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Soil microbiome engineering for sustainability in a changing environment

Nature Biotechnology volume 41, pages 1716–1728 (2023)Cite this article

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Abstract

Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth’s soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.

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Fig. 1: Soil microorganisms carry out key ecosystem services and have the potential to help mitigate a variety of deleterious anthropogenic impacts on soil ecosystems.
Fig. 2: The three pillars of soil microbiome engineering are isolate discovery, assembled communities and genetic manipulation.
Fig. 3: Design of tractable communities of soil microbes.
Fig. 4: Schematic of a co-abundance network for microbial taxa.
Fig. 5: Platforms to edit and evaluate genome modifications of soil microbiome isolates.
Fig. 6: Genome-editing approaches for soil microbiome engineering.

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Acknowledgements

This work was supported by the US Department of Energy (DOE) Office of Biological and Environmental Research as part of the Genomic Science Program and is a contribution of the Pacific Northwest National Laboratory (PNNL) Secure Biosystems Design Science Focus Area entitled ‘Persistence Control of Engineered Functions in Complex Soil Microbiomes’. PNNL is a multiprogram national laboratory operated by Battelle Memorial Institute for the DOE under contract DE-AC05-76RL01830.

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  1. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA

    Janet K. Jansson, Ryan McClure & Robert G. Egbert

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  1. Janet K. Jansson
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Jansson, J.K., McClure, R. & Egbert, R.G. Soil microbiome engineering for sustainability in a changing environment. Nat Biotechnol 41, 1716–1728 (2023). https://doi.org/10.1038/s41587-023-01932-3

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