- Volume 55, Issue 1, 2005

A global phylogeny of major eukaryotic lineages is a significant and ongoing challenge to molecular phylogenetics. Currently, there are five hypothesized major lineages or ‘supergroups' of eukaryotes. One of these, the chromalveolates, represents a large fraction of protist and algal diversity. The chromalveolate hypothesis was originally based on similarities between the photosynthetic organelles (plastids) found in many of its members and has been supported by analyses of plastid-related genes. However, since plastids can move between eukaryotic lineages, it is important to provide additional support from data generated from the nuclear-cytosolic host lineage. Genes coding for six different cytosolic proteins from a variety of chromalveolates (yielding 68 new gene sequences) have been characterized so that multiple gene analyses, including all six major lineages of chromalveolates, could be compared and concatenated with data representing all five hypothesized supergroups. Overall support for much of the phylogenies is decreased over previous analyses that concatenated fewer genes for fewer taxa. Nevertheless, four of the six chromalveolate lineages (apicomplexans, ciliates, dinoflagellates and heterokonts) consistently form a monophyletic assemblage, whereas the remaining two (cryptomonads and haptophytes) form a weakly supported group. Whereas these results are consistent with the monophyly of chromalveolates inferred from plastid data, testing this hypothesis is going to require a substantial increase in data from a wide variety of organisms.

The Judicial Commission of the International Committee for Systematics of Prokaryotes decided that strain NBRC (formerly IFO) 3782 (=No. 43797), which was the originally designated type strain, has to replace ATCC 21273 as the type strain of Streptomyces rameus. ATCC 21273 was given as the type strain in the Approved Lists 1980.

The Judicial Commission of the International Committee for Systematics of Prokaryotes decided that the type species of the genus Paenibacillus is Paenibacillus polymyxa.

The Judicial Commission of the International Committee for Systematics of Prokaryotes has decided to place the genus Pelczaria with the species Pelczaria aurantia on the list of nomina rejicienda, due to the lack of an authentic type or neotype strain.

The Judicial Commission of the International Committee on Systematics of Prokaryotes has corrected the nomenclatural types of 12 orders: Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales.

The Judicial Commission of the International Committee for Systematics of Prokaryotes has decided that the type species of the genus Salmonella Lignieres 1900 is Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 and that the type strain of this species is strain LT2T. In addition, the epithet enterica in Salmonella enterica is conserved over all earlier epithets that may be applied to this species.

The nomenclature of the genus Salmonella has reached an unsatisfactory state of affairs, with two systems of nomenclature in circulation. One system, proposed in the 1980s by Le Minor and Popoff, has received wide acceptance, although it does not conform to the rules of the Bacteriological Code. The other system, which conforms to the rules of the Bacteriological Code, is being used by an ever-decreasing minority. As a result of a number of recent Requests for an Opinion, the Judicial Commission of the International Committee on the Systematics of Prokaryotes has issued an Opinion (Opinion 80) with the intention that it should solve these discrepancies. However, like all Opinions, it is limited to matters of nomenclature and does not help to interpret the taxonomic consequences. The Judicial Commission has therefore asked experts in the field of nomenclature and taxonomy to write a commentary on the nomenclatural and taxonomic consequences of Opinion 80. The present article explains the nomenclatural consequences of Opinion 80, together with a clear presentation of the taxonomy that results when applying the currently widely accepted interpretation that the genus Salmonella currently includes only two species.