ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Terrestrial Microbiology
This article is part of the Research TopicSoil Microbiome and Agroecosystem MultifunctionalityView all 9 articles
Geno-pheno characterization of crop rhizospheres: An integrated Raman spectroscopy and microbiome approach in conventional and organic agriculture
Provisionally accepted
- 1Cornell University Horticulture Section, Ithaca, United States
- 2Cornell University School of Civil and Environmental Engineering, Ithaca, United States
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In this study, we investigated phenotypic and compositional patterns in rhizosphere microbial communities across conventional and organic farms to assess agricultural impacts on soil microbiomes. We characterized microbial communities from 10 conventionally and 12 organically cultivated horticultural crops across multiple New York State farms using 16S rRNA gene sequencing and a newly developed single-cell Raman microspectroscopy (SCRS) approach. - Farming practice strongly influenced microbiome clustering, regardless of site or plant species differences. SCRS-based phenotyping detected distinct microbial biochemical profiles: organic systems favored lipid-accumulating phenotypes linked to energy storage and stress resilience, while conventional systems promoted carbon-rich phenotypes associated with rapid carbon assimilation and biomass production. Network analysis identified Pseudomonas and nitrogen-fixing taxa as ecological hubs in conventional systems, while organic soils were enriched in Bacilli-class plant growth promoting rhizobacteria (PGPR) (e.g., Tumebacillus, Bacillus, Paenibacillus, Brevibacillus) and harbored microorganisms bearing antibiotic resistance genes, suggesting that management regimes shape distinct microbial functional traits and community structures. Our results underscore the value of integrating genotypic and phenotypic analyses, particularly microbial phenotyping via SCRS, to reveal adaptive traits in agricultural microbiomes. This approach provides new insight into how plant production systems influence microbial assembly and function, informing sustainable soil health and agroecosystem resilience strategies.
Keywords: soil microorganisms, Organic Agriculture, Conventional agriculture, agriculturalmicrobiome, Raman single cell spectroscopy, Food security
Received: 08 Oct 2025; Accepted: 13 Nov 2025.
Copyright: © 2025 Son, He, Baldwin, Li, Wang, Gu and Kao-Kniffin. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Jenny Kao-Kniffin, jtk57@cornell.edu
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