Abstract Environmental biotechnology is a discipline that aims to use both natural and augmented biological systems as a resource for sustainable, ‘green’
Environmental biotechnology is a discipline that aims to use both natural and augmented biological systems as a resource for sustainable, ‘green’ technologies. This includes applications such as the use of natural microbial communities to treat waste water and remediate land, to genetically engineering strains of microbes to produce biofuels in industrial-scale bioreactors. Recently, the academic discipline of synthetic biology has joined this initiative by developing advanced molecular biology techniques to accelerate the conversion of microbial strains into novel biotechnologies. The future of synthetic biology envisions scientists designing an “optimal” genome electronically, synthesizing it and inserting it into a host organism, after which it will grow, reproduce, and perform the desired function at profitable scales. To pave the way for this envisioned future of optimal genome design, lab microbial strains such as Escherichia coli (E. coli) are having their genomes minimised and converted into a ‘chassis’. All this facilitates predictable growth properties, with promising results when tested at lab-scale. The next major challenge is getting these populations of lab-optimized organisms to thrive in environments such as lagoons that facilitate waste water treatment or in industrial-scale reactors with mixed feedstocks. In addition to the obvious disparity in size, these are fluctuating, stressful environments that are vastly more unpredictable compared with controlled lab conditions. Thus, the success of these fledgling biotechnologies is highly dependent on whether these organisms can thrive here.
The main aim of the current work was to investigate whether this genome minimizing strategy would come at an evolutionary cost in these non-ideal environments. To interrogate this, I conducted evolution experiments using the E. coli biotechnology chassis. Strains were evolved in continuous culture under prolonged starvation stress (a typical environmental stress) while emerging mutations were assayed. The spectrum of mutations was then captured via ultra(deep) sequencing on the Illumina hi-SeqÒ platform and used to analyse the evolutionary impact of a non-ideal environment on this minimal genome. I found that the genome minimised strains mutated quickly in non-ideal environments, which over time, could compromise the effectiveness of the biotechnology applications they underpin. Thus to prevent this, more resilient genomes will need to be designed that compensate for the effect of these mutations. This will help ensure the success of these biotechnologies in their ultimate engineering environments.
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Maria Tello Ramos, Niki Khan, Nick Jones