Habitat loss causes long extinction transients in small trophic chains

Transients in ecology are extremely important since they determine how equilibria are approached. The debate on the dynamic stability of ecosystems has been largely focused on equilibrium states. However, since ecosystems are constantly changing due to climate conditions or to perturbations driven by the climate crisis or anthropogenic actions (habitat destruction, deforestation, or defaunation), it is important to study how dynamics can proceed till equilibria. This article investigates the dynamics and transient phenomena in small food chains using mathematical models. We are interested in the impact of habitat loss in ecosystems with vegetation undergoing facilitation. We provide a dynamical study of a small food chain system given by three trophic levels: primary producers, i.e., vegetation, herbivores, and predators. Our models reveal how habitat loss pushes vegetation towards tipping points, how the presence of herbivores in small habitats could promote ecosystem's extinction (ecological meltdown), or how the loss of predators produce a cascade effect (trophic downgrading). Mathematically, these systems exhibit many of the possible local bifurcations: saddle-node, transcritical, Andronov-Hopf, together with a global bifurcation given by a heteroclinic bifurcation. The associated transients are discussed, from the ghost dynamics to the critical slowing down tied to the local and global bifurcations. Our work highlights how the increase of ecological complexity (trophic levels) can imply more complex transitions. This article shows how the pernicious effects of perturbations (i.e., habitat loss or hunting pressure) on ecosystems could not be immediate, producing extinction delays. These theoretical results suggest the possibility that some ecosystems could be currently trapped into the (extinction) ghost of their stable past

Terraforming Earth's ecosystems : engineering ecosystems to avoid anthropogenic tipping points

The idea of Terraformation comes from the science fiction literature, where humans have the capability of changing a non-habitable planet to an Earth-like one. Nowadays, Nature is changing rapidly, the poles are melting, oceans biodiversity is vanishing due to plastic pollution, and the deserts are advancing at an unstoppable rhythm. This thesis is a first step towards the exploration of new strategies that could serve to change this pernicious tendencies jeopardising ecosystems. We suggest it may not only be possible by adding new species (alien species), but also engineering autochthonous microbial species that are already adapted to the environment. Such engineering may improve their functions and capabilities allowing them to recover the (host) ecosystem upon their re-introduction. These new functionalities should make the microbes be able to induce a bottom-up change in the ecosystem: from the micro-scale (microenvironment) to the macro-scale (even changing the composition of species in the entire the ecosystem). To make this possible, the so-called Terraformation strategy needs to fuse many different fields of knowledge. The focus of this thesis relies on studying the outcome of the interactions between species and their environment (Ecology), on making the desired modifications by means of genetic engineering of the wild-type species (Synthetic Biology), and on monitoring the evaluation of the current ecosystems’ states, testing the possible changes, and predicting the future development of possible interventions (Dynamical Systems). In order to do so, in this thesis, we have gathered the tools provided by these different fields of knowledge. The methodology is based on loops between observation, designing, and prediction. For example, if there is a lack of humidity in semiarid ecosystems, we then propose to engineer e.g. Nostoc sp. to enhace its capability to produce extracellular matrix (increasing water retention). With this framework, we perform a model to understand the different possible dynamics, by means of dynamical equations to evaluate e.g. when a synthetic strain will remain in the ecosystem and the effects it will produce. We have also studied spatial models to predict their ability to modify the spatial organization of vegetation. Transient dynamics depend on the kind of transition underlying the occurring tipping point. For this reason, we have studied different systems: vegetation dynamics with facilitation (typical from drylands), a cooperator-parasite system, and a trophic chain model where different human interventions can be tested (i.e. hunting, deforestation, soil degradation, habitat destruction). All of these systems are shown to promote different types of transitions (i.e. smooth and catastrophic transitions). Each transition has its own dynamical fingerprint and thus knowing them can help monitoring and anticipating these transitions even before they happen, taking advantage of the so-called early warning signals. In this travel, we have found that transients can be an important phenomena in the current changing world. The ecosystems that we observe can be trapped into a seemingly stable regime, but be indeed in an unstable situation driving to a future sudden collapse (Fig 1) For this reason, we need to investigate novel intervention methods able to sustain the current ecosystems, for instance: Terraformation

Bacteriophage-based synthetic biology

Treball de fi de grau en BiomèdicaTutor: Javier MaciàThe biology is complex and there is a sort of organisms that interacts worldwide. In that big system, there are the viruses, organisms that are not “alive” while they are out of the host organism. When viruses enter inside the host cell, immediately start to use their own molecular machinery in combination with the host one, in order to produce the molecules that are encoded in their genes. The first interactions between the host (inner medium, cell cycle state, etc.), and the viruses affects to behaviour will develop the virus. The behaviours are: produce copies of the viruses (lytic state) or be inserted to the host genome and be silenced until dangers for the virus became (lysogenic state). The aim of this project is to develop new applications that allow controlling -phage virus (bacteriophage) in several scenarios. The control was reached with synthetic genetic construct that interacts with the wild type genome of the virus in order to control the transition between the lysogenic and lytic states. This study was a computational approach where we use the simple model from Hasty [1] that describes CI-CRO genetic circuit, responsible of the virus bistability, and we add in this system the parts that describes our synthetic circuits. Using this approaches we have finally obtained circuits that make the bacteria immune to the -phage virus infection, lyses the cells using an external effector and finally a population control of infected cells via coupling Quorum sensing [2] with the regulation of the viral genome. For all these systems we have agent-based simulations using Netlogo. These simulations and the simplicity of the synthetic circuits give us good perspectives in order to be implemented in the wet-lab

Ecological firewalls for synthetic biology

It has been recently suggested that engineered microbial strains could be used to protect ecosystems from undesirable tipping points and biodiversity loss. A major concern in this context is the potential unintended consequences, which are usually addressed in terms of designed genetic constructs aimed at controlling overproliferation. Here we present and discuss an alternative view grounded in the nonlinear attractor dynamics of some ecological network motifs. These ecological firewalls are designed to perform novel functionalities (such as plastic removal) while containment is achieved within the resident community. That could help provide a self-regulating biocontainment. In this way, engineered organisms have a limited spread while-when required-preventing their extinction. The basic synthetic designs and their dynamical behavior are presented, each one inspired in a given ecological class of interaction. Their possible applications are discussed and the broader connection with invasion ecology outlined

Dynamics in a time-discrete food-chain model with strong pressure on preys

Discrete-time dynamics, mainly arising in boreal and temperate ecosystems for species with non-overlapping generations, have been largely studied to understand the dynamical outcomes due to changes in relevant ecological parameters. The local and global dynamical behaviour of many of these models is difficult to investigate analytically in the parameter space and, typically, numerical approaches are employed when the dimension of the phase space is large. In this article we provide topological and dynamical results for a map modelling a discrete-time, three-species food chain with two predator species interacting on the same prey. The domain where dynamics live is characterised, as well as the so-called escaping regions, which involve species extinctions. We also provide a full description of the local stability of equilibria within a volume of the parameter space given by the prey’s growth rate and the predation rates. We have found that the increase of the pressure of predators on the prey results in chaos via a supercritical Neimark-Sacker bifurcation. Then, period-doubling bifurcations of invariant curves take place. Interestingly, an increasing predation directly on preys can shift the extinction of top predators to their survival, allowing an unstable persistence of the three species by means of periodic and chaotic attractors

Synthetic criticality in cellular brains

Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to such critical boundaries consistent with self-organized criticality (SOC). Is this also taking place in small-scale living systems, such as cells? Here, we explore a recent model of engineered gene networks that have been shown to exploit the feedback between order and control parameters (as defined by expression levels of two coupled genes) to achieve an SOC state. We suggest that such SOC motif could be exploited to generate adaptive behavioral patterns and might help design fast responses in synthetic cellular and multicellular organisms.This work was supported by the Spanish Ministry of Economy and Competitiveness, Grant PID2019-111680GB-I00, an MICIN Grant PID2019-111680GB-I00 and an AGAUR FI 2018 Grant. JS has been partially funded by the CERCA Programme of the 'Generalitat de Catalunya', by 'Agencia Estatal de Investigación' Grant RTI2018-098322-B-I00 and by the 'Ramón y Cajal' contract RYC-2017-22243. AG has been funded by the AGAUR Grant 2017-SGR-1049 and by the MINECO-FEDER-UE Grants PGC-2018-098676-B-100 and RTI2018-093860-B-C21. JP was funded by FPI 202

Critical slowing down close to a global bifurcation of a curve of quasineutral equilibria

Critical slowing down arises close to bifurcations and involves long transients. Despite slowing down phenomena have been widely studied in local bifurcations i.e., bifurcations of equilibrium points, less is known about transient delay phenomena close to global bifurcations. In this paper, we identify a novel mechanism of slowing down arising in the vicinity of a global bifurcation i.e., zip bifurcation, identified in a mathematical model of the dynamics of an autocatalytic replicator with an obligate parasite. Three different dynamical scenarios are first described, depending on the replication rate of cooperators, $(L)$, and of parasites, $(K)$. If $KL$ the system is monostable and both species become extinct. In the case $K=L$ coexistence of both species takes place in a Curve of Quasi-Neutral Equilibria (CQNE). The novel slowing down mechanism identified is due to an underlying ghost CQNE for the cases $K \lesssim L$ and $K \gtrsim L$. We show, both analytically and numerically, that the delays caused by the ghost CQNE follow scaling laws of the form $\tau \sim|K-L|^{-1}$ for both $K \lesssim L$ and $K \gtrsim L$. We propose the ghost CQNE as a novel transientgenerator mechanism in ecological systems

Synthetic lateral inhibition in periodic pattern forming microbial colonies

Multicellular entities are characterized by intricate spatial patterns, intimately related to the functions they perform. These patterns are often created from isotropic embryonic structures, without external information cues guiding the symmetry breaking process. Mature biological structures also display characteristic scales with repeating distributions of signals or chemical species across space. Many candidate patterning modules have been used to explain processes during development and typically include a set of interacting and diffusing chemicals or agents known as morphogens. Great effort has been put forward to better understand the conditions in which pattern-forming processes can occur in the biological domain. However, evidence and practical knowledge allowing us to engineer symmetry-breaking is still lacking. Here we follow a different approach by designing a synthetic gene circuit in E. coli that implements a local activation long-range inhibition mechanism. The synthetic gene network implements an artificial differentiation process that changes the physicochemical properties of the agents. Using both experimental results and modeling, we show that the proposed system is capable of symmetry-breaking leading to regular spatial patterns during colony growth. Studying how these patterns emerge is fundamental to further our understanding of the evolution of biocomplexity and the role played by self-organization. The artificial system studied here and the engineering perspective on embryogenic processes can help validate developmental theories and identify universal properties underpinning biological pattern formation, with special interest for the area of synthetic developmental biology.This study was supported by a European Research Council Advanced Grant (SYNCOM), the Botin Foundation, by Banco Santander through its Santander Universities Global Division and by a MINECO Grant FIS2015-67616-P. This work has also received support by the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya and by the Santa Fe Institute

Population dynamics of synthetic terraformation motifs

Ecosystems are complex systems, currently experiencing several threats associated with global warming, intensive exploitation and human-driven habitat degradation. Because of a general presence of multiple stable states, including states involving population extinction, and due to the intrinsic nonlinearities associated with feedback loops, collapse in ecosystems could occur in a catastrophic manner. It has been recently suggested that a potential path to prevent or modify the outcome of these transitions would involve designing synthetic organisms and synthetic ecological interactions that could push these endangered systems out of the critical boundaries. In this paper, we investigate the dynamics of the simplest mathematical models associated with four classes of ecological engineering designs, named Terraformation motifs (TMs). These TMs put in a nutshell different ecological strategies. In this context, some fundamental types of bifurcations pervade the systems' dynamics. Mutualistic interactions can enhance persistence of the systems by means of saddle-node bifurcations. The models without cooperative interactions show that ecosystems achieve restoration through transcritical bifurcations. Thus, our analysis of the models allows us to define the stability conditions and parameter domains where these TMs must work.This study was supported by a European Research Council Advanced Grant (SYNCOM), by the Botin Foundation, by Banco Santander through its Santander Universities Global Division, by grant FIS2015-67616-P, by the PR01018-EC-H2020-FET-Open MADONNA project and by the Santa Fe Institute. This work has also counted with the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya. J.S. has been also partially funded by a ‘Ramón y Cajal’ Fellowship (RYC-2017-22243) and by the CERCA Programme of the Generalitat de Catalunya. The research leading to these results has received funding from ‘la Caixa’ Foundatio

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.N.C.-P., B.V., R.S., and V.L. have been funded by PR01018-EC-H2020-FET-Open MADONNA project. Moreover, N.C.-P., B.V. and R.S. were partialy funded by European Research Council Advanced Grant (SYNCOM), and the Botin Foundation (Banco Santander through its Santander Universities Global Division). R.S. also counted with the support of the FIS2015-67616-P grant, the Santa Fe Institute, and the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya. J.S. has been funded by a “Ramón y Cajal” contract RYC-2017-22243, and by the MINECO grant MTM2015-71509-C2-1-R and the Spain’s “Agencia Estatal de Investigación” grant RTI2018-098322-B-I00, as well as by the CERCA Programme of the Generalitat de Catalunya. F.T.M acknowledges the support by the European Research Council (ERC Grant Agreements 242658 [BIOCOM] and 647038 [BIODESERT], and also acknowledges support from Generalitat Valenciana (CIDEGENT/2018/041). M.D.B. acknowledges support from the Marie Sklodowska-Curie Actions of the Horizon 2020 Framework Program H2020-MSCA-IF-2016 under REA grant agreement 702057 and acknowledges support from a Juan de la Cierva Formación grant from Spanish Ministry of Science (FJCI-2018-036520-I)