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Different microbiome and Bacillus thuringiensis diversity and dynamics of field soils of sole rain fed rice, and deep/shallow water rice-fish cultivation systems of National Rice Research Institute was assessed to enrich knowledge on functionalities of active microbial guilds of aforementioned micro-ecologies. Diversity and dynamics (x105 cfu/g soil, approx.) of microbial guilds viz. heterotrophs (1.04-7.87), spore formers (0.37-0.99), Gram negative bacteria (0.87-9.44), asymbiotic N2 fixers (0.10-0.17), nitrifiers (0.04-0.38), denitrifiers (0.09-0.38), spore crystal formers (0.003-0.02), actinobacteria (0.004-0.005) and fungi (0.003-0.01), as well as, indices (0.07-0.19 x 10-2) of spore-crystal forming bacteria i.e. Bacillus thuringiensis (Bt) were highly diverse in rain fed rice and deep/shallow water rice-fish farming field soils. Four spore-crystal forming bacterial isolates viz. TB426 and 432 of rice field, and TB436 of deep water rice-fish and TB442 of shallow water rice-fish farming field soils were diverse in phenotypic characters, antibiotic/salt (6–11% NaCl) tolerance, crystal composition (bipyramidal but variable sizes) etc. The Bt isolates (Bts) had 62.10-76.87 kbp genomic DNA (gDNA) and single plasmid (24.33- 42.50 kbp). The Bts (TB 426/432) had 12-14 cellular proteins (9.88-540.7 kDa). Phenotypic identities of TB426 and 432 were Bacillus thuringiensis (Bt) var. galleriae, TB436 was Bt var. thompsoni/coreanensis and TB442 was Bt var. dendrolimus/sotto. The results proved structural and functional diversity of Bt population in NRRI rice soils of different micro-ecologies. The resident Bt with different toxin composition would be potent natural biocide and can be exploited for suppression of different rice field pests to sustain productivity.