Characterization of the effects of different soil storage protocol on microbial community structure, vitality and metabolism in strawberry soil
Preserving soil microbial communities is essential for maintaining biodiversity, ensuring accurate microbiome research and supporting biotechnological applications in sustainable agriculture. This study evaluates the effects of three common preservation methods—cryopreservation at -80°C, refrigeration at 4°C, and lyophilization—on the microbial viability, diversity and metabolic functionality of soil microbiomes associated with strawberry cultivation. Soil samples from untreated and solarized strawberry fields were analyzed at 0, 6 months, and 12 months of storage. 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. Results showed that cryopreservation effectively maintained total bacterial counts, preserved the balance between oligotrophic and copiotrophic communities, and retained high alpha diversity indices over 12 months, closely resembling fresh soil conditions. 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 initial timepoint, while lyophilized samples diverged substantially. Functional analyses also revealed reduced metabolic activity in lyophilized soils, underscoring the negative impact on microbiome ecological roles. These findings identify cryopreservation as the most effective storage method for maintaining soil microbiome integrity, providing critical guidance for soil sample preservation in microbiome research and sustainable agricultural biotechnology.
Preserving soil microbial communities is essential for maintaining biodiversity, ensuring accurate microbiome research and supporting biotechnological applications in sustainable agriculture. This study evaluates the effects of three common preservation methods—cryopreservation at -80°C, refrigeration at 4°C, and lyophilization—on the microbial viability, diversity and metabolic functionality of soil microbiomes associated with strawberry cultivation. Soil samples from untreated and solarized strawberry fields were analyzed at 0, 6 months, and 12 months of storage. 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. Results showed that cryopreservation effectively maintained total bacterial counts, preserved the balance between oligotrophic and copiotrophic communities, and retained high alpha diversity indices over 12 months, closely resembling fresh soil conditions. 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 initial timepoint, while lyophilized samples diverged substantially. Functional analyses also revealed reduced metabolic activity in lyophilized soils, underscoring the negative impact on microbiome ecological roles. These findings identify cryopreservation as the most effective storage method for maintaining soil microbiome integrity, providing critical guidance for soil sample preservation in microbiome research and sustainable agricultural biotechnology.
university of turin