Nebraska, USA, provide habitat for two sympatric, grassland-obligate species of grouse, the greater prairie-chicken (Tympanuchus cupido pinnatus) and the plains sharp-tailed grouse (Tympanuchus phasianellus jamesi). Collectively referred to as prairie grouse, these birds are monitored and managed jointly by wildlife practitioners who face the novel challenge of conserving historically allopatric species in shared range. We reconstructed region-wide and route-specific prairie grouse population trends in the Sandhills, using a 63-year timeseries of breeding ground counts aggregated from old reports and paper archives. Our objective was to repurpose historical data collected for harvest management to address questions pertinent to the conservation of prairie grouse, species whose populations have declined precipitously throughout their respective ranges. Because we cannot change the sampling protocol of historical data to answer new questions, we applied 3 different methods of data analysis—traditional regional mean counts used to adjust harvest regulations, spatially implicit, site-specific counts, and spatially explicit trends. Prairie-chicken populations have increased since the 1950s, whereas sharp-tailed grouse populations have remained stable or slightly declined. However, each species exhibited unique shifts in abundance and distribution over time, and regional indices masked important aspects of population change. Our findings indicate that legacy data have the capacity to tell new stories apart from the questions they were collected to answer. By integrating concepts from landscape ecology—a discipline that emerged decades after the collection of our count data began—we demonstrate the potential of historical data to address questions of modern-day conservation concern, using prairie grouse as a case study.

Making the competitive exclusion principle operational at the biogeographical scale using fuzzy logic

In biogeography the competitive exclusion principle (CEP) has been confirmed in some cases but not in others. This has fueled an unresolved debate between those advocating niche theory or the neutral theory in biodiversity and biogeography. We suggest that this situation mainly arises from the use of crisp logic, where the CEP is defined as either completely true or false. We propose the application of the fuzzy concepts of favorability (the degree to which environmental conditions are propitious for the occurrence of individual species) and favorableness (the degree to which environmental conditions are simultaneously favorable for competing species) to operationalize a fuzzy version of the CEP. Favorability was obtained by performing species distribution models applying favorability functions, while favorableness was derived from the application of the fuzzy intersection between the favorability for competing species. Then we plotted individual favorability values along the gradient of favorableness. Two potentially competing species would coexist in high-favorableness locations, as the demands of both species would be well fulfilled. In locations of low favorableness, the result would be either autecological exclusion of both species or autecological segregation, as abiotic conditions are unfavorable for at least one of the species. Competitive exclusion would occur at the intermediate stretch of the favorableness gradient, as the conditions would be good enough for persistence of each species separately but not enough for permanent coexistence. According to this theoretical framework, the observed probability that a location belongs to the intermediate favorableness area given that the two species co-occur in this location should be lower than expected according to the environmental probability models for the two species. We tested this prediction on published data about the distribution of pairs of native and introduced deer species in Great Britain, using a Bayesian approach. In two thirds of comparisons between a native and an introduced deer species the predictions of the fuzzy CEP were corroborated, which suggests that these are the pairs of species and the specific geographical areas affected by competitive exclusion. This is important both theoretically and for biodiversity conservation planning.

New insights into microbial interactions and putative competitive mechanisms during the hydrogen production from tequila vinasses

This study aimed to characterize the prokaryotic community and putative microbial interactions involved in hydrogen (H₂) production during the dark fermentation (DF) process, applying principal components analysis (PCA) to correlate changes in operational, physicochemical, and biological variables. For this purpose, a continuous stirred-tank reactor-type digester fed with tequila vinasses was operated at 24, 18, and 12 h of hydraulic retention times (HRTs) to apply organic loading rates of 20, 36, and 54 g-COD L^-1 d^-1, corresponding to stages I, II, and III, respectively. Results indicated high population dynamics for Archaea during the DF process toward a decrease in total sequences from 6299 to 99. Concerning the Bacteria community, lactic acid bacteria (LAB) were dominant reaching a relative abundance of 57.67%, while dominant H₂-producing bacteria (HPB) decreased from 25.76% to 21.06% during stage III. Putative competitive exclusion mechanisms such as competition for substrates, bacteriocins production, and micronutrient depletion carried out by Archaea and non-H₂-producing bacteria (non-HPB), especially LAB, could negatively impact the dominance of HPB such as Ethanoligenens harbinense and Clostridium tyrobutyricum. As a consequence, low maximal volumetric H₂ production rate (672 mL-H₂ L^-1 d^-1) and yield (3.88 mol-H₂ assimilated sugars^-1) were obtained. The global scenario obtained by PCA correlations suggested that C. tyrobutyricum positively impacted H₂ molar yield through butyrate fermentation using the butyryl-CoA:acetate CoA transferase pathway, while the most abundant HPB E. harbinense decreased its relative abundance at the shortest HRT toward the dominance of non-HPB. This study provides new insights into the microbial interactions and helps to better understand the DF performance for H₂ production using tequila vinasses as substrate. KEY POINTS: • E. harbinense and C. tyrobutyricum were responsible for H₂ production. • Clostridiales used acetate and butyrate fermentations for H₂ production. • LAB won the competition for sugars against Clostridiales during DF. • Putative bacteriocins production and micronutrients depletion could favor LAB.

The effects of random and seasonal environmental fluctuations on optimal harvesting and stocking

We analyze the harvesting and stocking of a population that is affected by random and seasonal environmental fluctuations. The main novelty comes from having three layers of environmental fluctuations. The first layer is due to the environment switching at random times between different environmental states. This is similar to having sudden environmental changes or catastrophes. The second layer is due to seasonal variation, where there is a significant change in the dynamics between seasons. Finally, the third layer is due to the constant presence of environmental stochasticity-between the seasonal or random regime switches, the species is affected by fluctuations which can be modelled by white noise. This framework is more realistic because it can capture both significant random and deterministic environmental shifts as well as small and frequent fluctuations in abiotic factors. Our framework also allows for the price or cost of harvesting to change deterministically and stochastically, something that is more realistic from an economic point of view. The combined effects of seasonal and random fluctuations make it impossible to find the optimal harvesting-stocking strategy analytically. We get around this roadblock by developing rigorous numerical approximations and proving that they converge to the optimal harvesting-stocking strategy. We apply our methods to multiple population models and explore how prices, or costs, and environmental fluctuations influence the optimal harvesting-stocking strategy. We show that in many situations the optimal way of harvesting and stocking is not of threshold type.

Evolutionary coexistence in a metacommunity: Competition-colonization trade-off, ownership effects, environmental fluctuations

We study the adaptive dynamics of the colonization rate of species living in a patchy habitat when there is a trade-off with the competitive strength for individual patches. To that end, we formulate a continuous-time competition-colonization model that also includes ownership effects as well as random disturbance affecting the mortality rate. We find that intermediate disturbance (as measured by the fluctuation intensity of the mortality rate), a strong competition-colonization trade-off, and a weak ownership effect are necessary conditions for evolutionary branching and hence for the emergence of polymorphisms (i.e., coexistence) by small evolutionary steps. Specifically, concerning ownership we find that with low-intermediate disturbance, a weak ownership advantage favours evolutionary branching while ownership disadvantage does not. This asymmetry disappears at the higher-intermediate disturbance. Moreover, at a low-intermediate disturbance, the effect of the strength of the competition-colonization trade-off on evolutionary branching is non-monotonic disappears because the possibility of branching disappears again when the trade-off is too strong. We also find that there can be multiple evolutionary attractors for polymorphic populations, each with its own basin of attraction. With small but non-zero random evolutionary steps and depending on the initial polymorphic condition just after branching, a coevolutionary trajectory may come arbitrarily close to the shared boundary of two such basins and may even jump from one side to the other, which can lead to various kinds of long-term evolutionary dynamics, including evolutionary branching-extinction cycles.

Effective Resource Competition Model for Species Coexistence

Local coexistence of species in large ecosystems is traditionally explained within the broad framework of niche theory. However, its rationale hardly justifies rich biodiversity observed in nearly homogeneous environments. Here we consider a consumer-resource model in which a coarse-graining procedure accounts for a variety of ecological mechanisms and leads to effective spatial effects which favor species coexistence. Herein, we provide conditions for several species to live in an environment with very few resources. In fact, the model displays two different phases depending on whether the number of surviving species is larger or smaller than the number of resources. We obtain conditions whereby a species can successfully colonize a pool of coexisting species. Finally, we analytically compute the distribution of the population sizes of coexisting species. Numerical simulations as well as empirical distributions of population sizes support our analytical findings.

Prokaryotic population dynamics and interactions in an AnSBBR using tequila vinasses as substrate in co-digestion with acid hydrolysates of Agave tequilana var. azul bagasse for hydrogen production

AIMS

The purpose of this study was to characterize the prokaryotic community and putative microbial interactions between H₂ -producing bacteria (HPB) and non-HPB using two anaerobic sequencing batch biofilm reactors (AnSBBRs) fed with tequila vinasses in co-digestion with acid hydrolysates of Agave tequilana var. azul bagasse (ATAB).

METHODS AND RESULTS

Two AnSBBRs were operated for H₂ production to correlate changes in physicochemical and biological variables by principal component analysis (PCA). Results indicated that H₂ yield was supported by Ethanoligenens harbinense and Clostridium tyrobutyricum through the PFOR pathway. However, only E. harbinense was able to compete for sugars against non-HPB. Competitive exclusion associated with competition for sugars, depletion of essential trace elements, bacteriocin production and resistance to inhibitory compounds could be carried out by non-HPB, increasing their relative abundances during the dark fermentation (DF) process.

CONCLUSIONS

The global scenario obtained by PCA correlated the decrease in H₂ production with the lactate:acetate molar ratio in the influent. At the beginning of co-digestion, this ratio had the minimum value considered for a net gain of ATP. This fact could cause the reduction of the relative abundance of C. tyrobutyricum.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study that demonstrated the feasibility of H₂ production by Clostridiales from acid hydrolysates of ATAB in co-digestion with tequila vinasses.

Stationary distributions of persistent ecological systems

We analyze ecological systems that are influenced by random environmental fluctuations. We first provide general conditions which ensure that the species coexist and the system converges to a unique invariant probability measure (stationary distribution). Since it is usually impossible to characterize this invariant probability measure analytically, we develop a powerful method for numerically approximating invariant probability measures. This allows us to shed light upon how the various parameters of the ecosystem impact the stationary distribution. We analyze different types of environmental fluctuations. At first we study ecosystems modeled by stochastic differential equations. In the second setting we look at piecewise deterministic Markov processes. These are processes where one follows a system of differential equations for a random time, after which the environmental state changes, and one follows a different set of differential equations-this procedure then gets repeated indefinitely. Finally, we look at stochastic differential equations with switching, which take into account both the white noise fluctuations and the random environmental switches. As applications of our theoretical and numerical analysis, we look at competitive Lotka-Volterra, Beddington-DeAngelis predator-prey, and rock-paper-scissors dynamics. We highlight new biological insights by analyzing the stationary distributions of the ecosystems and by seeing how various types of environmental fluctuations influence the long term fate of populations.

Freshwater phytoplankton diversity: models, drivers and implications for ecosystem properties

Our understanding on phytoplankton diversity has largely been progressing since the publication of Hutchinson on the paradox of the plankton. In this paper, we summarise some major steps in phytoplankton ecology in the context of mechanisms underlying phytoplankton diversity. Here, we provide a framework for phytoplankton community assembly and an overview of measures on taxonomic and functional diversity. We show how ecological theories on species competition together with modelling approaches and laboratory experiments helped understand species coexistence and maintenance of diversity in phytoplankton. The non-equilibrium nature of phytoplankton and the role of disturbances in shaping diversity are also discussed. Furthermore, we discuss the role of water body size, productivity of habitats and temperature on phytoplankton species richness, and how diversity may affect the functioning of lake ecosystems. At last, we give an insight into molecular tools that have emerged in the last decades and argue how it has broadened our perspective on microbial diversity. Besides historical backgrounds, some critical comments have also been made.