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Naming photosynthetic bacteria

Howard Gest hgest at bio.indiana.edu
Tue Oct 13 15:55:28 EST 1998


Dear Colleague,

        Confusion is being introduced in the scientific literature by a
rash of new "proposals" for changing the names of bacterial species that
have been the subjects of numerous basic studies over many decades. Aside
from other problems, profligate renaming of species will obviously hamper
communication. There is widespread discontent among investigators who
consider rampant name changing as misguided and premature, and who are
mystified when new names suddenly appear in the literature for organisms
thay have worked with for many years. This communication discusses the
counterproductive and narrowly-based "proposals" of some contemporary
taxonomists, and is being sent to numerous interested parties.
        We recently drew attention to increasing problems in nomenclature
of anoxyphototrophs (Gest and Favinger, ASM News 64: 434 (1998)). Numerous
name changes have been proposed by individuals who believe that 16s rRNA
sequences accurately reveal more authentic taxonomic relationships
requiring new generic and species designations. Aside from the fact that
changing the name of an organism that has been the subject of hundreds of
published investigations introduces confusion in the literature (and a
great burden on those involved in updating information retrieval), there
are good reasons to question this new hobbyhorse of taxonomists. As one
example in this connection, we note Mayr's recent analysis, which supports
the conclusion that "Archaea" are in fact bacteria, and not a separate
"empire." (E. Mayr, Proc. Nat. Acad. Sci. 95: 9720, 1998).
        As far as we have been able to determine, taxonomy committees meet
occasionally to discuss proposed name changes, which in fact enter the
literature as faits accomplis. Theoretically, there is a procedure by which
one can question proposed name changes, but it is obscure. In effect,
scientists actively investigating the organisms in question are by-passed.

        Some investigators prefer to cite Bergey's Manual of Systematic
Bacteriology as the authority for names of anoxyphototrophs. They should
always also cite the original names of the organisms, but they frequently
fail to do so. Eventually, some of the name changes used in revised
editions of the Systematic Manual will prove to be scientifically
justified, but we believe many will not. This conviction stems from our
belief that we have much to learn about evolutionary phylogeny. We marvel
at the naivete of the crusaders who campaign for the notion that a single
molecular Rosetta Stone can decipher the complexities of microbial
evolution.
        We now offer a suggestion, namely, that in our research papers and
in dealing with editors, we should simply ignore the new "proposals" and
use the  Ninth Edition of Bergey's Manual of DETERMINATIVE Bacteriology
(Williams & Wilkins,1994) as the authority for validated names of
anoxyphototrophs currently under active investigation; in other words,
names we are used to and which are very extensively cited in the
literature. In 1980, R.E. Dickerson (Nature, vol. 283, p. 210) noted the
concern that "molecular information might be of little use in deciphering
bacterial phylogeny because of the possibility of lateral transfer of genes
and the consequent scrambling of the genetic record." Genomes of bacteria
are being sequenced at an accelerating pace, and when the genomes of a
number of representative anoxyphototrophs become available we will have a
much better picture of the natural relationships of these organisms and how
the partial information from 16s rRNA sequences may relate to cellular
evolution.
        There is no compelling reason for an end-of-millenium panic to
change names of anoxyphototrophs. We note also that excessive zeal of
taxonomists is not a new phenomenon. In 1974, S.T. Cowan commented: "It is
often easier to create a new genus or species than to do the comparative
work necessary to put an organism into its rightful place in an existing
genus or species. The temptation to designate a new genus or species should
be resisted; it would be if people realized that the ability of a
taxonomist is judged as inversely proportional to the number of new taxa he
has created." (Manual for the Identification of Medical Bacteria; Cambridge
University Press, 2nd ed.)
        It should also be reemphasized that appropriate nomenclature serves
several purposes; indicating phylogenetic relations is only one aspect.
This was clearly recognized by C.B. Van Niel, who published a penetrating
analysis in 1946 of "The classification and natural relationships of
bacteria" (Cold Spring Harbor Symposia, vol. 11, p.285-301).
        Some patience is in order, and we hope that those who agree with
our suggestion will communicate their views in letters to relevant journals
such as American Society for Microbiology News [1325 Massachusetts Ave.,
N.W. Washington,DC 20005-4171; M.I. Goldberg, Editor In Chief]. For those
who do not have ready access to the Determinative Manual, we list below
names given in the manual for a number of species of particular interest to
current investigators.

Rhodobacter: adriaticus, capsulatus, euryhalinus, sphaeroides,
sulfidophilus, veldkampii [Table 10.10] Rhodocyclus: gelatinosus,
purpureus, tenuis [Table 10.11]
Rhodopseudomonas: acidophila, blastica, marina, palustris, rutila,
sulfoviridis, viridis [Table 10.12]
Rhodospirillum: centenum, fulvum, mediosalinum, molischianum,
photometricum, rubrum, salexigens, salinarum [Table 10.13]

Howard Gest and Jeffrey Favinger         Terry Meyer
Photosynthetic Bacteria Group            Department of Biochemistry
Biology Department                       University of Arizona
Indiana University                       Tucson, AZ 85721
Bloomington, IN 47408



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