The ecological aspects of the transfer and spread of mobile genetic elements (MGE) are reviewed in the context of the emerging evidence for the dominant role that horizontal gene transfer (HGT) has played in the evolutionary shaping of bacterial communities. Novel tools are described that allow a refined analysis of HGT in natural settings. The occurrence of HGT processes in soil and water, as affected by environmental factors, is then discussed. Examples are provided that illustrate how MGE can influence the behavior of microorganisms in their natural habitats. The occurrence of microorganisms as groups of cells in structured communities, such as those found in biofilms, is used as a framework in order to review the data and pose further questions on the evolutionary role and significance of contemporary gene transfer processes in nature. Selection by the environment is likely to be the dominant force in shaping the genetic make-up of bacterial communities. In fact, selective force can act as an apparent accelerator of gene transfer processes, mainly as a result of the enhancement of survival and persistence of favorably selected products of gene transfer processes (genes, metabolic pathways, microbial cells and communities). However, the current understanding of the triggering and impact of HGT in nature remains limited by our lack of understanding of the very nature and variety of the selective forces that act on microorganisms in situ. Hence, the relevant questions with respect to these triggers acting in natural habitats need to be answered using advanced approaches for studying HGT processes in nature, such as those discussed in this review.