Synthetic soil microcosms as emerging model systems to study the rhizosphere

TY - JOUR

T1 - Synthetic soil microcosms as emerging model systems to study the rhizosphere

AU - Mair, Andrew

AU - Patko, Daniel

AU - Liu, Yangminghao

AU - Engelhardt, Ilonka

AU - Dupuy, Lionel X.

N1 - Copyright: © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2025.

PY - 2025/5/21

Y1 - 2025/5/21

N2 - Background: Root and soil interactions are generally difficult for biologists to study due to the challenges of obtaining measurements deep within soil. Nowadays, techniques from other disciplines are increasingly being adopted to build soil microcosms from artificial substrates and engineered microbiota, and conducting experiments within these new model systems is facilitating collection of higher quality data.Scope: This article reviews the emergence of such synthetic soil microcosms and covers the materials and technologies used to construct their various components. For example, synthetic soils, microfluidic systems, and integrated sensors, as well as the methods employed to assemble synthetic microbial communities and incorporate biochemical compounds released by roots. Synthetic soil microcosms are drastically improving the availability and richness of data on rhizosphere processes, and we explain how this is advancing the development of models and theory to better understand root and soil interactions.Conclusions: The development of synthetic soil microcosms is still in its early stages, with current literature primarily comprised of feasibility studies and proof-of-concept reports. Nevertheless, the consolidation of knowledge, tools and techniques should, with time, lead to fully developed systems, which can be routinely applied in laboratories and considerably enhance our ability to predict rhizosphere responses to environmental conditions.

AB - Background: Root and soil interactions are generally difficult for biologists to study due to the challenges of obtaining measurements deep within soil. Nowadays, techniques from other disciplines are increasingly being adopted to build soil microcosms from artificial substrates and engineered microbiota, and conducting experiments within these new model systems is facilitating collection of higher quality data.Scope: This article reviews the emergence of such synthetic soil microcosms and covers the materials and technologies used to construct their various components. For example, synthetic soils, microfluidic systems, and integrated sensors, as well as the methods employed to assemble synthetic microbial communities and incorporate biochemical compounds released by roots. Synthetic soil microcosms are drastically improving the availability and richness of data on rhizosphere processes, and we explain how this is advancing the development of models and theory to better understand root and soil interactions.Conclusions: The development of synthetic soil microcosms is still in its early stages, with current literature primarily comprised of feasibility studies and proof-of-concept reports. Nevertheless, the consolidation of knowledge, tools and techniques should, with time, lead to fully developed systems, which can be routinely applied in laboratories and considerably enhance our ability to predict rhizosphere responses to environmental conditions.

KW - Microcosm

KW - Model systems

KW - Rhizosphere

KW - Synthetic soils

UR - https://www.scopus.com/pages/publications/105005875112

U2 - 10.1007/s11104-025-07495-3

DO - 10.1007/s11104-025-07495-3

M3 - Review article

AN - SCOPUS:105005875112

SN - 0032-079X

JO - Plant and Soil

JF - Plant and Soil

ER -