@article{Ascensao2023,

title = {Quantifying the local adaptive landscape of a nascent bacterial community},

author = {Joao A. Ascensao and Kelly M. Wetmore and Benjamin H. Good and Adam P. Arkin and Oskar Hallatschek},

doi = {10.1038/s41467-022-35677-5},

issn = {2041-1723},

year  = {2023},

date = {2023-12-00},

journal = {Nat Commun},

volume = {14},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractThe fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this adaptive landscape changes over evolutionary times, especially upon ecological diversification and changes in community composition, remains poorly understood. We sought to fill this gap by analyzing a stable community of two closely related ecotypes (“L” and “S”) shortly after they emerged within the E. coli Long-Term Evolution Experiment (LTEE). We engineered genome-wide barcoded transposon libraries to measure the invasion fitness effects of all possible gene knockouts in the coexisting strains as well as their ancestor, for many different, ecologically relevant conditions. We find consistent statistical patterns of fitness effect variation across both genetic background and community composition, despite the idiosyncratic behavior of individual knockouts. Additionally, fitness effects are correlated with evolutionary outcomes for a number of conditions, possibly revealing shifting patterns of adaptation. Together, our results reveal how ecological and epistatic effects combine to shape the adaptive landscape in a nascent ecological community.},

keywords = {General Biochemistry, General Chemistry, General Physics and Astronomy, Genetics and Molecular Biology, Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Averesch2023,

title = {Microbial biomanufacturing for space-exploration—what to take and when to make},

author = {Nils J. H. Averesch and Aaron J. Berliner and Shannon N. Nangle and Spencer Zezulka and Gretchen L. Vengerova and Davian Ho and Cameran A. Casale and Benjamin A. E. Lehner and Jessica E. Snyder and Kevin B. Clark and Lewis R. Dartnell and Craig S. Criddle and Adam P. Arkin},

doi = {10.1038/s41467-023-37910-1},

issn = {2041-1723},

year  = {2023},

date = {2023-12-00},

journal = {Nat Commun},

volume = {14},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractAs renewed interest in human space-exploration intensifies, a coherent and modernized strategy for mission design and planning has become increasingly crucial. Biotechnology has emerged as a promising approach to increase resilience, flexibility, and efficiency of missions, by virtue of its ability to effectively utilize in situ resources and reclaim resources from waste streams. Here we outline four primary mission-classes on Moon and Mars that drive a staged and accretive biomanufacturing strategy. Each class requires a unique approach to integrate biomanufacturing into the existing mission-architecture and so faces unique challenges in technology development. These challenges stem directly from the resources available in a given mission-class—the degree to which feedstocks are derived from cargo and in situ resources—and the degree to which loop-closure is necessary. As mission duration and distance from Earth increase, the benefits of specialized, sustainable biomanufacturing processes also increase. Consequentially, we define specific design-scenarios and quantify the usefulness of in-space biomanufacturing, to guide techno-economics of space-missions. Especially materials emerged as a potentially pivotal target for biomanufacturing with large impact on up-mass cost. Subsequently, we outline the processes needed for development, testing, and deployment of requisite technologies. As space-related technology development often does, these advancements are likely to have profound implications for the creation of a resilient circular bioeconomy on Earth.},

keywords = {cubes, General Biochemistry, General Chemistry, General Physics and Astronomy, Genetics and Molecular Biology, Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Mutalik2022,

title = {A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens},

author = {Vivek K. Mutalik and Adam P. Arkin},

doi = {10.1016/j.isci.2022.104121},

issn = {2589-0042},

year  = {2022},

date = {2022-04-00},

journal = {iScience},

volume = {25},

number = {4},

publisher = {Elsevier BV},

keywords = {Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}