Abstract
In a recent publication the name Solimonadaceae Losey et al. 2013 has been proposed as a replacement name for the family name Sinobacteraceae Zhou et al. 2008. This course of action contravenes the current Code governing the nomenclature of prokaryotes, making Solimonadaceae Losey et al. 2013 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 2005.
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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. 2008 was validly published in 2008 (Zhou et al., 2008), with Sinobacter flavus Zhou et al., 2008 as the type and only species in the 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. 2008 should be placed in a single genus (Sheu et al. 2011), together with Solimonas soli Kim et al. 2007 (Kim et al. 2007), Solimonas aquatica Sheu et al. 2011 (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. 2011 and Solimonas variicoloris (Friedrich & Lipski 2008) Sheu et al. 2011, as well as providing emended descriptions of the species Solimonas soli Kim et al. 2007 emend. Sheu et al. 2011 and the genus Solimonas Kim et al. 2007 emend. Sheu et al. 2011. 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. 2008 to be a later heterotypic synonym of Solimonas Kim et al. 2007 emend. Sheu et al. 2011, the genus Sinobacter Zhou et al. 2008 remains the type of the family Sinobacteraceae Zhou et al. 2008. The family Sinobacteraceae Zhou et al. 2008 evidently contained a single genus, Solimonas, that is regarded as an earlier heterotypic synonym of the genera Sinobacter Zhou et al. 2008 and Singularimonas Friedrich and Lipski, 2008 according to Sheu et al. (2011), i.e. Sinobacteraceae Zhou et al. 2008 emend. Sheu et al. 2011. 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. 2008 emend. Xu et al. 2011. 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. 2013 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. 2007 emend Sheu et al. 2011 and Fontimonas Losey et al. 2013 (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. 2008 and the family name Sinobacteraceae Zhou et al. 2008 remain validly published. Despite the fact that the genus name Sinobacter Zhou et al. 2008 is considered to be a synonym of the genus name Solimonas Kim et al. 2007 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), 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. 2013 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. 2013 and Sinobacteraceae Zhou et al. 2008 emend. Sheu et al. 2011 are synonyms or that the family name Solimonadaceae Losey et al. 2013 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. 2011 and Solimonas variicoloris (Friedrich & Lipski, 2008) Sheu et al. 2011. The use of the genus name with an author citation Solimonas Kim et al. 2007 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. 2007 emend. Sheu et al. 2011 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. 2008 and Solimonas Kim et al. 2007 are synonyms and that Sinobacter flavus Zhou et al. 2008 is to be treated as Solimonas flava (Zhou et al., 2008) Sheu et al. 2011 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. 2007 are to be treated as synonyms as proposed by Sheu et al. (2011), i.e. Solimonas Kim et al. 2007 emend. Sheu et al. 2011. 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 (). 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.