International Code of Nomenclature of Prokaryotes . Appendix 9 : Orthography

Correspondence Hans G. Trüper hgtrueper@googlemail.com Jean P. Euzéby email address can be found at www.bacterio.net Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität, Meckenheimer Allee 168, D-53115 Bonn, Germany Société de Bactériologie Systématique et Vétérinaire (SBSV) and École Nationale Vétérinaire de Toulouse (ENVT), BP 87614, F-31076 Toulouse cedex 3, France


Preamble
When naming an organism, authors should be aware of the fact that there is no guarantee that all strains of a newly named species or all species of a newly named genus possess the property or properties used for the formation of that name.

A. Formation of Compound Names
(1) Compound names are formed by combining two or more words or word elements of Latin and/or Greek origin into one generic name or specific epithet.In most cases two word elements are used (e.g.Thio/bacillus, thio/parus), but up to four elements may be found (e.g.Ecto/thio/rhodo/ spira).The combination of word elements follows four basic rules: (a) Except for the last word element only the word stems are to be used.(b) The connecting vowel is -o-when the preceding word element is of Greek origin, it is -i-when the preceding word element is of Latin origin.Greek is more flexible than Latin about the connecting vowel, and other connecting vowels than -o-may be used if a precedent is found in Greek.Example: Corynebacterium.(c) A connecting vowel is dropped when the following word element starts with a vowel.(d) Hyphens and diacritic signs are not allowed (see Rules 12a and 64, respectively).
(2) Exemptions from these regulations exist only for the following cases: (a) When well-established word elements from chemistry or physics are used, their use in these sciences must be followed.Examples: thio-for sulfur does not lose the -o-in combinations such as Thioalkalibacter and thiooxidans (following the usage in chemistry: thioether, thioester); likewise radio-would not lose the -o-in combinations such as 'Radioalkalibacter' or 'radioegens' (following the usage in physics: radioactive).(b) As in inorganic chemistry the vowels -o and -i are used to indicate different oxidation levels of cations (e.g.ferro, ferri, cupro, cupri, etc.); they do not fall under the Greek/Latin ruling for connection vowels when used in prokaryote names.Examples: Ferroglobus is an Fe 2+ oxidizer, while Ferrimonas is an Fe 3+ reducer.(c) In word components like bio-, geo-, halo-, neo-, macro-, micro-, etc., the connecting vowel -o-may be kept when a component follows that begins with a vowel (for reasons of clarity or of previous usage).
(2) Both Latin and Greek know three genders, i.e. contain nouns of masculine, feminine and neuter gender.
Adjectives associated with nouns follow these in gender.
For the correct formation of specific epithets (as adjectives) it is therefore necessary to know the gender of the genus name or of its last component, as appropriate.
(3) The gender of a new genus must be indicated with the etymology given in the description.
C. Specific (and subspecific) epithets (1) Rule 12c of the Code demands that specific (or subspecific) epithets must be treated in one of the three following ways: (a) as an adjective that must agree in gender with the generic name; (b) as a substantive (noun) in apposition in the nominative case; (c) as a substantive (noun) in the genitive case.
(2) Adjectives and participles as specific epithets (a) Latin adjectives belong to the 1st, 2nd or 3rd declension.Those of the 1st and 2nd declension have different endings in the three genders.In the 3rd declension the situation is more complicated, as there are adjectives that don't change with gender, others that do and some that are identical in the masculine and feminine gender and different in the neuter.
Table 1 gives some examples.Note that comparative adjectives are also listed.It is recommended always to look up an adjective in a dictionary before using it for the formation of a name.(c) Infinitive (also named 'present') participles in the singular do not change with gender.According to the four conjugations of Latin they end in -ans (first conjugation, e.g.vorans devouring, from vorare to devour, voro I devour), -ens (second conjugation, e.g.inhibens inhibiting, from inhibere to inhibit, inhibeo I inhibit), -ens (third conjugation, e.g.exigens demanding, from exigere to demand, exigo I demand), -iens (third conjugation, e.g.faciens making, from facere to make, facio, I make), -iens (fourth conjugation, e.g.oboediens obeying, from oboedire to obey, oboedio I obey).Note that knowledge of the ending of the first person singular in the present is decisive!(d) Perfect participles change their endings with gender and are handled like adjectives of the first and second declension, e.g.aggregatus (masc.),aggregata (fem.), aggregatum (neut.)(aggregated, from aggregare to get together), flexus, flexa, flexum (bent, from flectere to bend), latus, lata, latum (carried, from the irregular verb ferre to carry), diminutus, diminuta, diminutum (smashed, from diminuere to smash).
(3) Nominative nouns in apposition as specific epithets (a) Nominative nouns in apposition must make sense to be acceptable.In grammar, apposition means 'the placing of a word or expression beside another so that the second explains and has the same grammatical construction as the first'; i.e. the added nominative noun has an explanatory specifying function for the generic name, thus, e.g.Desulfovibrio gigas may be understood as Desulfovibrio dictus gigas and translated as 'Desulfovibrio, called the giant', which, with reference to the unusual cell size of this species, makes sense.
(b) All specific epithets ending with the Latin suffixes -cola (derived from incola, 'the inhabitant, dweller') and -cida ('the killer') fulfil the above-mentioned requirement.

D. Formation of prokaryote names from personal names
(1) Persons may be honoured by using their name in forming a generic name or a specific epithet.The Code, however, strongly recommends refraining from naming genera (and subgenera) after persons that are not connected with bacteriology or at least with natural science (Recommendation 10a) and, in the case of specific epithets, to ensure that, if taken from the name of a person, it recalls the name of one who discovered or described it, or was in some way connected with it (Recommendation 12c).
(2) It is good practice to ask the person to be honoured by a scientific name for permission (as long as she/he is alive).Authors should refrain from naming bacteria after themselves or co-authors after each other in the same publication, as this is considered immodest by the majority of the scientific community [see Recommendation 6 (10)].
(3) Personal names in generic names (a) The Code provides two ways to form a generic name from a personal name: either directly by adding the ending -a, -ea, -nia or -ia or as a diminutive by adding, usually, the ending -ella, -iella or -nella.(4) Personal names in specific epithets (a) To form specific epithets from personal names there are principally two possibilities: the adjective form and the genitive noun form.The adjective form has no means to recognize the sex of the honoured person, which, in principle, is not necessary for nomenclatural purposes.The personal names receive appropriate endings according to the gender of the generic name as indicated in Table 3.Thus an adjective epithet is formed that has the meaning of 'pertaining/relating/belonging to ... (the person)'.
(b) When the genitive of a Latinized personal name is formed for a specific epithet, the sex of the person to be honoured may be taken into consideration as indicated in Table 4.
On the basis of classical, medieval and Neo-Latin usage, any of the forms of Latinization listed in Table 4 may be chosen.As evident from Table 4, the formation of specific epithets from personal names as genitive nouns poses certain problems only with names ending in -a and -o.
(c) The recommendations and rules for genus names as given above [D (3), (c)-(f)] are also applicable for specific epithets.Appropriate examples are given there.

E. Formation of prokaryote names from geographical names
(1) The formation of prokaryote names from geographical names has no geopolitical meaning, i.e. such names cannot be used to express geopolitical claims.
(2) Unlike epithets derived from personal names, epithets on the basis of geographical names cannot be formed as substantives in the genitive case.They must be adjectives and are usually constructed by adding the ending -ensis (masculine or feminine gender) or -ense (neuter gender) to the geographical name in agreement with the latter's gender.Only if the name of the locality ends in -a or -e or -en, these letters are dropped before adding -ensis/-ense (e.g.jenensis from Jena, californiensis from California, drentensis from Drente, bremensis from Bremen).If the locality's name ends in -o, the ending becomes -nensis/ -nense (e.g. the name of the Japanese city Sapporo: sapporonensis, sapporonense).
(b) Participles are treated as if they are adjectives, i.e. they fall under Rule 12c (2) of the Code.

Table 1 .
Examples of Latin adjectives *Most common types.DInfinitive participle used as adjective.International Journal of Systematic and Evolutionary Microbiology 59 Downloaded from www.microbiologyresearch.orgby IP: 54.70.40.11On: Sun, 04 Aug 2019 20:05:13 Both kinds are always in the feminine gender.Examples are provided in Table2.(b)Somepersonalnames in Europe were already Latinized before 1800 and kept since.If they end in -us, replace the ending by -a or -ella (diminutive) respectively (e.g. the name Bucerius would result in 'Buceria' or 'Buceriella').Beware, however, of Lithuanian names like Didlaukus, Zeikus, etc.! These are not Latinized but genuine forms and would receive the ending -ia according to Table2.(c)Not more than one person can be honoured in one generic name or epithet.
(d) If an organism is named after a person, the name cannot be shortened, e.g.'Wigglesia' after Wigglesworth, 'Stackia' after Stackebrandt or 'Goodfellia' after Goodfellow, etc., but must appear fully.Personal titles(Sir, Lord, Duke, Baron, Graf, Conte, etc.)are not included in prokaryote names, although they may belong to the name according to the laws of the respective country.Prefixes and particles should be treated as follows:(i) The Scottish patronymic prefixes 'Mac', 'Mc' and 'M', meaning 'son of', should be written 'mac' and be united with the rest of the name (e.g.'Macdonellia' or 'macdonellii' after MacDonell; Macginleya or macginleyi after McGinley).(ii) The Irish patronymic prefix 'O' should be united with the rest of the name or omitted (e.g.

Table 2 .
Ways to form generic names from personal names Some names may be hypothetical examples.Oconnoria' or 'Connoria' or 'oconnorii' or 'connorii' after O'Connor).(iii) A prefix consisting of an article (e.g.le, la, l', les, el, il, lo, de), or containing an article (e.g.du, de la, des, del, della, do, da), may be omitted or united to the name (e.g.Rochalimaea after da Rocha-Lima; *This name of Lithuanian origin is not a genuine Latinized name.If it were, the genus names 'Zeikia' or 'Zeik(i)ella' might have been possible.'(e)Rarely, generic names or specific epithets have been formed from forenames (first names, given names, Christian names), i.e. not from the family name.Examples: Erwinia was named after Erwin F. Smith; the first name Arletta appears in Staphylococcus arlettae (N.L. gen.n.arlettae of Arletta, named after Arlette van de Kerckhove).First names may be chosen in order to avoid rather long family names or unusually long (hyphenated) double names.(f)In cases of very frequent family names where the honoured person is not easily identifiable, first and family name may be contracted without connecting vowel or hyphenation, but otherwise treated like a single family name.Examples: Owenweeksia, Elizabethkingia.

Table 3 .
Formation of specific epithets from personal names in the adjective form Some names may be hypothetical examples.
Woods Hole, Cape Cod, Monte Carlo, etc.).The formation of specific epithets from such localities' names may pose a problem, as the use of the adjectival suffix -ensis, -ense may lead to rather strange looking or awkward constructions, such as 'deeplakensis' or 'bluemountainense', although they would be formally correct.If a name of a locality lends itself to translation into Latin, specific epithets may as well be formed as genitive substantives of the two components and concatenating them without hyphenation, like the existing ones lacusprofundi (of Deep Lake), marisnigri (of the Black Sea), marismortui (of the Dead Sea) or, of two nouns, vallismortis (of Death Valley).Note that in Latin

Table 4 .
Formation of specific epithets from personal names as genitive nouns Some names may be hypothetical examples.