Magnetically responsive nanocultures for direct microbial assessment in soil environments

Usman, Huda [Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.] (ORCID:0000000224949400); Molaei, Mehdi [Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA.] (ORCID:000000020956211X); House, Stephen D. [Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM, USA.] (ORCID:0000000320356373); Haase, Martin F. [Van’t Hoff Laboratory of Physical and Colloid Chemistry, Department of Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands.] (ORCID:000000021355151X); Dennis, Cindi L. [National Institute of Standards and Technology, Gaithersburg, MD, USA.] (ORCID:0000000268739237); Niepa, Tagbo H. R. [Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.] (ORCID:0000000230185419)

doi:10.1126/sciadv.ady2654

DOE OSTI · 3508087

Magnetically responsive nanocultures for direct microbial assessment in soil environments

Usman, Huda [Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.] (ORCID:0000000224949400)·Molaei, Mehdi [Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA.] (ORCID:000000020956211X)·House, Stephen D. [Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM, USA.] (ORCID:0000000320356373)·Haase, Martin F. [Van’t Hoff Laboratory of Physical and Colloid Chemistry, Department of Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands.] (ORCID:000000021355151X)·Dennis, Cindi L. [National Institute of Standards and Technology, Gaithersburg, MD, USA.] (ORCID:0000000268739237)·Niepa, Tagbo H. R. [Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.] (ORCID:0000000230185419)

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Abstract

Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing now unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover previously unidentified biotherapeutics. We present magnetic nanocultures—a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semipermeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for bioprospecting previously uncultured or unknown microbial species.

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Usman, Huda [Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.] (ORCID:0000000224949400), Molaei, Mehdi [Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA.] (ORCID:000000020956211X), House, Stephen D. [Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM, USA.] (ORCID:0000000320356373), Haase, Martin F. [Van’t Hoff Laboratory of Physical and Colloid Chemistry, Department of Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands.] (ORCID:000000021355151X), Dennis, Cindi L. [National Institute of Standards and Technology, Gaithersburg, MD, USA.] (ORCID:0000000268739237), Niepa, Tagbo H. R. [Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.] (ORCID:0000000230185419). 2025-11-21. Magnetically responsive nanocultures for direct microbial assessment in soil environments. https://doi.org/10.1126/sciadv.ady2654

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