The acquisition of foreign DNA is a fundamental process in the diversification and adaptation of most bacterial species. Horizontal transfer of plasmids, bacteriophages, transposons, integrons, conjugative transposons, integrative conjugative elements (ICEs) and genomic islands is of particular importance to many plant and human pathogens. These integrative elements can encode functions that increase bacterial fitness under different environmental conditions or in different niches. Genomic islands are large chromosomal regions that have aberrant base composition compared to the whole genome, encode an integrase and insert at tRNA loci. The term ‘pathogenicity islands’ was first coined by Hacker to describe unstable regions present in pathogenic isolates of Escherichia coli that were unlike any previously described integrative element. The regions were called pathogenicity islands because they encoded several virulence factors. Subsequently, the term genomic island was introduced to describe regions that contained a diverse range of functions, such as (i) the ability to utilize novel carbon and nitrogen sources (metabolic islands); (ii) the ability to break down novel compounds (degradation islands); (iii) resistance to antibiotic and heavy metals (resistance islands); and (iv) the ability to cause disease (pathogenicity islands). Within each subset of islands, the gene content can vary considerably, even within a species.
Acquisition of genomic islands plays a central part in bacterial evolution as a mechanism of diversification and adaptation. Genomic islands are non-self-mobilizing integrative and excisive elements that encode diverse functional characteristics but all contain a recombination module comprised of an integrase, associated attachment sites and, in some cases, a recombination directionality factor. Here, we discuss how a group of related genomic islands are evolutionarily ancient elements unrelated to plasmids, phages, integrons and integrative conjugative elements. In addition, we explore the diversity of genomic islands and their insertion sites among Gram-negative bacteria and discuss why they integrate at a limited number of tRNA genes.