I don't think that it is really a 'debate'. There are different species concepts that are used depending on the needs of the situation (http://en.wikipedia.org/wiki/Species#Other_species_concepts). A single definition cannot be found for less divergent groups because speciation is really a continuous process. Also the mechanisms and course of the process differs between taxonomic groups and, in some cases, may never be 'complete'.
The case of horizontal gene transfer mentioned below occurs in eukaryotes as well (http://en.wikipedia.org/wiki/Horizontal_gene_transfer#Eukary...).