Niche adaptation refers to the ability of some organisms to adapt to changing environments, or niches. Genetic mechanisms of this adaptation include horizontal gene transfer, gene duplication, and gene shuffling. Adaptations are the result of Evolution and allow an organism to live in new environments. All organisms must fill some ecological niche and at some point, species must adapt to fill newer niches if they are to survive in a changing world. Mechanisms involved in evolving new abilities to exploit new environments happen on the genetic scale. Genes mix and match in processes like horizontal gene transfer and gene or genome duplications. Transposable elements and plasmid or phage introduced genomic islands also provide organisms with the genetic tools they need to adapt to newer environments.
Adaptations can result in obviously visible morphological differences or increased metabolic pathways that are not as easily detectable and require genetic analysis to confirm. For pathogenic organisms, this usually means increasing virulence. In the case of wilt-fungi like Verticillium dahliae and Verticillium albo-atrum, the increased virulence is dependent on homologs genes picked up from some incidence of horizontal gene transfer with a bacterium early in its evolutionary history. For ocean dwelling cyanobacteria, adapting to colonize new territories has led to clades of Prochlorococcus becoming specialized to thrive in the low light and colder temperatures of the deeper depths in the ocean. Additionally, resistance to harsh compounds is also important for adaptation. The aerobic ammonia oxidizing bacteria Nitrosomonas eutropha C91 contains genomic islands that house genes important in providing resistance to heavy metals and oxidizing nitrogen. As a result, the species occupies environments with elevated N2 concentrations. Some of these genes are unique to this species meaning no other ammonia oxidizing bacteria could survive in the climates that N. eutropha C91 does, giving it a significant fitness advantage.