Integrating Raman spectroscopy with microbiome methods for both phenotypic and genotypic characterization of organic and conventional agricultural soils

While prior research has explored soil microbiome differences between conventional and organic farming systems, this study distinguishes itself by examining not only the microbial community's taxonomic makeup but also its functional phenotypes. We integrated newly developed single-cell Raman microspectroscopy (SCRS)-based community phenotypic profiling analysis with microbiome 16S rRNA gene amplicon sequencing to compare the soil microbial communities of alfalfa, carrot, corn, lettuce, potato, soybean, squash, tomato, triticale, wheat, oat, and pea grown under either conventional agriculture or organic agriculture across farms in New York State (U.S.A.). Our findings showed that, despite site and plant species variations, conventionally grown plants shared similar characteristics in terms of microbial compositions within their group and organic plants, although differences by plant family and species and production practices (conventional vs. organic) were significant factors of microbial community structure. Leveraging the SCRS-based microbial phenotyping technology, we revealed distinctive microbial phenotypic profiles that were influenced by agricultural practices. SCRS showed that organic agricultural soils featured microbial phenotypes related to intracellular lipid accumulation. The results suggest that the increased carbon availability may have led to higher carbon inclusion into microbial biomass in conventionally farmed systems. Using network analysis to map ecological hub species, we identified a plant growth-promoting rhizobacteria (PGPR), Pseudomonas, and several nitrogen fixing prokaryotes as core members. In the organically farmed systems, there were several PGPR taxa belonging to the Bacilli class and the presence of bacteria with antibiotic resistance genes, which could indicate the greater presence of antibiotic resistance genes in organically managed farms. Overall, we found that the novel inclusion of microbial phenotyping methods, such as SCRS, can describe unique linkages between microbiome structure and physiology that vary between conventional and organic agricultural systems.