The consistent use of the taxonomic system of binomial nomenclature (genus and species) was firstpopularized by Linnaeus nearly three-hundred years ago to classify mainly plants and animals. Hismain goal was to give labels that would ensure that biologists could agree on which organism wasunder investigation. One-hundred fifty years later, Darwin considered the term species as one ofconvenience and not essentially different from variety. In the modern era, exploration of theworld's niches together with advances in genomics have expanded the number of named speciesto over 1.8 million, including many microorganisms. However, even this large number excludesover 90% of microorganisms that have yet to be cultured or classified. In naming new isolates inthe microbial world, the challenge remains the lack of a universally held and evenly applied standardfor a species. The definition of species based on the capacity to form fertile offspring is notapplicable to microorganisms and 70% DNA-DNA hybridization appears rather crude in light ofthe many completed genome sequences. The popular phylogenetic marker, 16S rRNA, is tricky forclassification since it does not provide multiple characteristics or phenotypes used classically forthis purpose. Using most criteria, agreement may usually be found at the genus level, but specieslevel distinctions are problematic. These observations lend credence to the proposal that thespecies concept is flawed when applied to prokaryotes. In order to address this topic, we haveexamined the taxonomy of extremely halophilic Archaea, where the order, family, and even a genusdesignation have become obsolete, and the naming and renaming of certain species has led to muchconfusion in the scientific community.

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