Quantitative analysis of horizontal gene transfer in complex systems

•Microbial HGT is a complex process influenced by a variety of modulating factors, including cellular genetics and environmental conditions.•HGT dynamics are governed by the underlying biochemical kinetic rate of gene transfer.•Quantification of HGT rates can be done at various complementary levels of experimental complexity, which necessarily seek to strike a balance between precision and fidelity to natural systems.•In vitro, in vivo, and in situ rate measurements are often complementary; these studies engender a deeper understanding of transfer dynamics, and will lead to future insights and applications. Horizontal gene transfer (HGT) plays a significant role in rapidly propagating diverse traits throughout bacterial populations, thereby accelerating natural evolution and leading to complex community structures. Critical gene transfer rates underlying these occurrences dictate the efficiency and speed of gene spread; these rates are often highly specific to HGT mechanism and environmental context, and have historically been challenging to reliably quantify. In this review, we examine recent works that leverage rigorous quantitative methods to precisely measure these rates in a variety of settings beginning with in vitro studies and advancing to in situ measurements; we emphasize contexts where quantification across multiple scales of complexity has led to fundamental biological insights. Finally, we highlight the applications of these measurements and suggest potential methodological advances to improve our understanding.