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

Korean Natural Farming (KNF) practices claim to cultivate and transfer "indigenous microorganisms (IMOs)" to donor soils as a method of probiotic soil enhancement. We investigated whether IMO cultivation can propagate unique microbiomes and maintain microbial diversity through successive IMO stages for restoration of flood contaminated soils. Employing a balanced study design using soil samples from salt marsh, deciduous forest, and urban greenspace (plus sterilized controls), samples underwent the first two IMO cultivation steps followed by 16S rRNA and ITS metagenomic sequencing. Notably, IMO 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 also revealed distinct clustering by inoculum source (i.e. human-altered, human-transported vs. natural vs. sterile) that persisted throughout cultivation. Our evidence suggests that the IMO process enriches for specific taxa likely adapted to cultivated conditions and fails to maintain fungal diversity, contrasting greatly with KNF's proposed benefit of propagating locale-specific, fungal-dominated indigenous microbiomes. However, our results demonstrate that early IMO cultures may capture and sustain bacterial diversity in soil, opening the door for future studies of KNF efficacy and sustainability.