While the focus of the discussion of HGT is often on events in single cells, the possibility that a HGT event could pose an environmental or health risk depends upon the gene persisting at some level in a population of cells. This occurs only if there is no fitness cost associated with the newly acquired gene. Furthermore, the probability that a HGT event will have environmental or health effects, depends upon the frequency of the new gene in the population. An increase in gene frequency depends upon selective pressure that favors the spread of that gene throughout the population. Therefore, implicit in the issues described above are questions about differences in selective advantages and disadvantages provided by transgenes and other genes.

The majority of the transgenes in biotech crops being currently grown by farmers would not be expected to impart a selective advantage to soil microbes and might, instead, confer a detrimental “growth drag” on them. This fitness cost would decrease the probability the new gene would survive in the host. However, because scientists do not understand all the selective pressures acting on soil microbes, it cannot be said with absolute certainty that a crop transgene would not confer some unexpected selective advantage. However, naturally occurring plants, animals and microbes release significantly more transforming DNA into the soil than biotech crops. Many of the microbial genes have proven survival value for soil microbes, so one would expect the persistence of these naturally occurring genes to exceed transgene persistence.