Korean Natural Farming practices are dominated by a limited number of microbes and decrease fungal diversity

PurposeKorean Natural Farming (KNF) practices claim to cultivate and transfer "indigenous micro-organisms" (IMOs) to donor soils as a method of probiotic soil enhancement, yet lack peer-reviewed scientific validation. We investigated whether IMO cultivation can propagate unique microbiomes and maintain microbial diversity through successive IMO stages for restoration of flood contaminated soils. MethodsWe employed a balanced study design using soil samples from three New York metropolitan ecological sites: salt marsh, deciduous forest, and urban greenspace, plus sterilized controls. Samples underwent the first two IMO cultivation steps via inoculation on rice and fermentation in unrefined sugar. We extracted environmental DNA and performed 16S rRNA and ITS metagenomic sequencing using the AVITI platform and analyzed 84 libraries with QIIME2. Dynamics of microbial community composition and soil biodiversity, as a function of both ecological source and IMO cultivation, were assessed using Jaccard Index, Unweighted UniFrac, and ANCOM-BC analysis. ResultsIMO cultivation was dominated by limited bacterial taxa (Enterobacterales, Pseudomonadales, Bacillales) and fungal taxa (Rhizopodaceae, particularly R. oryzae). While bacterial diversity was maintained or increased during two IMO stages, fungal diversity consistently decreased. Principal Coordinates Analysis revealed distinctclustering by inoculum source (i.e. manmade vs. natural vs. sterile) that persistedthroughout cultivation. ConclusionsOur evidence suggests that the IMO process selects for specific taxa likely adapted to cultivated conditions and fails to maintain fungal diversity. This greatly contrasts IMOs proposed benefit of propagating locally-specific, fungal-dominated indigenous microbiomes. However, our results demonstrate that IMO cultures may capture and sustain bacterial diversity in soil, while it is unclear how such diversity mayarise. The possibility remains that the early stages of IMO studied here could fosterfurther microbial community expansions, but further study is required.