Synthetic Ecosystems Research Articles

From synthetic communities to synthetic ecosystems: exploring causalities in plant-microbe-environment interactions.

The plant microbiota research field has rapidly shifted from efforts aimed at gaining a descriptive understanding of microbiota composition to a focus on acquiring mechanistic insights into microbiota functions and assembly rules. This evolution was driven by our ability to establish comprehensive collections of plant-associated microbes and to reconstruct meaningful microbial synthetic communities (SynComs). We argue that this powerful deconstruction-reconstruction strategy can be used to reconstitute increasingly complex synthetic ecosystems (SynEcos) and mechanistically understand high-level biological organization. The transitioning from simple to more advanced, fully tractable and programmable gnotobiotic SynEcos is ongoing and aims at rationally simplifying natural ecosystems by engineering them. Such reconstitution ecology approaches represent an untapped strategy for bridging the gap between ecology and functional biology and for unraveling plant-microbiota-environment mechanisms that modulate ecosystem health, assembly, and functioning.

Synthetic microbial ecology: engineering habitats for modular consortia.

Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.

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.

Biodiversity and Constrained Information Dynamics in Ecosystems: A Framework for Living Systems.

The increase in ecosystem biodiversity can be perceived as one of the universal processes converting energy into information across a wide range of living systems. This study delves into the dynamics of living systems, highlighting the distinction between ex post adaptation, typically associated with natural selection, and its proactive counterpart, ex ante adaptability. Through coalescence experiments using synthetic ecosystems, we (i) quantified ecosystem stability, (ii) identified correlations between some biodiversity indexes and the stability, (iii) proposed a mechanism for increasing biodiversity through moderate inter-ecosystem interactions, and (iv) inferred that the information carrier of ecosystems is species composition, or merged genomic information. Additionally, it was suggested that (v) changes in ecosystems are constrained to a low-dimensional state space, with three distinct alteration trajectories-fluctuations, rapid environmental responses, and long-term changes-converging into this state space in common. These findings suggest that daily fluctuations may predict broader ecosystem changes. Our experimental insights, coupled with an exploration of living systems' information dynamics from an ecosystem perspective, enhance our predictive capabilities for natural ecosystem behavior, providing a universal framework for understanding a broad spectrum of living systems.

Synthetic ecosystems: an emerging opportunity for science and society?

For millenia, humans have modified aspects of natural ecosystems to meet their social, economic and ecological needs. With advancing technology and global movement of species, modification has shifted to designing and creating new ecologies in cityscapes, building interiors, agricultural settings and more. We call intentional ecosystems that combine biodiversity and technology with little to no shared history, synthetic ecosystems. Fields, from microbial ecology to agroecology, build synthetic ecosystems under different names but share the same properties of: Being human‐designed, assembled and controlled, having novel components and/or interactions, and creating systems distinctly different from what came before at a site. Creating synthetic ecosystems represents a design challenge, but also an opportunity for real‐world impact – which we illustrate with a biodiverse, indoor synthetic ecosystem for food production. Overall, synthetic ecosystems may advance socioecological goals in six ways. They can: 1) replace ecological deadzones with living systems (e.g. building green roofs), 2) enhance existing ecosystem processes (e.g. boosting agricultural yields), 3) create new ecosystem functions (e.g. bioelectricity), 4) establish new ecosystem controls (e.g. biological control), 5) foster knowledge synthesis (e.g. testing ecological theory) and 6) reshape human‐nature relationships (e.g. improve wellbeing). To realize these potentials, future work must more fully evaluate whereandwhen synthetic ecosystems are appropriate to build, whatarchitectures and aspects of diversity (biological and technological) make them most functional and how knowledge from across cultures and eras can be integrated in solutions.

Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor.

Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a community, functionally specialized strains can perform different yet complementary steps within a linear pathway, a phenomenon termed metabolic division of labor (MDOL). However, little is known about how such metabolic behaviors shape microbial communities. Here, we derive a theoretical framework to define the assembly of a community that degrades an organic compound through MDOL. The framework indicates that to ensure community stability, the strains performing the initial steps should hold a growth advantage (m) over the "private benefit" (n) of the strain performing the last step. The steady-state frequency of the last strain is then determined by the quotient of n and m. Our experiments show that the framework accurately predicts the assembly of our synthetic consortia that degrade naphthalene through MDOL. Our results provide insights for designing and managing stable microbial systems for metabolic pathway optimization.

Identification of Environmental Buffer Areas in Urbanized Catchments Based on Synthetic Ecosystem Functions

The Saldan river basin in the northwest of the metropolitan area of Córdoba, Argentina, was defined as a unit for the observation of ecosystem services of water regulation. The capacity of the system to retain excess rainfall through vegetation in areas with slopes was analyzed. The observation area was a wildland-urban interface. From there, a model capable of synthesizing the behavior of the most relevant variables in the event of an extraordinary rainfall event was adjusted. The result was the definition of buffer areas or exosystemic protection in the interface. The testing and adjustment of this model defined a REP indicator that was proposed as an input in the planning of the sector. For validation, soil moisture permanence values from LWI were used. The derivative was calculated for each pixel value in the basin, for both dry and wet periods, and the areas with the lowest loss in both periods were compared with those with the highest retention obtained in the model. The zones identified by both methods show great similarities.

Construction of Synthetic Microbial Ecosystems and the Regulation of Population Proportion

With the development of synthetic biology, the design and application of microbial consortia have received increasing attention. However, the construction of synthetic ecosystems is still hampered by our limited ability to rapidly develop microbial consortia with the required dynamics and functions. By using modular design, we constructed synthetic competitive and symbiotic ecosystems with Escherichia coli. Two ecological relationships were realized by reconfiguring the layout between the communication and effect modules. Furthermore, we designed inducible synthetic ecosystems to regulate subpopulation ratios. With the addition of different inducers, a wide range of strain ratios between subpopulations was achieved. These inducible synthetic ecosystems enabled a larger volume of population regulation and simplified culture conditions. The synthetic ecosystems we constructed combined both basic and applied functionalities and expanded the toolkit of synthetic biology research.

Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia

Bacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere). Interactions between eukaryotes and bacteria range from cooperative to competitive, with the associated microorganisms affecting their host`s development, growth and health. Since the advent of non-culture dependent analytical techniques such as metagenome sequencing, consortia have been described at the phylogenetic level but rarely functionally. Multifaceted analysis of the microbial consortium of the ancient phytoplankton Botryococcus as an attractive model food web revealed that its all abundant bacterial members belong to a niche of biotin auxotrophs, essentially depending on the microalga. In addition, hydrocarbonoclastic bacteria without vitamin auxotrophies seem adversely to affect the algal cell morphology. Synthetic rearrangement of a minimal community consisting of an alga, a mutualistic and a parasitic bacteria underpins the model of a eukaryote that maintains its own mutualistic microbial community to control its surrounding biosphere. This model of coexistence, potentially useful for defense against invaders by a eukaryotic host could represent ecologically relevant interactions that cross species boundaries. Metabolic and system reconstruction is an opportunity to unravel the relationships within the consortia and provide a blueprint for the construction of mutually beneficial synthetic ecosystems.

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.

Rock-paper-scissors: Engineered population dynamics increase genetic stability.

Advances in synthetic biology have led to an arsenal of proof-of-principle bacterial circuits that can be leveraged for applications ranging from therapeutics to bioproduction. A unifying challenge for most applications is the presence of selective pressures that lead to high mutation rates for engineered bacteria. A common strategy is to develop cloning technologies aimed at increasing the fixation time for deleterious mutations in single cells. We adopt a complementary approach that is guided by ecological interactions, whereby cyclical population control is engineered to stabilize the functionality of intracellular gene circuits. Three strains of Escherichia coli were designed such that each strain could kill or be killed by one of the other two strains. The resulting "rock-paper-scissors" dynamic demonstrates rapid cycling of strains in microfluidic devices and leads to an increase in the stability of gene circuit functionality in cell culture.

Stabilizing synthetic gene circuits

Synthetic Biology Making synthetic gene circuits in bacteria is one thing, but making them stable under selective pressure with high mutation rates is another. Liao et al. addressed this problem with an ecological strategy in which they created three strains of bacteria, each of which could kill or be killed by one of the other strains (see the Perspective by Johnston and Collins). Once the first strain of bacteria hosting the engineered circuit underwent mutations that decreased function, the system could be “rebooted” by addition of another strain that killed the first but also contained the desired synthetic circuit, allowing its function to proceed unperturbed. This strategy provides a way to control synthetic ecosystems and maintain synthetic gene circuits without using traditional selection to maintain plasmids with antibiotics. Science , this issue p. [1045][1]; see also p. [986][2] [1]: /lookup/doi/10.1126/science.aaw0542 [2]: /lookup/doi/10.1126/science.aay3157

Homeorhesis and ecological succession quantified in synthetic microbial ecosystems

The dynamics of ecological change following a major perturbation, known as succession, are influenced by random processes. Direct quantitation of the degree of contingency in succession requires chronological study of replicate ecosystems. We previously found that population dynamics in carefully controlled, replicated synthetic microbial ecosystems were strongly deterministic over several months. Here, we present simplified, two-species microbial ecosystems consisting of algae and ciliates, imaged in toto at single-cell resolution with fluorescence microscopy over a period of 1 to 2 weeks. To directly study succession in these ecosystems, we deliberately varied the initial cell abundances over replicates and quantified the ensuing dynamics. The distribution of abundance trajectories rapidly converged to a nearly deterministic path, with small fluctuations, despite variations in initial conditions, environmental perturbations, and intrinsic noise, indicative of homeorhesis. Homeorhesis was also observed for certain phenotypic variables, such as partitioning of the ciliates into distinct size classes and clumping of the algae. Although the mechanism of homeorhesis observed in these synthetic ecosystems remains to be elucidated, it is clear that it must emerge from the ways each species controls its own internal states, with respect to a diverse set of environmental conditions and ecological interactions.

Synthetic Bistability and Differentiation in Yeast.

Engineered systems that control cellular differentiation and pattern formation are essential for applications like tissue engineering, biomaterial fabrication, and synthetic ecosystems. Synthetic circuits that can take on multiple states have been made to engineer multicellular systems. However, how to use these states to drive interesting cellular behavior remains challenging. Here, we present a cellular differentiation program involving a novel synthetic bistable switch coupled to an antibiotic resistance gene that affects growth in yeast ( S.cerevisiae). The switch is composed of a positive feedback loop involving a novel transcription factor and can be switched ON and OFF via two different transient inducer inputs. By further coupling the bistable switch with an antibiotic resistance gene, we obtained a growth differentiation circuit, where yeast cells can be switched to stable HIGH or LOW growth rate states via transient inducer inputs. This work demonstrates a rationally designed and experimentally validated cellular differentiation behavior in yeast.

A synthetic ecosystem for the multi-level modelling of heterotroph-phototroph metabolic interactions

Marine ecosystems are characterized by an intricate set of interactions. One of the most important occurs through the exchange of dissolved organic matter (DOM) provided by phototrophs and used by heterotrophic bacteria as their main carbon and energy source. This metabolic interaction represents the foundation of the entire ocean food-web.Here we have assembled a synthetic ecosystem to assist the systems-level investigation of this biological association. This was achieved by building an integrated, genome-scale metabolic reconstruction using two model organisms (a diatom Phaeodactylum tricornutum and an heterotrophic bacterium, Pseudoalteromonas haloplanktis). The model was initially analysed using a constraint-based approach (Flux Balance Analysis, FBA) and then turned into a dynamic (dFBA) model to simulate a diatom-bacteria co-culture and to study the effect of changes in growth parameters on such a system. Furthermore, we developed a simpler dynamic Ordinary Differential Equations (ODEs) system that, fed with dFBA results, was able to qualitatively describe this synthetic ecosystem and allowed performing stochastic simulations to assess the effect of noise on the overall balance of this co-culture.We show that our model represents known metabolic cross-talks of a phototroph-heterotroph system, including mutualism and competition for inorganic ions (i.e., phosphate and sulphate). In addition, the dynamic simulation predicts realistic growth rates for both the diatom and the bacterium and a steady-state balance between diatom and bacterial cell concentration that matches those determined in experimental co-cultures. This steady state, however, is reached following an oscillatory trend, a behaviour that is typically observed in the presence of metabolic co-dependencies. Finally, we show that, at high diatom/bacteria cell concentration ratio, stochastic fluctuations can lead to the extinction of bacteria from the co-culture, causing an explosion of diatom population. We anticipate that the developed synthetic ecosystem will serve as a basis for the generation of testable hypotheses and as a scaffold for integrating and interpreting -omics data from experimental co-cultures.

Error propagation during inverse modeling leads to spurious correlations and misinterpretation of lake metabolism

AbstractInverse modeling is a common practice to decompose observed processes into constituents that are unobservable or difficult to measure. To achieve this goal, a mechanistic model is calibrated to fit the observations and thereby the model produces a coherent set of constituent estimates. A disadvantage of this procedure is that any disagreement between the model assumptions and reality potentially introduces bias and other statistical artifacts into the constituents and their relations. Lake metabolism is recently most often followed by high‐frequency measurements of dissolved oxygen, and inverse modeling with simple conceptual models is used to couple oxygen dynamics to ecosystem‐wide aggregated metabolic rates, such as net ecosystem production (NEP). These models rely on estimates of gas exchange and community respiration. Using a model of a simple ecosystem and field data, we demonstrate that typical relations between modeled metabolic rates frequently do not follow patterns expected from synthetic ecosystems and that estimation errors strongly influence calculations by producing strong, spurious correlations. Correlation artifacts can be expected during inverse modeling, whenever observed time series are decomposed into poorly known or unmeasured processes that can compensate for the effect of each other.

Modifying Saccharomyces cerevisiae Adhesion Properties Regulates Yeast Ecosystem Dynamics.

Physical contact between yeast species, in addition to better-understood and reported metabolic interactions, has recently been proposed to significantly impact the relative fitness of these species in cocultures. Such data have been generated by using membrane bioreactors, which physically separate two yeast species. However, doubts persist about the degree that the various membrane systems allow for continuous and complete metabolic contact, including the exchange of proteins. Here, we provide independent evidence for the importance of physical contact by using a genetic system to modify the degree of physical contact and, therefore, the degree of asexual intraspecies and interspecies adhesion in yeast. Such adhesion is controlled by a family of structurally related cell wall proteins encoded by the FLO gene family. As previously shown, the expression of specific members of the FLO gene family in Saccharomyces cerevisiae dramatically changes the coadhesion patterns between this yeast and other yeast species. Here, we use this differential aggregation mediated by FLO genes as a model to assess the impact of physical contact between different yeast species on the relative fitness of these species in simplified ecosystems. The identity of the FLO gene has a marked effect on the persistence of specific non-Saccharomyces yeasts over the course of extended growth periods in batch cultures. Remarkably, FLO1 and FLO5 expression often result in opposite outcomes. The data provide clear evidence for the role of physical contact in multispecies yeast ecosystems and suggest that FLO gene expression may be a major factor in such interactions.IMPORTANCE The impact of direct (physical) versus indirect (metabolic) interactions between different yeast species has attracted significant research interest in recent years. This is due to the growing interest in the use of multispecies consortia in bioprocesses of industrial relevance and the relevance of interspecies interactions in establishing stable synthetic ecosystems. Compartment bioreactors have traditionally been used in this regard but suffer from numerous limitations. Here, we provide independent evidence for the importance of physical contact by using a genetic system, based on the FLO gene family, to modify the degree of physical contact and, therefore, the degree of asexual intraspecies and interspecies adhesion in yeast. Our results show that interspecies contact significantly impacts population dynamics and the survival of individual species. Remarkably, different members of the FLO gene family often lead to very different population outcomes, further suggesting that FLO gene expression may be a major factor in such interactions.

Designing microbial consortia with defined social interactions.

Designer microbial consortia are an emerging frontier in synthetic biology that enable versatile microbiome engineering. However, the utilization of such consortia is hindered by our limited capacity in rapidly creating ecosystems with desired dynamics. Here we present the development of synthetic communities through social interaction engineering that combines modular pathway reconfiguration with model creation. Specifically, we created six two-strain consortia, each possessing a unique mode of interaction, including commensalism, amensalism, neutralism, cooperation, competition and predation. These consortia follow distinct population dynamics with characteristics determined by the underlying interaction modes. We showed that models derived from two-strain consortia can be used to design three- and four-strain ecosystems with predictable behaviors and further extended to provide insights into community dynamics in space. This work sheds light on the organization of interacting microbial species and provides a systematic framework-social interaction programming-to guide the development of synthetic ecosystems for diverse purposes.

SPEW: Synthetic Populations and Ecosystems of the World

ABSTRACTAgent-based models (ABMs) simulate interactions between autonomous agents in constrained environments over time and are often used for modeling the spread of infectious diseases. ABMs use information about agents and their environments as input, together referred to as a “synthetic ecosystem.” Previous approaches for generating synthetic ecosystems have some limitations: they are not open-source, cannot be adapted to new or updated input data sources, or do not allow for alternative methods for sampling agent characteristics and locations. We introduce a general framework for generating synthetic ecosystems, called “Synthetic Populations and Ecosystems of the World” (SPEW). SPEW lets researchers choose from a variety of sampling methods for agent characteristics and locations and is implemented as an open-source R package. We analyze the accuracy and computational efficiency of SPEW, given different sampling methods for agent characteristics and locations, and provide a suite of statistical and graphical tools to screen our generated ecosystems. SPEW has generated over five billion human agents across approximately 100,000 geographic regions in over 70 countries available online.

Constructing Synthetic Ecosystems with Biopolymer Fluitrodes

AbstractModeling the complex interactions among organisms found within microbiomes is of great interest for the development of new biological technologies. Challenges remain in culturing cells of multiple species with spatial resolutions similar to microbial communities. Here, a fluitrode concept in microfluidics using biofabrication of functional biopolymers is demonstrated to efficiently assemble multiple cell populations in 3D hydrogels of spatial and biological relevance. The fluitrodes are freestanding biopolymer membranes that, similar to electrodes in transmitting electrons, transmit ions and small molecules with spatiotemporal programmability. The individually addressable fluitrodes allow for controlled delivery of nutrients and chemical molecules of interest in situ, live imaging of biological events, effluent collection to perform ex situ diagnostics, and finally, release of cells for downstream molecular and biochemical analyses. This novel coculturing platform can model in vitro ecosystems comprised of multiple species or kingdoms to elucidate cell–cell interactions in complex communities and aid in high throughput screening for drug discovery.