Evolutionary stability of coexistence due to the storage effect in a two-season model

The current progress of tandem chemical and biological plastic upcycling

Each year, millions of tons of plastics are produced for use in such applications as packaging, construction, and textiles. While plastic is undeniably useful and convenient, its environmental fate and transport have raised growing concerns about waste and pollution. However, the ease and low cost of producing virgin plastic have so far made conventional plastic recycling economically unattractive. Common contaminants in plastic waste and shortcomings of the recycling processes themselves typically mean that recycled plastic products are of relatively low quality in some cases. The high cost and high energy requirements of typical recycling operations also reduce their economic benefits. In recent years, the bio-upcycling of chemically treated plastic waste has emerged as a promising alternative to conventional plastic recycling. Unlike recycling, bio-upcycling uses relatively mild process conditions to economically transform pretreated plastic waste into value-added products. In this review, we first provide a précis of the general methodology and limits of conventional plastic recycling. Then, we review recent advances in hybrid chemical/biological upcycling methods for different plastics, including polyethylene terephthalate, polyurethane, polyamide, polycarbonate, polyethylene, polypropylene, polystyrene, and polyvinyl chloride. For each kind of plastic, we summarize both the pretreatment methods for making the plastic bio-available and the microbial chassis for degrading or converting the treated plastic waste to value-added products. We also discuss both the limitations of upcycling processes for major plastics and their potential for bio-upcycling.

Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches

How natural communities maintain their remarkable biodiversity and which species survive in complex communities are central questions in ecology. Resource competition models successfully explain many phenomena but typically predict only as many species as resources can coexist. Here, we demonstrate that sequential resource utilization, or diauxie, with periodic growth cycles can support many more species than resources. We explore how communities modify their own environments by sequentially depleting resources to form sequences of temporal niches, or intermediately depleted environments. Biodiversity is enhanced when community-driven or environmental fluctuations modulate the resource depletion order and produce different temporal niches on each growth cycle. Community-driven fluctuations under constant environmental conditions are rare, but exploring them illuminates the temporal niche structure that emerges from sequential resource utilization. With environmental fluctuations, we find most communities have more stably coexisting species than resources with survivors accurately predicted by the same temporal niche structure and each following a distinct optimal strategy. Our results thus present a new niche-based approach to understanding highly diverse fluctuating communities.

Stability of consumer-resource interactions in periodic environments

Periodic fluctuations in abiotic conditions are ubiquitous across a range of temporal scales and regulate the structure and function of ecosystems through dynamic biotic responses that are adapted to these external forces. Research has suggested that certain environmental signatures may play a crucial role in the maintenance of biodiversity and the stability of food webs, while others argue that coupled oscillators ought to promote chaos. As such, numerous uncertainties remain regarding the intersection of temporal environmental patterns and biological responses, and we lack a general understanding of the implications for food web stability. Alarmingly, global change is altering the nature of both environmental rhythms and biological rates. Here, we develop a general theory for how continuous periodic variation in productivity, across temporal scales, influences the stability of consumer-resource interactions: a fundamental building block of food webs. Our results suggest that consumer-resource dynamics under environmental forcing are highly complex and depend on asymmetries in both the speed of forcing relative to underlying dynamics and in local stability properties. These asymmetries allow for environmentally driven stabilization under fast forcing, relative to underlying dynamics, as well as extremely complex and unstable dynamics at slower periodicities. Our results also suggest that changes in naturally occurring periodicities from climate change may lead to precipitous shifts in dynamics and stability.

Eco-evolutionary maintenance of diversity in fluctuating environments

Growing evidence suggests that temporally fluctuating environments are important in maintaining variation both within and between species. To date, however, studies of genetic variation within a population have been largely conducted by evolutionary biologists (particularly population geneticists), while population and community ecologists have concentrated more on diversity at the species level. Despite considerable conceptual overlap, the commonalities and differences of these two alternative paradigms have yet to come under close scrutiny. Here, we review theoretical and empirical studies in population genetics and community ecology focusing on the 'temporal storage effect' and synthesise theories of diversity maintenance across different levels of biological organisation. Drawing on Chesson's coexistence theory, we explain how temporally fluctuating environments promote the maintenance of genetic variation and species diversity. We propose a further synthesis of the two disciplines by comparing models employing traditional frequency-dependent dynamics and those adopting density-dependent dynamics. We then address how temporal fluctuations promote genetic and species diversity simultaneously via rapid evolution and eco-evolutionary dynamics. Comparing and synthesising ecological and evolutionary approaches will accelerate our understanding of diversity maintenance in nature.

Periodic temporal environmental variations induce coexistence in resource competition models

Natural ecosystems, in particular on the microbial scale, are inhabited by a large number of species. The population size of each species is affected by interactions of individuals with each other and by spatial and temporal changes in environmental conditions, such as resource abundance. Here, we use a generic population dynamics model to study how, and under what conditions, a periodic temporal environmental variation can alter an ecosystem's composition and biodiversity. We demonstrate that using timescale separation allows one to qualitatively predict the long-term population dynamics of interacting species in varying environments. We show that the notion of Tilman's R* rule, a well-known principle that applies for constant environments, can be extended to periodically varying environments if the timescale of environmental changes (e.g., seasonal variations) is much faster than the timescale of population growth (doubling time in bacteria). When these timescales are similar, our analysis shows that a varying environment deters the system from reaching a steady state, and stable coexistence between multiple species becomes possible. Our results posit that biodiversity can in part be attributed to natural environmental variations.

Seasonal specialization drives divergent population dynamics in two closely related butterflies

Seasons impose different selection pressures on organisms through contrasting environmental conditions. How such seasonal evolutionary conflict is resolved in organisms whose lives span across seasons remains underexplored. Through field experiments, laboratory work, and citizen science data analyses, we investigate this question using two closely related butterflies (Pieris rapae and P. napi). Superficially, the two butterflies appear highly ecologically similar. Yet, the citizen science data reveal that their fitness is partitioned differently across seasons. Pieris rapae have higher population growth during the summer season but lower overwintering success than do P. napi. We show that these differences correspond to the physiology and behavior of the butterflies. Pieris rapae outperform P. napi at high temperatures in several growth season traits, reflected in microclimate choice by ovipositing wild females. Instead, P. rapae have higher winter mortality than do P. napi. We conclude that the difference in population dynamics between the two butterflies is driven by seasonal specialization, manifested as strategies that maximize gains during growth seasons and minimize harm during adverse seasons, respectively.

Life-history responses to temperature and seasonality mediate ectotherm consumer-resource dynamics under climate warming

Climate warming is altering life cycles of ectotherms by advancing phenology and decreasing generation times. Theoretical models provide powerful tools to investigate these effects of climate warming on consumer-resource population dynamics. Yet, existing theory primarily considers organisms with simplified life histories in constant temperature environments, making it difficult to predict how warming will affect organisms with complex life cycles in seasonal environments. We develop a size-structured consumer-resource model with seasonal temperature dependence, parameterized for a freshwater insect consuming zooplankton. We simulate how climate warming in a seasonal environment could alter a key life-history trait of the consumer, number of generations per year, mediating responses of consumer-resource population sizes and consumer persistence. We find that, with warming, consumer population sizes increase through multiple mechanisms. First, warming decreases generation times by increasing rates of resource ingestion and growth and/or lengthening the growing season. Second, these life-history changes shorten the juvenile stage, increasing the number of emerging adults and population-level reproduction. Unstructured models with similar assumptions found that warming destabilized consumer-resource dynamics. By contrast, our size-structured model predicts stability and consumer persistence. Our study suggests that, in seasonal environments experiencing climate warming, life-history changes that lead to shorter generation times could delay population extinctions.

Phenological Coadaptation Can Stabilize Predator–Prey Dynamics

In recent years, phenology – the seasonal timing of biological life cycles – has received increasing attention as climate change threatens to shift phenology. Phenology is crucial to the life cycle of organisms and their interactions with intimate partner species; hence, phenology has important fitness consequences suggesting that phenology can change through adaptive processes caused by species interaction. However, to date, there is limited understanding of how phenological adaptation occurs among interacting species and consequently affects ecological population dynamics. In this study, a phenological predator–prey co-adaptation model was evaluated to determine how adaptive phenological changes occur in prey and predator and how phenological coadaptation affects their coexistence. Population fluctuations tend to decrease and become stabilized when adaptation occurs rapidly. Furthermore, when adaptation is slow, predator–prey dynamics can be stabilized or destabilized depending on the initial difference in phenological timing between species. These results suggest that phenology shaped by slow coevolution can shift with changes in activity timing caused by environmental changes and simultaneously alter the stability of predator–prey dynamics. In contrast, phenology caused by rapid adaptation, such as phenotypic plasticity, may be robust to environmental change and maintain the stability of predator–prey dynamics. Understanding the types of adaptative processes that shape species phenologies may be crucial for predicting the ecological effects of climate change.

Construction of Environmental Synthetic Microbial Consortia: Based on Engineering and Ecological Principles

In synthetic biology, engineering principles are applied to system design. The development of synthetic microbial consortia represents the intersection of synthetic biology and microbiology. Synthetic community systems are constructed by co-cultivating two or more microorganisms under certain environmental conditions, with broad applications in many fields including ecological restoration and ecological theory. Synthetic microbial consortia tend to have high biological processing efficiencies, because the division of labor reduces the metabolic burden of individual members. In this review, we focus on the environmental applications of synthetic microbial consortia. Although there are many strategies for the construction of synthetic microbial consortia, we mainly introduce the most widely used construction principles based on cross-feeding. Additionally, we propose methods for constructing synthetic microbial consortia based on traits and spatial structure from the perspective of ecology to provide a basis for future work.

Stabilising role of seed banks and the maintenance of bacterial diversity

Coexisting species often exhibit negative frequency dependence due to mechanisms that promote population growth and persistence when rare. These stabilising mechanisms can maintain diversity through interspecific niche differences, but also through life-history strategies like dormancy that buffer populations in fluctuating environments. However, there are few tests demonstrating how seed banks contribute to long-term community dynamics and the maintenance of diversity. Using a multi-year, high-frequency time series of bacterial community data from a north temperate lake, we documented patterns consistent with stabilising coexistence. Bacterial taxa exhibited differential responses to seasonal environmental conditions, while seed bank dynamics helped maintain diversity over less-favourable winter periods. Strong negative frequency dependence in rare, but metabolically active, taxa suggested a role for biotic interactions in promoting coexistence. Together, our results provide field-based evidence that niche differences and seed banks contribute to recurring community dynamics and the long-term maintenance of diversity in nature.

Character displacement in the presence of multiple trait differences: Evolution of the storage effect in germination and growth

Ecological character displacement is a prominent hypothesis for the maintenance of ecological differences between species that are critical to stable coexistence. Models of character displacement often ascribe interspecific competitive interactions to a single character, but multiple characters contribute to competition, and their effects on selection can be nonadditive. Focusing on one character, we ask if other characters that affect competition alter evolutionary outcomes for the focal character. We address this question using the variable environment seed bank model for two species with two traits. The focal trait is the temporal pattern of germination, which is evolutionary labile. The other trait is the temporal pattern of plant growth, which is assumed fixed. We ask whether evolutionary divergence of germination patterns between species depends on species differences in plant growth. Patterns of growth can affect selection on germination patterns in two ways. First, cues present at germination can provide information about future growth. Second, germination and growth jointly determine the biomass of plants, which determines demand for resources. Germination and growth contribute to the selection gradient in distinct components, one density-independent and the other density-dependent. Importantly, the relative strengths of the components are key. When the density-dependent component is stronger, displacement in germination patterns between species is larger. Stronger cues at germination strengthen the density-independent component by increasing the benefits of germinating in years of favorable growth. But cues also affect the density-dependent component by boosting a species' biomass, and hence its competitive effect, in good years. Consequently, cues weaken character displacement when growth patterns are similar for two competitors, but favor displacement when growth patterns are species-specific. Understanding how these selection components change between contexts can help understand the origin and maintenance of species differences in germination patterns in temporally fluctuating environments.

Interspecific competition between resident and wintering birds: experimental evidence and consequences of coexistence

The contribution of interspecific competition to structuring population and community dynamics remains controversial and poorly tested. Interspecific competition has long been thought to influence the structure of migrant-resident bird communities in winter, yet experimental evidence remains elusive. The arrival of billions of songbirds into Neotropical habitats, where they co-exist with residents, provides a unique opportunity to assess interspecific competition and its consequences. Working in 15 ha of Jamaican black mangrove forest, we used removal experiments to test whether dominant resident Yellow Warblers compete interspecifically with subordinate wintering American Redstarts; we also used observational evidence (interspecific territorial overlap) to understand whether this coexistence influences physical condition, spring departure dates or annual return rates. Consistent with interspecific competition, after experimental removal of the resident, yearling male Redstarts (but not females or adult males) immediately moved into vacated Yellow Warbler territories, increasing their overlap with the space by 7.3%. Yearling Redstarts also appeared to adjust their territorial space use by actively avoiding Yellow Warblers; for example, Redstarts departing the wintering grounds as yearlings and returning the following winter shifted such that their territories overlapped 32% less with those of Yellow Warblers. Adult Redstarts showed no such territorial flexibility. Adult male Redstarts also showed evidence supporting the consequences of coexistence: territorial overlap with Yellow Warblers was negatively correlated with body condition and annual return rates. Adult male Redstarts with <25% territorial overlap with Yellow Warblers were more than three times as likely to return between seasons than those with 100% overlap. We propose that the territorial inflexibility of adult male Redstarts produces these consequences, which may be due to their years-long investment in that particular territory. More generally, the temporary nature of migrant-resident interspecific competition is likely what allows coexistence during winter, the most resource-poor time of year. Interspecific competition and the consequences of coexistence are likely age- and sex-specific and the product of intraspecific dominance hierarchy in Redstarts. Our observations suggest that interspecific coexistence has measurable consequences, and our experiments support the long-held, but previously untested belief that resident birds compete interspecifically with wintering migrants.

Stabilization of extensive fine-scale diversity by ecologically driven spatiotemporal chaos

It has recently become apparent that the diversity of microbial life extends far below the species level to the finest scales of genetic differences. Remarkably, extensive fine-scale diversity can coexist spatially. How is this diversity stable on long timescales, despite selective or ecological differences and other evolutionary processes? Most work has focused on stable coexistence or assumed ecological neutrality. We present an alternative: extensive diversity maintained by ecologically driven spatiotemporal chaos, with no assumptions about niches or other specialist differences between strains. We study generalized Lotka-Volterra models with antisymmetric correlations in the interactions inspired by multiple pathogen strains infecting multiple host strains. Generally, these exhibit chaos with increasingly wild population fluctuations driving extinctions. But the simplest spatial structure, many identical islands with migration between them, stabilizes a diverse chaotic state. Some strains (subspecies) go globally extinct, but many persist for times exponentially long in the number of islands. All persistent strains have episodic local blooms to high abundance, crucial for their persistence as, for many, their average population growth rate is negative. Snapshots of the abundance distribution show a power law at intermediate abundances that is essentially indistinguishable from the neutral theory of ecology. But the dynamics of the large populations are much faster than birth-death fluctuations. We argue that this spatiotemporally chaotic "phase" should exist in a wide range of models, and that even in rapidly mixed systems, longer-lived spores could similarly stabilize a diverse chaotic phase.

Microbial communities display alternative stable states in a fluctuating environment

The effect of environmental fluctuations is a major question in ecology. While it is widely accepted that fluctuations and other types of disturbances can increase biodiversity, there are fewer examples of other types of outcomes in a fluctuating environment. Here we explore this question with laboratory microcosms, using cocultures of two bacterial species, P. putida and P. veronii. At low dilution rates we observe competitive exclusion of P. veronii, whereas at high dilution rates we observe competitive exclusion of P. putida. When the dilution rate alternates between high and low, we do not observe coexistence between the species, but rather alternative stable states, in which only one species survives and initial species’ fractions determine the identity of the surviving species. The Lotka-Volterra model with a fluctuating mortality rate predicts that this outcome is independent of the timing of the fluctuations, and that the time-averaged mortality would also lead to alternative stable states, a prediction that we confirm experimentally. Other pairs of species can coexist in a fluctuating environment, and again consistent with the model we observe coexistence in the time-averaged dilution rate. We find a similar time-averaging result holds in a three-species community, highlighting that simple linear models can in some cases provide powerful insight into how communities will respond to environmental fluctuations.

The effect of environmental fluctuations on community structure and function is a fundamental question in ecology. A significant body of work suggests that fluctuations increase diversity due to a variety of proposed mechanisms. In this study, we compare the effects of constant and fluctuating dilution regimes on simple microbial communities with two or three species. We find that in all cases, the outcome in a fluctuating environment is the same as that in a constant environment in which the fluctuations are time-averaged. This surprising result highlights that in some communities, ecological stable states may be predicted by averaging environmental parameters, rather than by the variation itself.

Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection

Natural environments are rarely static; rather selection can fluctuate on timescales ranging from hours to centuries. However, it is unclear how adaptation to fluctuating environments differs from adaptation to constant environments at the genetic level. For bacteria, one key axis of environmental variation is selection for planktonic or biofilm modes of growth. We conducted an evolution experiment with Burkholderia cenocepacia, comparing the evolutionary dynamics of populations evolving under constant selection for either biofilm formation or planktonic growth with populations in which selection fluctuated between the two environments on a weekly basis. Populations evolved in the fluctuating environment shared many of the same genetic targets of selection as those evolved in constant biofilm selection, but were genetically distinct from the constant planktonic populations. In the fluctuating environment, mutations in the biofilm-regulating genes wspA and rpfR rose to high frequency in all replicate populations. A mutation in wspA first rose rapidly and nearly fixed during the initial biofilm phase but was subsequently displaced by a collection of rpfR mutants upon the shift to the planktonic phase. The wspA and rpfR genotypes coexisted via negative frequency-dependent selection around an equilibrium frequency that shifted between the environments. The maintenance of coexisting genotypes in the fluctuating environment was unexpected. Under temporally fluctuating environments, coexistence of two genotypes is only predicted under a narrow range of conditions, but the frequency-dependent interactions we observed provide a mechanism that can increase the likelihood of coexistence in fluctuating environments.

Evolutionarily stable communities: a framework for understanding the role of trait evolution in the maintenance of diversity

Biological diversity depends on the interplay between evolutionary diversification and ecological mechanisms allowing species to coexist. Current research increasingly integrates ecology and evolution over a range of timescales, but our common conceptual framework for understanding species coexistence requires better incorporation of evolutionary processes. Here, we focus on the idea of evolutionarily stable communities (ESCs), which are theoretical endpoints of evolution in a community context. We use ESCs as a unifying framework to highlight some important but under-appreciated theoretical results, and we review empirical research relevant to these theoretical predictions. We explain how, in addition to generating diversity, evolution can also limit diversity by reducing the effectiveness of coexistence mechanisms. The coevolving traits of competing species may either diverge or converge, depending on whether the number of species in the community is low (undersaturated) or high (oversaturated) relative to the ESC. Competition in oversaturated communities can lead to extinction or neutrally coexisting, ecologically equivalent species. It is critical to consider trait evolution when investigating fundamental ecological questions like the strength of different coexistence mechanisms, the feasibility of ecologically equivalent species, and the interpretation of different patterns of trait dispersion.