Holistic approach to study soil rhizosphere microbiomes and preservation strategies

Holistic approaches are essential to understand the distribution of microbial diversity and the functional profiles of soil microbiomes. The One Health approach, promoted by the World Health Organization, highlights soil as a critical factor for animal and human nutrition and underscores its preservation as vital for global well-being. This study evaluates the impact of different sample preservation techniques on rhizosphere soil microbial communities, focusing on the culturable fraction, microbiota composition, and metabolic fingerprint. Three storage conditions were tested: -80°C, lyophilization, and refrigeration at 4°C. Microbial community structures and growth strategies were analyzed through total microbial counts, copiotroph/oligotroph distributions, r-K strategies, and EPi indices. A total of 300 bacterial strains, 54 putative nitrogen-fixing strains, and 315 fungi were isolated for plant growth-promoting (PGP) activity assessment. Functional metabolic profiling using Biolog EcoPlates revealed widespread carbon source utilization in microbiomes with high population diversity (e.g., kiwifruit and strawberry rhizospheres) compared to soils with low species abundance, such as grapevine. These findings link microbial diversity distribution with ecosystem functionality and underline the importance of understanding community responses to environmental changes, particularly under preservation conditions. Further analyses after 6 and 12 months of storage will provide insights into microbiome structural shifts and functional alterations during long-term conservation. Additionally, microbial consortia will be developed from isolates with PGP traits to exploit native soil microbial communities (NatComs) as biofertilizers for enhancing crop productivity.