A method of integrating a donor DNA sequence into a target site on the genome of a Bacillus sp. cell without the integration of a selectable marker into said genome, the method comprising simultaneously introducing at least a linear recombinant DNA construct and a circular recombinant DNA construct into a Bacillus sp. cell, wherein said linear recombinant DNA construct comprises a donor DNA sequence, wherein said donor DNA sequence is flanked by an upstream homology arm (HR1) and a downstream arm (HR2), wherein each homology arm is greater than 1000 nucleotides in length, wherein said circular recombinant DNA construct comprises a DNA sequence encoding a guide RNA and a constitutive promoter operably linked to a nucleotide sequence encoding a Cas endonuclease, wherein said Cas9 endonuclease introduces a double-strand break at or near a target site in the genome of said Bacillus sp. cell.