Rhizosphere soil microbiome platform for organic rice farming validation and chitin-based biofertilizer development

Overview

This solution leverages rice rhizosphere soil microbiome analysis to address two critical challenges in sustainable agriculture: rapid validation of organic farming practices and improved rice productivity through targeted microbial enhancement. By characterizing bacterial and fungal communities in rhizosphere soil, the platform distinguishes organic from conventional rice cultivation methods, enabling faster and more reliable organic certification. In parallel, the research evaluates fermented chitin waste as an organic fertilizer designed to promote core microbiome development, with the goal of improving rice growth and yield without chemical inputs.

The work is particularly relevant for Thailand, a major global rice producer transitioning toward organic farming to reduce chemical use and improve soil health. Current organic validation processes are time-consuming; this microbiome-based approach offers a faster, science-backed alternative. The project combines expertise in microbiome ecology, plant science, and collaboration with the Rice Department of Thailand.

Technical specifications

Core capabilities:

• Microbial community profiling using next-generation amplicon sequencing targeting bacteria and fungi in rhizosphere soil samples
• Cultivation method differentiation through comparative microbiome analysis between organic and conventional rice farms across multiple geographic locations
• Core microbiome identification, including microbial network hubs and key species that persist across locations and farming methods
• Rapid organic farming validation protocol development adapted from established microbiome sequencing workflows
• Fermented chitin waste biofertilizer application to promote beneficial core microbiome growth in the rice rhizosphere
• Greenhouse cultivation trials using elite rice varieties to assess how core microbiome changes driven by chitin-based fertilizer affect rice growth and production

Validation approach:

• Phase 1 collects soil from five organic and five conventional rice farms, performs microbial DNA extraction and amplicon sequencing, then applies microbial ecology methods to develop the validation protocol
• Phase 2 uses collected soil to cultivate elite rice in greenhouse conditions, testing fermented chitin waste application and measuring effects on core microbiome dynamics and rice productivity

Technology readiness level

The fermented chitin waste fertilizer has prior validation showing it outperforms chemical fertilizers and certain organic alternatives in promoting rice growth and yield. The microbiome sequencing protocols are adapted from recently published work by the research group. The current project is in the active research and validation phase, with Phase 1 focused on protocol development across ten farm locations and Phase 2 centered on greenhouse-based fertilizer trials. The platform is advancing toward a deployable rapid validation tool for organic rice farming and a microbiome-enhancing biofertilizer solution for sustainable rice production.