The CRBC contains 1,817 undefined bacterial species. The maximum-likelihood phylogenetic tree contains 3,044 representative species of the CRBC and crop root bacteria in public databases (NCBI, IMG/M, and ENA;STAR Methods). The clades associated with phylogenetic branches of 2,212 CRBC unique bacterial species, which show ANI below 95% when compared with published genomes derived from crop roots, are designated as undefined in crops and highlighted in blue (n= 1,702, contributed by CRBC isolates) or green (n= 510, contributed by CRBC MAGs). Published bacterial species from crop roots (n= 832) are indicated in beige. The initial inner circle illustrates the taxonomy of representative species at the phylum level. Proteobacteria are displayed at the class level due to excessive species numbers. Black bars represent log10-transformed numbers of non-redundant genomes (ANI of <99.9%) within each representative bacterial species. The outermost circle indicates 1,817 undefined bacterial species (green,n= 1,817) in the CRBC when compared with bacterial genomes from GTDB with the threshold of 95% ANI.
