International Journal of Systematic and Evolutionary Microbiology (2014), 64,

Transcription

1 International Journal of Systematic and Evolutionary Microbiology (2014), 64, DOI /ijs Taxonomic Note The family name Solimonadaceae Losey et al is illegitimate, proposals to create the names Sinobacter soli comb.nov.and Sinobacter variicoloris contravene the Code, the family name Xanthomonadaceae Saddler and Bradbury 2005 and the order name Xanthomonadales Saddler and Bradbury 2005 are illegitimate and notes on the application of the family names Solibacteraceae Zhou et al. 2008, Nevskiaceae Henrici and Johnson 1935 (Approved Lists 1980) and Lysobacteraceae Christensen and Cook 1978 (Approved Lists 1980) and order name Lysobacteriales Christensen and Cook 1978 (Approved Lists 1980) with respect to the classification of the corresponding type genera Solibacter Zhou et al. 2008, Nevskia Famintzin 1892 (Approved Lists 1980) and Lysobacter Christensen and Cook 1978 (Approved Lists 1980) and importance of accurately expressing the link between a taxonomic name, its authors and the corresponding description/circumscription/emendation B. J. Tindall Correspondence B. J. Tindall bti@dsmz.de Leibniz-Institut DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, Braunschweig, Germany In a recent publication the name Solimonadaceae Losey et al has been proposed as a replacement name for the family name Sinobacteraceae Zhou et al This course of action contravenes the current Code governing the nomenclature of prokaryotes, making Solimonadaceae Losey et al an illegitimate name that neither has claim to priority nor can be used as a correct name. Closer examination of publications dealing with the taxonomy of members of the genera Solimonas and Sinobacter and the placement of these taxa at the rank of family and order reveal problems associated with the application of the family names Sinobacteraceae Zhou et al. 2008, Nevskiaceae Henrici and Johnson 1935 (Approved Lists 1980) and Lysobacteraceae Christensen and Cook 1978 (Approved Lists 1980) and the order names Lysobacterales Christensen and Cook 1978 (Approved Lists 1980) and Xanthomonadales Saddler and Bradbury For the purpose of clarity technical terms that are used in the International Code of Nomenclature of Bacteria are designated in bold face. The genus name Sinobacter Zhou et al was validly published in 2008 (Zhou et al., 2008), with Sinobacter flavus Zhou et al., 2008 as the type and only species in the G 2014 IUMS Printed in Great Britain 293

2 B. J. Tindall genus. The genus in turn serves as the type of the family Sinobacteraceae Zhou et al. 2008, with the name being based on the genus name Sinobacter and was validly published in the same publication that proposed both the genus name and the species combination. The family contained a single genus, Sinobacter. Subsequently, it was proposed that the species Sinobacter flavus Zhou et al should be placed in a single genus (Sheu et al. 2011), together with Solimonas soli Kim et al (Kim et al. 2007), Solimonas aquatica Sheu et al (Sheu et al. 2011) and Singularimonas variicoloris Friedrich and Lipski 2008 (Friedrich & Lipski 2008). Based on the principle of priority (Lapage et al., 1992) the earliest legitimate, validly published genus name is Solimonas Kim et al. 2007, resulting in the valid publication of the combinations Solimonas flava (Zhou et al. 2008) Sheu et al and Solimonas variicoloris (Friedrich & Lipski 2008) Sheu et al. 2011, as well as providing emended descriptions of the species Solimonas soli Kim et al emend. Sheu et al and the genus Solimonas Kim et al emend. Sheu et al Sheu et al. (2011) make no mention of the family Sinobacteraceae Zhou et al. 2008, although it remains validly published and despite the fact that Sheu et al. (2011) consider the type genus Sinobacter Zhou et al to be a later heterotypic synonym of Solimonas Kim et al emend. Sheu et al. 2011, the genus Sinobacter Zhou et al remains the type of the family Sinobacteraceae Zhou et al The family Sinobacteraceae Zhou et al evidently contained a single genus, Solimonas, that is regarded as an earlier heterotypic synonym of the genera Sinobacter Zhou et al and Singularimonas Friedrich and Lipski, 2008 according to Sheu et al. (2011), i.e. Sinobacteraceae Zhou et al emend. Sheu et al Note that an alternative taxonomic opinion has been effectively published (Xu et al., 2011), but currently no attempt appears to have been made to validly publish the names, where the authors propose the new combinations Sinobacter soli comb. nov. and Sinobacter variicoloris com. nov., together with an emended description of the genus Sinobacter Zhou et al emend. Xu et al The proposed new combinations contravene the Code (Lapage et al. 1992) and are also a potential source of confusion. In a recent publication, Losey et al. (2013) described a new genus Fontimonas Losey et al that contains a single species, Fontimonas thermophila Losey et al. 2013, that per definition is the type of the genus. In their publication, Losey et al. (2013) propose that the genus Fontimonas is to be placed in the same family as members of the genus Solimonas. Although the authors are aware that the genera Solimonas and Sinobacter are considered to be synonyms (Sheu et al., 2011), where the genus name Solimonas has priority the authors conclude with the genus name Sinobacter now defunct there is now an inconsistency in the nomenclature with the name Sinobacteraceae (Losey et al., 2013). At the same time they propose a new family, Solimonadaceae, to accommodate members of the genera Solimonas Kim et al emend Sheu et al and Fontimonas Losey et al (Losey et al., 2013). However, alterations have been made to the wording of the Bacteriological Code with the intention of clarifying a potentially ambiguous interpretation of Rule 15 (Garrity et al., 2011): The nomenclatural type, referred to in this Code as type, is that element of the taxon with which the name is permanently associated, whether as a correct name or as a later heterotypic synonym. The nomenclatural type is not necessarily the most typical or representative element of the taxon. It should also be remembered that if a name is validly published as defined by the Code, that name remains validly published even if it is shown to be a synonym and is not treated as a correct name. The Code does not appear to cater for the concept of defunct names. Consequently, the genus name Sinobacter Zhou et al and the family name Sinobacteraceae Zhou et al remain validly published. Despite the fact that the genus name Sinobacter Zhou et al is considered to be a synonym of the genus name Solimonas Kim et al emend Sheu et al. 2011, it remains the type of the family name Sinobacteraceae and that name is to be used for the taxon that contains the type, i.e. Sinobacter, irrespective of whether that name is treated as a synonym. The species Sinobacter flavus is treated by Sheu et al. (2011) as a member of the genus Solimonas and they have created the new combination Solimonas flava as well as proposing that the genera Sinobacter and Solimonas are synonyms. Rule 52b is fairly clear in that it states: Among the reasons for which a name may be illegitimate are the following. If the taxon to which the name was applied, as circumscribed by the author, included the nomenclatural type of a name which the author ought to have adopted under one or more of the Rules. In this particular case the family proposed by Losey et al. (2013) contains members of the genera Fontimonas and Solimonas, where the latter includes the genus name Sinobacter, treated as a synonym. Sinobacter is the type of the family Sinobacteraceae so it follows that the correct name of the taxon is Sinobacteraceae, and the family name Solimonadaceae contravenes the Code as defined in Rule 51b, making it an illegitimate name. It should be also noted that replacement names are catered for under Rule 54: A name or epithet illegitimate according to Rules 51b, 53, or 56a is replaced by the oldest legitimate name or epithet in a binary or ternary combination which in the new position will be in accordance with the Rules. If no legitimate name or epithet exists, one must be chosen. Since a specific epithet is not rendered illegitimate by publication in a species name in which the generic name is illegitimate (Rule 32b), 294 International Journal of Systematic and Evolutionary Microbiology 64

3 Solimonadaceae versus Sinobacteraceae an author may use such an epithet if he wishes, provided that there is no obstacle to its employment in the new position or sense; the resultant combination is treated as a new name and is to be ascribed to the author of the combination. The epithet is, however, ascribed to the original author. Based on this rule there is no evidence that the family name Sinobacteraceae is illegitimate and there is also no reason to create a replacement name as indicated in the title and the abstract of the paper by Losey et al. (2013). Documenting the fact that the family name Solimonadaceae Losey et al is an illegitimate name is not a superfluous exercise, because as Young (2009) has pointed out there is a tendency to use illegitimate names as candidates for correct names, despite the fact that the Code (Lapage et al., 1992) clearly rules that they are not to be used and that they are not to be taken into consideration with regards the principle of priority. Furthermore, any comment indicating that technically the family names Solimonadaceae Losey et al and Sinobacteraceae Zhou et al emend. Sheu et al are synonyms or that the family name Solimonadaceae Losey et al is illegitimate are missing from the Notification List that deals with names published in the first issue of volume 62 of the IJSEM (Euzéby, 2013). There is clearly a potential source of error and confusion. One of the key aspects of the Code (Lapage et al., 1992) is covered by: Principle 8 Each order or taxon of a lower rank with a given circumscription, position, and rank can bear only one correct name, i.e., the earliest that is in accordance with the Rules of this Code. and Rule 23a Each taxon above species, up to and including order, with a given circumscription, position, and rank can bear only one correct name, that is, the earliest that is in accordance with the Rules of this Code. If a name is to be use in such a fashion that it is clear which circumscription, position and rank is being referred to, due consideration must be given to each of these points. The issue that is often difficult to determine is the question of which circumscription is being used. Using the genus name Solimonas, for example, does not distinguish between the original opinion expressed by Kim et al. (2007) where a single species, Solimonas soli Kim et al. 2007, is included or the opinion expressed by Sheu et al. (2011) which includes the species Solimonas soli Kim et al. 2007, Solimonas aquatica Sheu et al. 2011, Solimonas flava (Zhou et al. 2008) Sheu et al and Solimonas variicoloris (Friedrich & Lipski, 2008) Sheu et al The use of the genus name with an author citation Solimonas Kim et al may also be ambiguous because it may be simply intended to refer to the authors who first created the name or to the circumscription published by those authors. Use of the genus name with the citation Solimonas Kim et al emend. Sheu et al is more accurate and clearly signifies which circumscription, position and rank is being used. Based on the wording used by Losey et al. (2013) it is clear that the authors are aware of the opinion that Sheu et al. (2011) consider that the genus names Sinobacter Zhou et al and Solimonas Kim et al are synonyms and that Sinobacter flavus Zhou et al is to be treated as Solimonas flava (Zhou et al., 2008) Sheu et al and that they appear to accept that opinion. However, there is no clear statement to that effect nor is it clear whether the genus Singularimonas Friedrich and Lipski 2008 and Solimonas Kim et al are to be treated as synonyms as proposed by Sheu et al. (2011), i.e. Solimonas Kim et al emend. Sheu et al There is also currently a trend to cite online sources to try to solve such issues, but as long as they change their content without documenting the dates of change or are simply lists of validly published names rather than associated taxonomic interpretation giving appropriate reference to the effectively published source of that interpretation, then this does not improve the situation and is certainly not any more accurate than using the genus name alone. A closer look at the placement of members of the genera Sinobacter and Solimonas in higher taxonomic ranks indicates that there may also be additional problems and there also seems to be a knock on effect. When originally described, the family Sinobacteraceae contained a single genus, Sinobacter (Zhou et al. 2008), but when Sheu et al. (2011) proposed that the genus names Sinobacter, Singularimonas and Solimonas were synonyms no statement was made about the effect that this rearrangement had on the family Sinobacteraceae. The issue is further compounded by the fact that Gutierrez et al. (2012) have published a figure (their figure 2) and wording that implies that members of the genera Sinobacter, Singularimonas, Solimonas, Nevskia, Steroidobacter, Alkanibacter, Panacagrimonas and Hydrocarboniphaga are all members of the family Sinobacteraceae. The authors provide no emended description and no direct reference to a publication where this opinion has been published and it is unclear whether this is meant to be a formal proposal or whether this should be simply considered to be equivalent of incidental mention as defined in Rule 28b (3) (Lapage et al., 1992) when applied to names and can be ignored. Although not currently recognized, members of the genus Polycyclovorans Gutierrez et al., 2013 also appear to have crept into the family in a similar fashion. In both publications, Gutierrez et al. (2012, 2013) also mention the synonymy of the genera Solimonas, Sinobacter and Singularimonas, but do not implement the nomenclatural consequences. At the time of writing (19 July 2013) some but not all of these genera mentioned by Gutierrez et al. (2012, 2013) are listed as members of the family Sinobacteraceae in the NCBI Taxonomy browser (

4 B. J. Tindall gov/taxonomy). Although such a website has no official status it is a source that is de facto used by the scientific community. Such an interpretation is also problematic because it does not take into account that the genus name Nevskia Famintzin, 1892 (Approved Lists 1980) (Skerman et al., 1980, 1989) is the type of the family Nevskiaceae Henrici and Johnson 1935 (Approved Lists 1980) (Skerman et al., 1980, 1989; Henrici & Johnson, 1935) that clearly has priority over the family name Sinobacteraceae Zhou et al. 2008, if one considers that members of the genera Nevskia and Sinobacter (even as a synonym of Solimonas) are to be placed in the same family. It is also interesting to note that in the second edition of Bergey s Manual of Systematic Bacteriology the genus Nevskia is placed in the family Xanthomonadaceae Saddler and Bradbury 2005 (Saddler & Bradbury, 2005b; Saddler & Bradbury, 2005d, a chapter that heads a section on the subordinate taxa and the subordinate taxa are named; Babenzen & Cypionka, 2005), a name that clearly fits the wording of Rule 51b and is consequently illegitimate, because the name Nevskiaceae Henrici and Johnson 1935 (Approved Lists 1980) is the name to be used. Even if the family Xanthomonadaceae Saddler and Bradbury, 2005 were to be emended to exclude the genus Nevskia the problem still exists that this family contains the genus Lysobacter Christensen and Cook 1978 (Approved Lists 1980), the type of the family name Lysobacteraceae Christensen and Cook 1978 (Approved Lists 1980) (Skerman et al., 1980, 1989; Christensen & Cook, 1978) which also has priority and continues to make the family name Xanthomonadaceae Saddler and Bradbury 2005 illegitimate. It should be mentioned that the order Xanthomonadales Saddler and Bradbury 2005 (Saddler & Bradbury, 2005a; Saddler & Bradbury, 2005c, a chapter that heads a section on the subordinate taxa; Christensen, 2005) is also illegitimate because it contains the genus Lysobacter Christensen and Cook 1978 (Approved Lists 1980), the type of the order Lysobacterales Christensen and Cook 1978 (Approved Lists 1980). The illegitimate names Xanthomonadaceae Saddler and Bradbury 2005 and Xanthomonadales Saddler and Bradbury 2005 are currently in use in the IJSEM. It would appear that there is already an interesting trend whereby names that are found unsuitable for diverse reasons are simply replaced and the wording of the Code ignored rather than applying the rules and providing appropriate emended descriptions of the taxa, further enhancing the principle of the stability of names (Principle 1, Lapage et al. 1992). If the ISCP is to further develop in the direction of a standards organization (Garrity & Oren, 2013) then there is a need for mechanisms of checking and eliminating such errors, particularly in the pages of the IJSEM, which is advertised as the official journal of the ICSP. Publication of names in the pages of the IJSEM is evidently not sufficient to guarantee that they are either legitimate or validly published. There would seem to be little point in creating a standards organization if the currently applicable standards, i.e. the Code, dealing with the nomenclature of prokaryotes (Lapage et al., 1992) are evidently not being implemented correctly in the official publication (the IJSEM). Clearly there is a need to either change that situation or to provide for other mechanisms whereby readers may be informed of the status of a name. Declaration of a potential conflict of interest The author is employed by an organization that commercially offers both taxonomic services as well as biological material to the scientific community. This may be perceived as a potential conflict of interest. References Babenzen, H.-D. & Cypionka, H. (2005). Genus I. Nevskia Famintzin AL.InBergey s Manual of Systematic Bacteriology, vol. 2, 2nd edn, pp Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer. Christensen, P. (2005). Genus IV. Lysobacter Christensen and Cook AL.InBergey s Manual of Systematic Bacteriology,vol.2,2ndedn, pp Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer. Christensen, P. & Cook, F. D. (1978). Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 28, Euzéby, J. P. (2013). Notification that new names and new combinations have appeared in volume 63, part 1, of the IJSEM. Int J Syst Evol Microbiol 63, Friedrich, M. M. & Lipski, A. (2008). Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov., hexanedegrading bacteria isolated from a hexane-treated biofilter. Int J Syst Evol Microbiol 58, Garrity, G. M. & Oren, A. (2013). Response to Sutcliffe et al.: regarding the International Committee on Systematics of Prokaryotes. Trends Microbiol 21, Garrity, G. M., Labeda, D. P. & Oren, A. (2011). Judicial Commission of the International Committee on Systematics of Prokaryotes. XIIth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 3, 4 and 6 August 2008, Istanbul, Turkey. Int J Syst Evol Microbiol 61, Gutierrez,T.,Green,D.H.,Whitman,W.B.,Nichols,P.D.,Semple,K.T. & Aitken, M. D. (2012). Algiphilus aromaticivorans gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from a culture of the marine dinoflagellate Lingulodinium polyedrum, and proposal of Algiphilaceae fam. nov. Int J Syst Evol Microbiol 62, Gutierrez, T., Green, D. H., Nichols, P. D., Whitman, W. B., Semple, K. T. & Aitken, M. D. (2013). Polycyclovorans algicola gen. nov., sp. nov., an aromatic-hydrocarbon-degrading marine bacterium found associated with laboratory cultures of marine phytoplankton. Appl Environ Microbiol 79, Henrici, A. T. & Johnson, D. E. (1935). Stalked bacteria, a new order of Schizomycetes. J Bacteriol 30, Kim, M. K., Kim, Y. J., Cho, D. H., Yi, T. H., Soung, N. K. & Yang, D. C. (2007). Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 57, Lapage, S. P., Sneath, P. H. A., Lessel, E. F., Skerman, V. B. D., Seeliger, H. P. R. & Clark, W. A. (editors) (1992). International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code. Washington, DC: American Society for Microbiology. 296 International Journal of Systematic and Evolutionary Microbiology 64

5 Solimonadaceae versus Sinobacteraceae Losey, N. A., Stevenson, B. S., Verbarg, S., Rudd, S., Moore, E. R. B. & Lawson, P. A. (2013). Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al Int J Syst Evol Microbiol 63, Saddler, G. S. & Bradbury, J. F. (2005a). Order Xanthomonadales ord. nov. In Validation of the publication of new names and new combinations previously effectively published outside the IJSEM, List no.106. Int J Syst Evol Microbiol 55, Saddler, G. S. & Bradbury, J. F. (2005b). Family Xanthomonadaceae fam. nov. In Validation of the publication of new names and new combinations previously effectively published outside the IJSEM, List no Int J Syst Evol Microbiol 55, Saddler, G. S. & Bradbury, J. F. (2005c). Order III. Xanthomonadales ord. nov. In Bergey s Manual of Systematic Bacteriology, vol. 2, 2nd edn, p. 63. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer. Saddler, G. S. & Bradbury, J. F. (2005d). Family I. Xanthomonadaceae fam. nov. In Bergey s Manual of Systematic Bacteriology, vol. 2, 2nd edn, p. 63. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer. Sheu, S. Y., Cho, N. T., Arun, A. B. & Chen, W. M. (2011). Proposal of Solimonas aquatica sp. nov., reclassification of Sinobacter flavus Zhou et al as Solimonas flava comb. nov. and Singularimonas variicoloris Friedrich and Lipski 2008 as Solimonas variicoloris comb. nov. and emended descriptions of the genus Solimonas and its type species Solimonas soli. Int J Syst Evol Microbiol 61, Skerman, V. B. D., McGowan, V. & Sneath, P. H. A. (1980). Approved lists of bacterial names. Int J Syst Bacteriol 30, Skerman, V. B. D., McGowan, V. & Sneath, P. H. A. (1989). Approved Lists of Bacterial Names (Amended). Washington, DC: American Society for Microbiology. Xu, J., Chen, X., Wang, X. & Zhou, Y. (2011). Reclassification of Solimonas soli (Kim et al., 2007) and Singularimonas variicoloris (Friedrich et al., 2008) as Sinobacter soli comb. nov. and Sinobacter variicoloris comb. nov. and emended description of the genus Sinobacter (Zhou et al., 2008). African J. Microbiol Res 5, Young, J. M. (2009). Legitimacy is an essential concept of the International Code of Nomenclature of Prokaryotes a major revision of the Code is called for. Int J Syst Evol Microbiol 59, Zhou, Y., Zhang, Y. Q., Zhi, X. Y., Wang, X., Dong, J., Chen, Y., Lai, R. & Li, W. J. (2008). Description of Sinobacter flavus gen. nov., sp. nov., and proposal of Sinobacteraceae fam. nov. Int J Syst Evol Microbiol 58,