I was following up on some questions during and after class today and found some interesting papers I thought I'd pass on. The first is a 2011 review in Frontiers in Microbiology, Horizontal Gene Exchange in Environmental Microbiota. This comes closest to an overview of the question 'How common is conjugation (and other methods of horizontal gene transfer (HGT)) in prokaryotes?
The main aim of this review is to give a brief account of the occurrence and diversity of MGEs (Mobile Genetic Elements) in natural ecosystems and of the environmental factors that may affect MGE-mediated HGT.
The high rate of horizontal gene exchange in natural ecosystems is evident from both retrospective and prospective types of studies. The microbial world around us can be seen as a giant microbiome, with the continuous flow of genes between its different compartments.
The second paper I found provides at least a theoretical answer to why plasmids may persist in a population without either going to fixation (ie 100% of individuals have plasmids) or extinction. From the journal Genetics in 2007: The Persistence of Parasitic Plasmids.
Plasmids thus make a major contribution to the accessory gene pool, but they are also considered to impose a fitness cost related to plasmid carriage and the time and resources required to replicate extra DNA. The precise magnitude and consistency of the fitness cost imposed by plasmids are currently a matter of debate.
In addition to conferring a potential fitness cost, plasmids may be lost stochastically during bacterial reproduction by failing to segregate into one of the daughter cells during binary fission.
(A) combination of fitness cost and stochastic loss should, over time, act to remove plasmids from the bacterial population. Much attention has therefore been focused on the nature of the opposing forces that act to maintain plasmids, and two such forces are widely considered important: the rate of infectious (horizontal) transfer between bacteria (in this case the dynamics are similar to the trade-offs in parasite–host dynamics) and the strength of the selective advantage conferred by plasmid genes. There are reasons to doubt the ability of either of these forces to maintain plasmid-bearing cells indefinitely.
The paper goes on to reexamine a model for plasmid persistence and conclude that:
In sum, we find no evidence to support the claims that a strong selective advantage or population heterogeneity is required for the maintenance of plasmids in bacterial populations and argue instead that even costly plasmids may persist in homogenous populations through undamped or (more realistically) damped oscillations with the plasmid-free class.