A roadmap to understanding and anticipating microbial gene transfer in soil communities

Gillett, David L.; Selinidis, Malyn; Seamons, Travis; George, Dalton; Igwe, Alexandria N.; Del Valle, Ilenne; Egbert, Robert G.; Hofmockel, Kirsten S.; Johnson, Alicia L.; Matthews, Kirstin R. W.; Masiello, Caroline A.; Stadler, Lauren B.; Chappell, James; Silberg, Jonathan J.

doi:10.1128/mmbr.00225-24

Title: A roadmap to understanding and anticipating microbial gene transfer in soil communities

Journal Article · Wed Jun 25 00:00:00 UTC 2025 · Microbiology and Molecular Biology Reviews

DOI: https://doi.org/10.1128/mmbr.00225-24 · OSTI ID:2998083

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Department of Biosciences, Rice University
Department of Biosciences, Rice University; School for the Future of Innovation in Society, Arizona State University
Department of Biological Sciences, Virginia Tech
Biosciences Division, Oak Ridge National Laboratory
Biological Sciences Division, Pacific Northwest National Laboratory
Baker Institute for Public Policy, Rice University
Department of Biosciences, Rice University; Department of Earth, Environmental and Planetary Sciences, Rice University
Department of Civil and Environmental Engineering, Rice University

Engineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. Here, we propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDA; USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725; AC05-76RL01830

OSTI ID:: 2998083

Report Number(s):: PNNL-SA--206807; PNNL-SA--216351

Journal Information:: Microbiology and Molecular Biology Reviews, Journal Name: Microbiology and Molecular Biology Reviews Journal Issue: 2 Vol. 89; ISSN 1092-2172; ISSN 1098-5557

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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