Gaia and natural selection

Persistence selection between simulated biogeochemical cycle variants for their distinct effects on the Earth system

The average long-term impact of Darwinian evolution on Earth's habitability remains extremely uncertain. Recent attempts to reconcile this uncertainty by "Darwinizing" nonreplicating biogeochemical processes subject to persistence-based selection conform with the historicity of the geochemical record but lack mechanistic clarity. Here, we present a theoretical framework showing how: 1) A biogeochemical "cycle-biota-variant" (CBV) can be defined non-arbitrarily as one biologically facilitated pathway for net recycling of an essential element, plus the genotypes driving the relevant interconversion reactions. 2) Distinct CBVs can be individuated if they have climatic or geochemical side effects that feed-back on relative persistence. 3) The separation of spatial/temporal scales between the dynamics of such effects and those of conventional Darwinian evolution can introduce a degree of randomness into the relationship between CBVs and their Earth system impact properties, loosely analogous to that between the biochemical causes and evolutionary effects of genetic mutation. 4) Threshold behavior in climate feedback can accentuate biotic impacts and lead to CBV-level "competitive exclusion". 5) CBV-level persistence selection is observationally distinguishable from genotype-level selection by strong covariance between "internal" CBV properties (genotypes and reactions) and "external" climatic effects, which we argue is analogous to the covariance between fitness and traits under conventional Darwinian selection. These factors cannot circumvent the basic fact that local natural selection will often favor phenotypes that ultimately destabilize large-scale geochemical/climatic properties. However, we claim that our results nevertheless demonstrate the theoretical coherence of persistence-selection between non-replicating life-environment interaction patterns and therefore have broad biogeochemical applicability.

One Earth-One Health (OE-OH): Antibacterial Effects of Plant Flavonoids in Combination with Clinical Antibiotics with Various Mechanisms

Background/Objectives: Antimicrobial resistance (AMR) poses a significant threat to human health, and combination therapy has proven effective in combating it. It has been reported that some plant flavonoids can enhance the antibacterial effects of antibiotics and even reverse AMR. This study systematically evaluated the synergistic effects of plant flavonoids and clinical antibiotics. Methods: The antibacterial activities of thirty-seven plant flavonoids and nine clinical antibiotics with various antimicrobial mechanisms were determined using the microbroth dilution method. Subsequently, the combined effects of twelve plant flavonoids presenting definite MICs against Staphylococcus aureus with these nine antibiotics were determined using the checkerboard test, together with those of thirty-two plant flavonoids presenting definite MICs against Escherichia coli with these nine antibiotics. Results: Plant flavonoids in combination with antibiotics present extensive synergistic effects, and 25% of combinations exhibited synergy against S. aureus and 50% against E. coli, particularly with antibiotics affecting cell membranes or ribosomes. Conclusions: The findings align with the drug selection principle of synergistic combinations and suggest that plant flavonoids could extensively enhance antibiotic efficacy. Considering that various metabolites from microorganisms, plants, and animals on the Earth would definitely impact the evolution of AMR, together with the rules, key factors, and important principles of drug combination for preventing AMR, we further propose the "One Earth-One Health (OE-OH)" concept, emphasizing ecosystem interactions in AMR prevention.

A synthetic microbial Daisyworld: planetary regulation in the test tube

The idea that the Earth system self-regulates in a habitable state was proposed in the 1970s by James Lovelock, who conjectured that life plays a self-regulatory role on a planetary-level scale. A formal approach to such hypothesis was presented afterwards under a toy model known as the Daisyworld. The model showed how such life-geosphere homeostasis was an emergent property of the system, where two species with different properties adjusted their populations to the changing external environment. So far, this ideal world exists only as a mathematical or computational construct, but it would be desirable to have a real, biological implementation of Lovelock's picture beyond our one biosphere. Inspired by the exploration of synthetic ecosystems using genetic engineering and recent cell factory designs, here we propose a possible implementation for a microbial Daisyworld. This includes: (i) an explicit proposal for an engineered design of a two-strain consortia, using pH as the external, abiotic control parameter and (ii) several theoretical and computational case studies including two, three and multiple species assemblies. The special alternative implementations and their implications in other synthetic biology scenarios, including ecosystem engineering, are outlined.

Planetary Scale Information Transmission in the Biosphere and Technosphere: Limits and Evolution

Information transmission via communication between agents is ubiquitous on Earth, and is a vital facet of living systems. In this paper, we aim to quantify this rate of information transmission associated with Earth's biosphere and technosphere (i.e., a measure of global information flow) by means of a heuristic order-of-magnitude model. By adopting ostensibly conservative values for the salient parameters, we estimate that the global information transmission rate for the biosphere might be ∼1024 bits/s, and that it may perhaps exceed the corresponding rate for the current technosphere by ∼9 orders of magnitude. However, under the equivocal assumption of sustained exponential growth, we find that information transmission in the technosphere can potentially surpass that of the biosphere ∼90 years in the future, reflecting its increasing dominance.

Feedbacks in ecology and evolution

Ecology and evolutionary biology have focused on how organisms fit the environment. Less attention has been given to the idea that organisms can also modify their environment, and that these modifications can feed back to the organism, thus providing a key factor for their persistence and evolution. There are at least three independent lines of evidence emphasizing these biological feedback processes at different scales: niche construction (population scale); alternative biome states (community scale); and the Gaia hypothesis (planetary scale). These feedback processes make us rethink traditional concepts like niche and adaptation. We argue that organism-environment feedbacks must become a regular part of ecological thinking, especially now that the Earth is quickly changing.

Oxidative metabolisms catalyzed Earth’s oxygenation

The burial of organic carbon, which prevents its remineralization via oxygen-consuming processes, is considered one of the causes of Earth’s oxygenation. Yet, higher levels of oxygen are thought to inhibit burial. Here we propose a resolution of this conundrum, wherein Earth’s initial oxygenation is favored by oxidative metabolisms generating partially oxidized organic matter (POOM), increasing burial via interaction with minerals in sediments. First, we introduce the POOM hypothesis via a mathematical argument. Second, we reconstruct the evolutionary history of one key enzyme family, flavin-dependent Baeyer–Villiger monooxygenases, that generates POOM, and show the temporal consistency of its diversification with the Proterozoic and Phanerozoic atmospheric oxygenation. Finally, we propose that the expansion of oxidative metabolisms instigated a positive feedback, which was amplified by the chemical changes to minerals on Earth’s surface. Collectively, these results suggest that Earth’s oxygenation is an autocatalytic transition induced by a combination of biological innovations and geological changes.

How Earth’s atmosphere became oxygenated remains enigmatic. Here the authors use mathematical and phylogenetic analyses to find that Earth’s oxygenation is induced by the interactions of microbial oxidative metabolites with sediment minerals.

Selection principles for Gaia

The Gaia hypothesis considers the life-environment coupled system as a single entity that acts to regulate and maintain habitable conditions on Earth. In this paper we discuss three mechanisms which could potentially lead to Gaia: Selection by Survival, Sequential Selection and Entropic Hierarchy. We use the Tangled Nature Model of co-evolution as a common framework for investigating all three, using an extended version of the standard model to elaborate on Gaia as an example of an entropic hierarchy. This idea, which combines sequential selection together with a reservoir of diversity that acts as a 'memory', implies a tendency towards growth and increasing resilience of the Gaian system over time. We then discuss how Gaian memory could be realised in practice via the microbial seed bank, climate refugia and lateral gene transfer and conclude by discussing testable implications of an entropic hierarchy for the study of Earth history and the search for life in the universe. This paper adds to the existing taxonomy of Gaia hypotheses to suggest an "Entropic Gaia" where we argue that increasing biomass, complexity and enhanced habitability over time is a statistically likely feature of a co-evolving system.

Habitability Models for Astrobiology

Habitability has been generally defined as the capability of an environment to support life. Ecologists have been using Habitat Suitability Models (HSMs) for more than four decades to study the habitability of Earth from local to global scales. Astrobiologists have been proposing different habitability models for some time, with little integration and consistency among them, being different in function to those used by ecologists. Habitability models are not only used to determine whether environments are habitable, but they also are used to characterize what key factors are responsible for the gradual transition from low to high habitability states. Here we review and compare some of the different models used by ecologists and astrobiologists and suggest how they could be integrated into new habitability standards. Such standards will help improve the comparison and characterization of potentially habitable environments, prioritize target selections, and study correlations between habitability and biosignatures. Habitability models are the foundation of planetary habitability science, and the synergy between ecologists and astrobiologists is necessary to expand our understanding of the habitability of Earth, the Solar System, and extrasolar planets.

Survival of the Systems

Since Darwin, individuals and more recently genes, have been the focus of evolutionary thinking. The idea that selection operates on nonreproducing, higher-level systems including ecosystems or societies, has met with scepticism. But research emphasising that natural selection can be based solely on differential persistence invites reconsideration of their evolution. Self-perpetuating feedback cycles involving biotic as well as abiotic components are critical to determining persistence. Evolution of autocatalytic networks of molecules is well studied, but the principles hold for any 'self-perpetuating' system. Ecosystem examples include coral reefs, rainforests, and savannahs. Societal examples include agricultural systems, dominant belief systems, and economies. Persistence-based selection of feedbacks can help us understand how ecological and societal systems survive or fail in a changing world.

Modeling the evolution of interconnected processes: It is the song and the singers: Tracking units of selection with interaction networks

Recently, Doolittle and Inkpen formulated a thought provoking theory, asserting that evolution by natural selection was responsible for the sideways evolution of two radically different kinds of selective units (also called Domains). The former entities, termed singers, correspond to the usual objects studied by evolutionary biologists (gene, genomes, individuals, species, etc.), whereas the later, termed songs, correspond to re-produced biological and ecosystemic functions, processes, information, and memes. Singers perform songs through selected patterns of interactions, meaning that a wealth of critical phenomena might receive novel evolutionary explanations. However, this theory did not provide an empirical approach to study evolution in such a broadened context. Here, we show that analyzing songs and singers, using patterns of interaction networks as a common ontology for both, offers a novel, actionable, inclusive and mathematical way to analyze not only the re-production but also the evolution and fitness of biological and ecosystemic interconnected processes.

Resilience Viewed through the Lens of Climate Change and Water Management

Resilience is not a new idea but there has been an upsurge in efforts to operationalize the concept within water management. This review begins with a synopsis of related themes around persistent and emerging pressures on freshwaters; environmental thresholds (or tipping points); ‘safe’ operating conditions; multiple stable states; regime shifts. A case is made for viewing and managing the resilience of water systems at nested scales. Indicators are needed to track evolving climate risks as well as to measure socio-ecological responses. Catchment properties can identify those river systems that are more or less likely to return to a pre-disturbance state; resilience further depends on institutional and social landscapes. Ideally, allied notions of resistance and reliability are applied alongside resilience to broaden the portfolio of adaptation measures. Water managers would also benefit from more consistent use of resilience terminology; incentives to build back better after catastrophes; strategic monitoring of incipient threats and tipping points; availability of long-term adaptation indicators; coordinated efforts to reduce non-climatic pressures on freshwaters (especially in headwaters); evidence-based, practical guidance on adaptation measures that build resilience.

Synthetic Biology for Terraformation Lessons from Mars, Earth, and the Microbiome

What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can it be used to change endangered ecological communities and rescue them to prevent their collapse? What are the best strategies for such ecological engineering paths to succeed? Is it possible to create stable, diverse synthetic ecosystems capable of persisting in closed environments? Can synthetic communities be created to thrive on planets different from ours? These and other questions pervade major future developments within synthetic biology. The goal of engineering ecosystems is plagued with all kinds of technological, scientific and ethic problems. In this paper, we consider the requirements for terraformation, i.e., for changing a given environment to make it hospitable to some given class of life forms. Although the standard use of this term involved strategies for planetary terraformation, it has been recently suggested that this approach could be applied to a very different context: ecological communities within our own planet. As discussed here, this includes multiple scales, from the gut microbiome to the entire biosphere.

A Multipopulation-Based Multiobjective Evolutionary Algorithm

Multipopulation is an effective optimization component often embedded into evolutionary algorithms to solve optimization problems. In this paper, a new multipopulation-based multiobjective genetic algorithm (MOGA) is proposed, which uses a unique cross-subpopulation migration process inspired by biological processes to share information between subpopulations. Then, a Markov model of the proposed multipopulation MOGA is derived, the first of its kind, which provides an exact mathematical model for each possible population occurring simultaneously with multiple objectives. Simulation results of two multiobjective test problems with multiple subpopulations justify the derived Markov model, and show that the proposed multipopulation method can improve the optimization ability of the MOGA. Also, the proposed multipopulation method is applied to other multiobjective evolutionary algorithms (MOEAs) for evaluating its performance against the IEEE Congress on Evolutionary Computation multiobjective benchmarks. The experimental results show that a single-population MOEA can be extended to a multipopulation version, while obtaining better optimization performance.

Alternative mechanisms for Gaia

A long-standing objection to the Gaia hypothesis has been a perceived lack of plausible mechanisms by which life on Earth could come to regulate its abiotic environment. A null hypothesis is survival by pure chance, by which any appearance of regulation on Earth is illusory and the persistence of life simply reflects the weak anthropic principle - it must have occurred for intelligent observers to ask the question. Recent work has proposed that persistence alone increases the chance that a biosphere will acquire further persistence-enhancing properties. Here we use a simple quantitative model to show that such 'selection by survival alone' can indeed increase the probability that a biosphere will persist in the future, relative to a baseline of pure chance. Adding environmental feedback to this model shows either an increased or decreased survival probability depending on the initial conditions. Feedback can hinder early life becoming established if initial conditions are poor, but feedback can also prevent systems from diverging too far from optimum environmental conditions and thus increase survival rates. The outstanding question remains the relative importance of each mechanism for the historical and continued persistence of life on Earth.

Implications of Tides for Life on Exoplanets

As evident from the nearby examples of Proxima Centauri and TRAPPIST-1, Earth-sized planets in the habitable zone of low-mass stars are common. Here, we focus on such planetary systems and argue that their (oceanic) tides could be more prominent due to stronger tidal forces. We identify the conditions under which tides may exert a significant positive influence on biotic processes including abiogenesis, biological rhythms, nutrient upwelling, and stimulating photosynthesis. We conclude our analysis with the identification of large-scale algal blooms as potential temporal biosignatures in reflectance light curves that can arise indirectly as a consequence of strong tidal forces. Key Words: Tidal effects-Abiogenesis-Biological clocks-Planetary habitability-Temporal biosignatures. Astrobiology 18, 967-982.

Darwinizing Gaia

The Gaia hypothesis of James Lovelock was co-developed with and vigorously promoted by Lynn Margulis, but most mainstream Darwinists scorned and still do not accept the notion. They cannot imagine selection for global stability being realized at the level of the individuals or species that make up the biosphere. Here I suggest that we look at the biogeochemical cycles and other homeostatic processes that might confer stability - rather than the taxa (mostly microbial) that implement them - as the relevant units of selection. By thus focusing our attentions on the "song", not the "singers", a Darwinized Gaia might be developed. Our understanding of evolution by natural selection would however need to be stretched to accommodate differential persistence as well as differential reproduction.

Organismal homeostasis buffers the effects of abiotic change on community dynamics

The problem of linking fine-scale processes to broad-scale patterns remains a central challenge of ecology. As rates of abiotic change intensify, there is a critical need to understand how individual responses aggregate to generate compensatory dynamics that stabilize community processes. Notably, while local and global resource enhancement (e.g., nutrient and CO2 release) can reverse dominance relationship between key species (e.g., shifts from naturally kelp-dominated to turf-dominated systems), herbivores can counter these shifts by consuming the additional productivity of competing species (e.g., turfs). Here, we test whether consumer plasticity in energy intake to maintain growth in varying environments can underpin changes in consumption that buffer varying levels of productivity. In response to carbon and nutrient enrichment, herbivores increased consumption of higher-quality food, which acted as a buffer against enhanced production, while maintaining organismal processes across varying abiotic conditions (i.e., growth). These results not only suggest plasticity in feeding behavior, but also in energy acquisition and utilization to maintain organismal processes. Such plasticity may not only underpin organismal homeostasis, but also compensatory dynamics that emerge from the aggregate of these responses to buffer change in community processes.

The Cell as the First Niche Construction

Niche construction nominally describes how organisms can form their own environments, increasing their capacity to adapt to their surroundings. It is hypothesized that the formation of the first cell as 'internal' Niche Construction was the foundation for life, and that subsequent niche constructions were iterative exaptations of that event. The first instantation of niche construction has been faithfully adhered to by returning to the unicellular state, suggesting that the life cycle is zygote to zygote, not adult to adult as is commonly held. The consequent interactions between niche construction and epigenetic inheritance provide a highly robust, interactive, mechanistic way of thinking about evolution being determined by initial conditions rather than merely by chance mutation and selection. This novel perspective offers an opportunity to reappraise the processes involved in evolution mechanistically, allowing for scientifically testable hypotheses rather than relying on metaphors, dogma, teleology and tautology.

The Case for a Gaian Bottleneck: The Biology of Habitability

The prerequisites and ingredients for life seem to be abundantly available in the Universe. However, the Universe does not seem to be teeming with life. The most common explanation for this is a low probability for the emergence of life (an emergence bottleneck), notionally due to the intricacies of the molecular recipe. Here, we present an alternative Gaian bottleneck explanation: If life emerges on a planet, it only rarely evolves quickly enough to regulate greenhouse gases and albedo, thereby maintaining surface temperatures compatible with liquid water and habitability. Such a Gaian bottleneck suggests that (i) extinction is the cosmic default for most life that has ever emerged on the surfaces of wet rocky planets in the Universe and (ii) rocky planets need to be inhabited to remain habitable. In the Gaian bottleneck model, the maintenance of planetary habitability is a property more associated with an unusually rapid evolution of biological regulation of surface volatiles than with the luminosity and distance to the host star.

Forbidden phenotypes and the limits of evolution

Evolution has produced an astonishing array of organisms, but does it have limits and, if so, how are these overcome and how have they changed over the course of time? Here, I review models for describing and explaining existing diversity, and then explore parts of the evolutionary tree that remain empty. In an analysis of 32 forbidden states among eukaryotes, identified in major clades and in the three great habitat realms of water, land and air, I argue that no phenotypic constraint is absolute, that most constraints reflect a limited time-energy budget available to individual organisms, that natural selection is ultimately responsible for both imposing and overcoming constraints, including those normally ascribed to developmental patterns of construction and phylogenetic conservatism, and that increases in adaptive versatility in major clades together with accompanying new ecological opportunities have eliminated many constraints. Phenotypes that were inaccessible during the Early Palaeozoic era have evolved during later periods while very few adaptive states have disappeared. The filling of phenotypic space has proceeded cumulatively in three overlapping phases characterized by diversification at the biochemical, morphological and cultural levels.

Living organisms influence on environmental conditions: pH modulation by amphibian embryos versus aluminum toxicity

The LC10, 50 and 90/24h of aluminum for Rhinella arenarum embryos at complete operculum stage were 0.55, 0.75 and 1mgAl(3+)/L respectively. Those values did not change significantly by expanding the exposure period till 168h. The aluminum toxicity was evaluated in different pH conditions by means of a citrate buffer resulting for instance, 1mgAl(3+)/L at pH 4, 4.1, 5 and 6 in 100%, 70%, 35% and 0% of lethality respectively. As an outstanding feature, the embryos changed the pH of the maintaining media both in the case of Al(3+) or citrate buffer treatments toward neutral. 10 embryos in 40mL of AMPHITOX solution were able to increase the pH from 4.2 to 7.05, a fact related with a metabolic shift resulting in an increase in nitrogen loss as ammonia. Our study point out the natural selection of the most resistant amphibian embryos both for pH or aluminum as well as the capacity of living organisms (as a population) to alter their chemical environment toward optimal conditions for their survival. As these facts occur at early life stages, it expand the concept that living organisms at ontogenic stages are biomarker of environmental signatures of the evolutionary process (Herkovits, 2006) to a global Onto-Evo concept which imply also the feedback mechanisms from living organisms to shape environmental conditions in a way that benefits them.

Where do herbivore-induced plant volatiles go?

Herbivore induced plant volatiles (HIPVs) are specific volatile organic compounds (VOC) that a plant produces in response to herbivory. Some HIPVs are only produced after damage, while others are also produced by intact plants, but in lower quantities. Among the known functions of HIPVs are within plant volatile signaling to activate systemic plant defenses, the priming and activation of defenses in neighboring plants and the attraction of natural enemies of herbivores. When released into the atmosphere a plant's control over the produced compounds ends. However, many of the HIPVs are highly reactive with atmospheric oxidants and their atmospheric life times could be relatively short, often only a few minutes. We summarise the potential ecological and atmospheric processes that involve the reaction products of HIPVs in their gaseous, liquid and solid secondary organic aerosol (SOA) forms, both in the atmosphere and after deposition on plant surfaces. A potential negative feedback loop, based on the reactions forming SOA from HIPVs and the associated stimulation of sun screening cloud formation is presented. This hypothesis is based on recent field surveys in the geographical areas facing the greatest degree of global warming and insect outbreaks. Furthermore, we discuss how these processes could benefit the individual plant or conspecifics that originally released the HIPVs into the atmosphere. Further ecological studies should aim to elucidate the possible reasons for biosynthesis of short-lived volatile compounds to have evolved as a response to external biotic damage to plants.

The emergence of environmental homeostasis in complex ecosystems

The Earth, with its core-driven magnetic field, convective mantle, mobile lid tectonics, oceans of liquid water, dynamic climate and abundant life is arguably the most complex system in the known universe. This system has exhibited stability in the sense of, bar a number of notable exceptions, surface temperature remaining within the bounds required for liquid water and so a significant biosphere. Explanations for this range from anthropic principles in which the Earth was essentially lucky, to homeostatic Gaia in which the abiotic and biotic components of the Earth system self-organise into homeostatic states that are robust to a wide range of external perturbations. Here we present results from a conceptual model that demonstrates the emergence of homeostasis as a consequence of the feedback loop operating between life and its environment. Formulating the model in terms of Gaussian processes allows the development of novel computational methods in order to provide solutions. We find that the stability of this system will typically increase then remain constant with an increase in biological diversity and that the number of attractors within the phase space exponentially increases with the number of environmental variables while the probability of the system being in an attractor that lies within prescribed boundaries decreases approximately linearly. We argue that the cybernetic concept of rein control provides insights into how this model system, and potentially any system that is comprised of biological to environmental feedback loops, self-organises into homeostatic states.

Life on Earth is perhaps greater than three and a half billion years old and it would appear that once it started it never stopped. During this period a number of dramatic shocks and drivers have affected the Earth. These include the impacts of massive asteroids, runaway climate change and increases in brightness of the Sun. Has life on Earth simply been lucky in withstanding such perturbations? Are there any self-regulating or homeostatic processes operating in the Earth system that would reduce the severity of such perturbations? If such planetary processes exist, to what extent are they the result of the actions of life? In this study, we show how the regulation of environmental conditions can emerge as a consequence of life's effects. If life is both affected by and affects it environment, then this coupled system can self-organise into a robust control system that was first described during the early cybernetics movement around the middle of the twentieth century. Our findings are in principle applicable to a wide range of real world systems - from microbial mats to aquatic ecosystems up to and including the entire biosphere.

Origins of evolution: non-acquired characters dominates over acquired characters in changing environment

Natural Selection is so ubiquitous that we never wonder how it appeared as the evolution rule driving Life. We usually wonder how Life appeared, and seldom do we make an explicit distinction between Life and natural selection. Here, we apply the evolution concept commonly used for studying Life to evolution itself. More precisely, we developed two models aiming at selecting among different evolution rules competing for their supremacy. We explored competition between acquired (AQ) versus non-acquired (NAQ) character inheritance. The first model is parsimonious and non-spatial, in order to understand relationships between environmental forcings and rule selection. The second model is spatially explicit and studies the adaptation differences between AQ and NAQ populations. We established that NAQ evolution rule is dominating in case of changing environment. Furthermore, we observed that a more adapted population better fits its environmental constraints, but fails in rapidly changing environments. NAQ principle and less adapted populations indeed act as a reservoir of traits that helps populations to survive in rapidly changing environments, such as the ones that probably Life experienced at its origins. Although perfectible, our modeling approaches will certainly help us to improve our understanding of origins of Life and Evolution, on Earth or elsewhere.

Regime shift and robustness of organism-created environments: A model for microbial ecosystems

Organism-environment interactions are different from organism-resource interactions in two respects: (1) resources can only be consumed by organisms whereas environmental conditions can be increased or decreased depending on the species; (2) high resource conditions generally stimulate the growth of organisms, whereas extreme environmental conditions are not necessarily favored because each species usually has an optimum range for growth. To investigate the properties of an organism-environment feedback system, we analyze a model for microbial ecosystems in which a single microorganism species can modify the environmental pH. We demonstrate that the equilibrium level of the environmental pH can be partially regulated at a relatively constant value even if the pH in the influx to the ecosystem changes over a wide range. For species that acidify the medium, the equilibrium pH is somewhat lower than the pH optimal for the species. The pH-stabilizing effect of microorganisms is stronger if their growth is self-limited by the environmental pH. When the influx becomes sufficiently alkaline, the population of the organism suddenly disappears and the environmental pH changes abruptly. The system shows bi-stability and hysteresis and therefore differs from a standard resource competition model composed of a single species that consumes resources.

Parallel ecological networks in ecosystems

In ecosystems, species interact with other species directly and through abiotic factors in multiple ways, often forming complex networks of various types of ecological interaction. Out of this suite of interactions, predator-prey interactions have received most attention. The resulting food webs, however, will always operate simultaneously with networks based on other types of ecological interaction, such as through the activities of ecosystem engineers or mutualistic interactions. Little is known about how to classify, organize and quantify these other ecological networks and their mutual interplay. The aim of this paper is to provide new and testable ideas on how to understand and model ecosystems in which many different types of ecological interaction operate simultaneously. We approach this problem by first identifying six main types of interaction that operate within ecosystems, of which food web interactions are one. Then, we propose that food webs are structured among two main axes of organization: a vertical (classic) axis representing trophic position and a new horizontal 'ecological stoichiometry' axis representing decreasing palatability of plant parts and detritus for herbivores and detrivores and slower turnover times. The usefulness of these new ideas is then explored with three very different ecosystems as test cases: temperate intertidal mudflats; temperate short grass prairie; and tropical savannah.

Environmental regulation in a network of simulated microbial ecosystems

The Earth possesses a number of regulatory feedback mechanisms involving life. In the absence of a population of competing biospheres, it has proved hard to find a robust evolutionary mechanism that would generate environmental regulation. It has been suggested that regulation must require altruistic environmental alterations by organisms and, therefore, would be evolutionarily unstable. This need not be the case if organisms alter the environment as a selectively neutral by-product of their metabolism, as in the majority of biogeochemical reactions, but a question then arises: Why should the combined by-product effects of the biota have a stabilizing, rather than destabilizing, influence on the environment? Under certain conditions, selection acting above the level of the individual can be an effective adaptive force. Here we present an evolutionary simulation model in which environmental regulation involving higher-level selection robustly emerges in a network of interconnected microbial ecosystems. Spatial structure creates conditions for a limited form of higher-level selection to act on the collective environment-altering properties of local communities. Local communities that improve their environmental conditions achieve larger populations and are better colonizers of available space, whereas local communities that degrade their environment shrink and become susceptible to invasion. The spread of environment-improving communities alters the global environment toward the optimal conditions for growth and tends to regulate against external perturbations. This work suggests a mechanism for environmental regulation that is consistent with evolutionary theory.

Environmental regulation can arise under minimal assumptions

Models that demonstrate environmental regulation as a consequence of organism and environment coupling all require a number of core assumptions. Many previous models, such as Daisyworld, require that certain environment-altering traits have a selective advantage when those traits also contribute towards global regulation. We present a model that results in the regulation of a global environmental resource through niche construction without employing this and other common assumptions. There is no predetermined environmental optimum towards which regulation should proceed assumed or coded into the model. Nevertheless, polymorphic stable states that resist perturbation emerge from the simulated co-evolution of organisms and environment. In any single simulation a series of different stable states are realised, punctuated by rapid transitions. Regulation is achieved through two main subpopulations that are adapted to slightly different resource values, which force the environmental resource in opposing directions. This maintains the resource within a comparatively narrow band over a wide range of external perturbations. Population driven oscillations in the resource appear to be instrumental in protecting the regulation against mutations that would otherwise destroy it. Sensitivity analysis shows that the regulation is robust to mutation and to a wide range of parameter settings. Given the minimal assumptions employed, the results could reveal a mechanism capable of environmental regulation through the by-products of organisms.

A fitness based analysis of Daisyworld

The Gaia hypothesis [Lovelock, J., Margulis, L., 1974. Atmospheric homeostasis: the Gaia hypothesis. Tellus 26, 1], that the earth functions as a self-regulating system, has never sat particularly comfortably with ideas in mainstream biology [Anon, 2002. In pursuit of arrogant simplicities. Nature 416, 247]. A lack of any clear role for evolution in the model has led to claims of teleology-that self-regulation emerges because it is pre-ordained to do so [Doolittle, W.F., 1981. Is nature really motherly? CoEvol. Q. 58-63; Dawkins, R., 1979. The Extended Phenotype. Oxford University Press, Oxford]. The Daisyworld parable [Watson, A.J., Lovelock, J.E., 1983. Biological homeostasis of the global environment--the parable of Daisyworld. Tellus B 35, 284], a simple mathematical illustration of Gaia, went some way to addressing these critiques but, despite recent success in incorporating natural selection [Stocker, S.,1995. Regarding mutations in Daisyworld models. J. Theor. Biol. 175, 495; Lenton, T.M., 1998. Gaia and natural selection. Nature 394, 439; Lenton, T.M., Lovelock, J.E., 2001. Daisyworld revisited: quantifying biological effects on planetary self-regulation. Tellus B 53, 288; Wood, A.J., Ackland, G.J., Lenton, T.M., 2006. Mutation of albedo and growth response leads to oscillations in a spatial Daisyworld. J. Theor. Biol. 242, 188], it remains a widely held view that the ideas are inconsistent with biological principles. We show that standard methodology from quantitative genetics can be used to predict the stationary states and dynamic behaviour of Daisyworlds. The system regulates its temperature due to the low-level evolutionary dynamics of competition between the thermally coupled daisies, no higher level principle is invoked. A reconciliation of Gaia with evolutionary theory may allow further development of evolutionary arguments for the existence of global self-regulatory systems.

Do evolution and ecology need the Gaia hypothesis?

Gaia theory, which describes the life-environment system of the Earth as stable and self-regulating, has remained at the fringes of mainstream biological science owing to its historically inadequate definition and apparent incompatibility with individual-level natural selection. The key issue is whether and why the biosphere might tend towards stability and self-regulation. We review the various ways in which these issues have been addressed by evolutionary and ecological theory, and relate these to 'Gaia theory'. We then ask how this theory extends the perspectives offered by these disciplines, and how it might be tested by novel modelling approaches and laboratory experiments using emergent technologies.

Coexistence introducing regulation of environmental conditions

Interactions between environmental conditions and environment-affecting species have not been investigated extensively. In this study, the population dynamics of species yielding regulative feedback between temperature (a representative of environmental condition) and species with a temperature-altering trait was examined. We considered a simple closed model that described the population of two species (at least one of them had a temperature-altering trait) competing for one resource. The long-term outcomes of the competition and changes of temperature were explored against increasing background temperature. As a result of simulations, the regulation of temperature was accompanied by the coexistence of two species, which was contrary to the 'Gause's exclusion principle'. The steady-state analysis showed that (i) the temperature-altering trait allowed species to coexist and (ii) the coexistence of species with the trait could introduce the regulation of temperature. A 'trade-off' in their ability to utilize a resource plays a key role in this coexistence and homeostasis of temperature. This may imply that actual environmental conditions can be automatically stabilized by resource competition among species in natural ecosystems.