The present disclosure provides systems and methods for targeted nucleic acid deletions and inactivation of a gene of interest comprising a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated (Cas) (CRISPR-Cas) system comprising at least one Cas protein and a pair of guide RNAs (gRNAs), an engineered transposon system, at least one donor nucleic acid, and a recombinase. The present disclosure also provides methods for genetically modifying diverse bacterial communities comprising contacting a recipient bacterial community with donor bacteria, the donor bacteria comprising a vector encoding: an engineered CRISPR-Cas system, wherein the engineered CRISPR-Cas system comprises: at least one Cas protein and at least one guide RNA (gRNA); an engineered transposon system; at least one donor nucleic acid to be integrated comprising at least one transposon end sequence, and, optionally a recombinase, wherein the donor nucleic acid further comprises a recognitions site for the recombinase.