What happens when lake water microbiota is inoculated into pristine soil? While unconventional at first glance, addressing this question provides insight into how habitat filtering and microbiota origin can shape microbiome development – essential concepts for effective microbiome engineering.
In this study, we used standardized pristine soil habitats to grow three distinct microbial communities starting with either microbial cells purified from forest topsoil (SC), freshwater lake (LC), or composed from 21 soil isolates (SynCom). Regardless of their origins, both SC and LC inocula showed similar taxa-successions to clear soil microbiota compositions in comparison to global inventories of soil, sediment, and lake water microbiomes. When diluted into fresh soil microcosms, the soil-grown LC- and SC-microbiota developed again into communities with clear soil-like signatures, indicating that habitat filtering by the soil matrix was the driving factor for the soil microbiome formation. Mixing soil-grown SynCom with either LC or SC-microbiota in fresh soil habitats permanently changed the community growth trajectories compared to their non-merged diluted controls, but the SynCom members themselves declined to their natural background.
Our findings carry major implications for soil restoration and microbiome management; processes urgently needed amid global soil health crisis. Our results suggest that added synthetic microbiomes with specific functionalities may not proliferate very well, but their transient presence can steer community development in desired directions, depending on habitat filtering, functional redundancy, and interactions within the resident community. By revealing how habitat filtering dominates microbial assembly and merger outcomes, our study provides a framework for designing and guiding soil microbiomes for soil restoration.
Addressing the initial question posed, a highly diverse lake microbiota which is introduced into soil will be filtered by the habitat to resemble soil microbiome within the bounds of its seeding composition. This raises the question: could such cross-habitat introduction offer a successful strategy to restore soils with depleted microbial diversity?
Read the full journal article titled ‘Habitat filtering more than microbiota origin controls microbiome transplant outcomes in soil’ in The ISME Journal. This article has been selected as Editors’ Choice for the month of July 2025
Authors
- Senka Causevic, Department of Fundamental Microbiology, University of Lausanne, Switzerland
- Janko Tackmann, Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Switzerland
- Vladimir Sentchilo, Department of Fundamental Microbiology, University of Lausanne, Switzerland
- Lukas Malfertheiner, Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Switzerland
- Christian von Mering, Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Switzerland
- Jan Roelof van der Meer, Department of Fundamental Microbiology, University of Lausanne, Switzerland