Assessment of Stability of Preservation Techniques for Strawberry Soil Microbiomes: Exploring the Biotechnological Relevance for Sustainable Agriculture
Abstract
Preserving ex situ soil microbial communities is essential for bacterial biodiversity conservation in microbiome biobanking, accurate microbiome research, and future biotechnological applications in sustainable agriculture. The effect of three soil preservation methods-cryopreservation at -80 °C, refrigeration at 4 °C, and lyophilization-on the viability, diversity and metabolic functionality of the soil microbiome was evaluated using soil from untreated and solarized strawberry fields stored at 0, 6 and 12 months. Microbial viability, ecological strategies, functionality, and diversity were assessed using plate counts, r/K strategist profiling, BIOLOG EcoPlates, and 16S rRNA/ITS gene amplicon-based sequencing, respectively. Cryopreservation outperformed the other preservation strategies by generally maintaining total bacterial counts, especially in control soil, preserving the balance between oligotrophic and copiotrophic communities, and sustaining high alpha diversity indices over 12 months. Refrigeration provided moderate preservation, though microbial viability and community stability declined over time. In contrast, lyophilization significantly reduced microbial abundance, altered community composition, and diminished metabolic diversity and substrate utilization. Beta diversity analyses confirmed that cryopreserved samples remained similar in microbial structure to the initial timepoint, while lyophilized samples diverged substantially. Functional analyses also revealed reduced metabolic activity in lyophilized soils, underscoring the negative impact on the microbiome's ecological roles. Overall, the results of this study identify cryopreservation as the most effective storage method for maintaining soil microbiome integrity, providing critical guidance for preserving soil samples in microbiome research and sustainable agricultural biotechnology.
Related
- Biodiversity isn't measured in tons: Making sense of nature in the context of sustainable agriculture
- Biochar immobilized microbes for sustainable soil remediation and agriculture enhancement: from lab to farmland
- Green Pesantren: Best Practice of Integrating Green Technology and Sustainable Agriculture for Eco-friendly Education
- Knowledge, attitudes, and practices of farmers towards sustainable agriculture in the Barind Tract of Bangladesh
- Assessment of methods for collection, preservation, and storage of water samples for dissolved methane and nitrous oxide concentration measurements
BibTeX
@article{rillig2026assessment,
title = {{Assessment of Stability of Preservation Techniques for Strawberry Soil Microbiomes: Exploring the Biotechnological Relevance for Sustainable Agriculture}},
author = {Matthias Rillig and Laurent Philippot and Johannes Lehmann},
journal = {Microorganisms},
year = {2026},
month = jul,
doi = {10.3390/microorganisms14071547},
url = {https://hal.inrae.fr/hal-05771417v1},
note = {CC BY},
}
RIS
TY - JOUR
TI - Assessment of Stability of Preservation Techniques for Strawberry Soil Microbiomes: Exploring the Biotechnological Relevance for Sustainable Agriculture
AU - Matthias Rillig
AU - Laurent Philippot
AU - Johannes Lehmann
PY - 2026
DA - 2026/07/15
JO - Microorganisms
DO - 10.3390/microorganisms14071547
UR - https://hal.inrae.fr/hal-05771417v1
AB - Preserving ex situ soil microbial communities is essential for bacterial biodiversity conservation in microbiome biobanking, accurate microbiome research, and future biotechnological applications in sustainable agriculture. The effect of three soil preservation methods-cryopreservation at -80 °C, refrigeration at 4 °C, and lyophilization-on the viability, diversity and metabolic functionality of the soil microbiome was evaluated using soil from untreated and solarized strawberry fields stored at 0, 6 and 12 months. Microbial viability, ecological strategies, functionality, and diversity were assessed using plate counts, r/K strategist profiling, BIOLOG EcoPlates, and 16S rRNA/ITS gene amplicon-based sequencing, respectively. Cryopreservation outperformed the other preservation strategies by generally maintaining total bacterial counts, especially in control soil, preserving the balance between oligotrophic and copiotrophic communities, and sustaining high alpha diversity indices over 12 months. Refrigeration provided moderate preservation, though microbial viability and community stability declined over time. In contrast, lyophilization significantly reduced microbial abundance, altered community composition, and diminished metabolic diversity and substrate utilization. Beta diversity analyses confirmed that cryopreserved samples remained similar in microbial structure to the initial timepoint, while lyophilized samples diverged substantially. Functional analyses also revealed reduced metabolic activity in lyophilized soils, underscoring the negative impact on the microbiome's ecological roles. Overall, the results of this study identify cryopreservation as the most effective storage method for maintaining soil microbiome integrity, providing critical guidance for preserving soil samples in microbiome research and sustainable agricultural biotechnology.
SN - 2076-2607
ER -