Scientists show how to design ‘ecological firewalls’ for terraforming the biosphere

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Modern science has advanced to the point where scientists can design living systems or modify existing ones, thereby pushing or breaking the limits of nature, in some cases, to achieve specific goals.

Otherwise known as synthetic biology, this scientific field seeks to produce new functional designs based on living cells or subcellular microbes. Despite its promise, there are potential dangers surrounding synthetic biology’s impact on community dynamics that need to be explored.

Study: Ecological firewalls for synthetic biology. Image Credit: Kotkoa/Shutterstock.com

A new iScience The study discusses the use of ecological firewalls to predict and control microbiota communities into which synthetic organisms are released.

Introduction

Synthetic biology research has led to the development of tools capable of examining natural processes and new biomedical applications. Taken together, these advances have been exploited to design synthetic ecosystems, bioinformatics systems, and multicellular systems.

Systems biology is intrinsic to advances in synthetic biology. In fact, over the past decade, a type of systems biology known as community ecology has inspired several new ideas in the field of synthetic biology, in which the concepts of populations were screened for microbiota.

Additionally, researchers are increasingly interested in developing engineered microbes that can withstand various conditions caused by climate change. Some examples include specific waste-degrading bacteria, soil-improving cyanobacteria, or plant microbiomes.

Humans have caused a significant impact on the living world by polluting oceans and freshwater bodies, while reducing carbon dioxide removal and advancing the degradation of biodiversity. Thus, the development of these types of microorganisms could help conserve or restore ecosystems, especially those at risk of catastrophic climate-related events.

Despite their promise, there remains an urgent need to determine the effect of these synthetic designs on cellular communities. Notably, previous studies have been limited by moratoriums and modeling frameworks that have been largely absent.

Previous studies have reported the successful use of techniques based on microbial inoculation or the introduction of microorganisms into municipal waste. However, these methods introduce a number of microorganisms simultaneously, or even an entire microbiome, into the environment, which may have long-term effects that have yet to be explored.

Ecological firewalls for synthetic biology

Biocontainment Strategies

Biocontainment strategies currently used in synthetic biology remain a challenge, as most of these approaches eliminate any interaction between the modified strains and their surrounding environment. The basic operating principle of these methods is to develop a genetic “firewall” that works predictably and closely resembles known living organisms.

For example, developing such a firewall might involve designing a new cell. Moreover, the sequential modification of the codons in the engineered bacterial cells could move them away from the parental strains towards the artificial cell controlled by an unnatural genetic code.

In the present study, researchers discuss the concept of terraforming as an approach to solving the problem of population containment within the framework of synthetic biology.

The key concept here is that, ideally from a member of the resident community, a synthetic strain can be obtained to be reintroduced to serve a function while being constrained to limited spread in the given habitat..”

Research on ecosystems and their tipping points or alternate states demonstrates that the right intervention can transform or restore a degraded ecological community to a healthy one. In other words, there are certain common characteristics of an ecosystem, which guarantee states of attractor, which allow the ecosystem to enter one or more possible states of equilibrium.

The challenge these researchers faced was to modify or engineer organisms that could interact with other species in the resident community, such that the resulting robust attractor state would prevent the proliferation of synthetic organisms.

Previous studies on the ecology of invasion show that invasion by a new species is limited by the structure of the host community which ultimately prevents colonization by the new microorganism. The weakness of host communities or the extinction of large predators are examples of situations in which the invader easily takes hold. In some cases, the invading organism facilitates the establishment of diversity, thereby helping other organisms to survive.

The stability of the attractor is determined by how the different organisms in the ecosystem interact with each other. With a single stable attractor, an ecosystem could be designed where multiple species, including the synthetic strain, coexist indefinitely. In other words, the engineered characteristics of the synthetic organism could result in a dynamic and diverse ecosystem.

In this situation, the ecological firewall would successfully limit the proliferation of introduced synthetic species, while leaving them able to proliferate in response to an increase in the environmental problem, for example an oil spill.

Potential ecological firewalls

Five possible ecological firewalls are discussed in this article, each of which was designed based on different mechanisms, including the dynamic relationship between resources and consumers, mutualism, parasitism, indirect cooperation, and niche ecology. .

Each firewall represents a specific network of species interactions that are designed to function within a larger web or natural community that is responsible for a specific functional role. The scientists chose a set of models that uses a single species in a single dimension to simplify the theoretical problem and its result.

No specific gene construct was proposed in the present study. Instead, the researchers looked at examples where basic functional traits were assumed by the organism following its introduction into a given environment. In each type, the synthetic organism coexists with the existing community, although it may sometimes shrink to a very low level.

Resource Consuming Firewall

In the example of resource-consumer dynamics, the goal is to develop synthetic microorganisms capable of efficiently degrading certain anthropogenic xenobiotics such as plastic, recalcitrant chemicals or oil spills. As the microorganism becomes part of its community and anthropogenic substrate levels are reduced below certain predetermined limits, the synthetic strain should die out.

The model used in the present study made predictions that accurately resemble recent findings about the impact of current applications of synthetic biology. These include the exponential increase in plastic debris dumped in the ocean which has failed to increase the concentrations of sampled marine plastic. Simultaneously, an increasing number of plastic-eating bacteria are being detected across the world.

Synthetic Mutual Firewall

In the mutualistic firewall model, researchers examined how cyanobacteria could be engineered to improve soil moisture in arid areas. Such an approach would facilitate the growth of more plants in the soil, while improving soil quality and maintaining microbial diversity in the soil.

The behavior of the synthetic mutualistic firewall is ideal, as it improves moisture levels throughout the community, simultaneously improving the productive capabilities of the soil. Improved soil levels will subsequently benefit synthetic cyanobacteria, thus ensuring a coexistence attractor outcome.

Indirect Cooperation Firewall

In the example of the indirect cooperation firewall, the synthetic organisms that derive carbon from toxins in an oil spill support each other and the community, while helping to clean up the toxins. As oil levels decrease with increased removal, the synthetic strain becomes less abundant but does not die out.

Consequences

Scientists have demonstrated the feasibility of using ecological approaches designed to prevent the proliferation of synthetic microbial strains. Here, they considered different types of ecological networks to establish various firewall concepts that allow ecosystems to maintain their required level of diversity while remaining functional as desired.

Ecological firewalls will help address future bioremediation strategies.”

Further studies could help integrate genetic firewalls into this broader systems-level approach to improve the level of biocontainment. The introduction of a time limit is another potentially useful intervention.

Stochastic parameters would also be useful to build more detailed models, requiring an in-depth study of the interactions between species and abiotic factors.

Importantly, these EFWs should be used to test future terraforming strategies in a microcosm/mesocosm setting, where the presence and reliability of previous attractor states could be investigated under realistic conditions..”

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