https://doi.org/10.1038/s41564-022-01214-9

Supplementary information

SeqCode: a nomenclatural code forprokaryotes described from sequence data
In the format provided by theauthors and unedited

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SeqCode, a nomenclatural code for prokaryotes described from sequence data
Brian P. Hedlund, Maria Chuvochina, Philip Hugenholtz, Konstantinos T. Konstantinidis, Alison
E. Murray, Marike Palmer, Donovan H. Parks, Alexander J. Probst, Anna-Louise Reysenbach,Luis M. Rodriguez-R, Ramon Rossello-Mora, Iain C. Sutcliffe, Stephanus N. Venter, and William
B. Whitman*

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8* Correspondence to: William B. Whitman, whitman@uga.edu

9Supplementary Information

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The Code of Nomenclature of Prokaryotes Described from Sequence Data
Glossary
Example cases of validation of names under the SeqCode
Example of path 1: family Wolframiiraptoraceae and child taxa
Table S1: Example spreadsheet format for nomenclature proposals
SeqCode Pre-registration
Example of path 2: Macondimonas diazotrophica
Example of combination of paths 1 and 2: class Kryptonia and child taxa
Table S2. Etymology and typification of higher taxa for Kryptonium thompsonii
References

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The Code of Nomenclature of Prokaryotes Described from Sequence Data

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Edited by William B Whitmana, Maria Chuvochinab, Brian P Hedlundc, Philip Hugenholtzb,
Konstantinos T Konstantinidisd, Alison E Murraye, Marike Palmerc, Donovan H Parksb, Alexander
J Probstf, Anna-Louise Reysenbachg, Luis M Rodriguez-Rh, Ramon Rossello-Morai, Iain Sutcliffej
and Stephanus N Venterk

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a

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b

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c

School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA

32dSchool of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA

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eDivision of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA

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Department of Microbiology, University of Georgia, Athens, GA, USA

The University of Queensland, School of Chemistry and Molecular Biosciences, Australian
Centre for Ecogenomics, Australia

Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for
Aquatic Microbial Ecology and Centre of Water and Environmental Research(ZWU), University of Duisburg-Essen, Essen, Germany.
Biology Department, Portland State University, Portland, OR, USA

Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck,
Innrain 15 / 01-05, Innsbruck 6020, Austria
Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean
Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK

Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural
Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa

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CHAPTER 1. GENERAL CONSIDERATIONSGeneral Consideration 1
The progress of prokaryotic microbiology requires a precise system of nomenclature accepted by
the majority of microbiologists. For practical purposes, the term prokaryotes is a synonym for
Archaea and Bacteria.
General Consideration 2
To achieve order in nomenclature, it is essential that scientific names be regulated byinternationally accepted rules.
General Consideration 3
The rules that govern the scientific nomenclature used in the biological sciences are embodied incodes of nomenclature.
General Consideration 4
Rules of nomenclature do not govern the delimitation of taxa or determine their relations. The rules
are primarily for assessing the correctness of the names applied to defined taxa; they also prescribe
procedures for creating and proposing new names.
General Consideration 5
The Code of Nomenclature of Prokaryotes Described from Sequence Data applies to the namingof all prokaryotes where the lower taxa (species and subspecies) are typified by a DNA
sequence. This code is colloquially referred to as the SeqCode to distinguish it from theInternational Code of Nomenclature of Prokaryotes (ICNP), which applies to the naming of all
prokaryotes where the lower taxa (species and subspecies) are typified by either a strain or
illustration/description. The nomenclature of eukaryotic microbial groups is provided for byother Codes: fungi and algae by the International Code of Nomenclature for algae, fungi andplants; protozoa by the International Code of Zoological Nomenclature. The nomenclature ofviruses is provided for by the International Code of Virus Classification and Nomenclature.
General Consideration 6
The Committee on the Systematics of Prokaryotes Described from Sequence Data, colloquially
the SeqCode Committee, has been established to provide mechanisms to emend, interpret, andconsider exemptions to the rules of the SeqCode.
General Consideration 7
The SeqCode is divided into principles, rules and recommendations. The principles (Chapter 2)
form the basis of the Code, and the rules and recommendations are derived from them. The rules(Chapter 3) are designed to implement the principles. The recommendations (Chapter 3)
supplement some of the rules and do not have the force of rules. They are intended as guides todesirable practice. Names contrary to recommendations cannot be rejected for this reason.
Appendices may be added to assist in the application of this Code and do not form the legislative
part of this Code.

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General Consideration 8
Nomenclature deals with the application of names to the following taxonomic ranks, i.e.,“subspecies”, “species”, “genus”, “family”, “order”, “class”, and “phylum”.
General Consideration 9
The SeqCode is an instrument of scientific communication.
CHAPTER 2. PRINCIPLES
Principle 1
The SeqCode has one fundamental aim, which is to provide a standardized, robust, and stablesystem of nomenclature for prokaryotes that is compatible with the freedom of scientists to classify
prokaryotes according to taxonomic opinion. Nothing in the SeqCode may be construed to restrict
the freedom of taxonomic opinion or action.
Principle 2
The nomenclature of prokaryotes is not independent of botanical, zoological and viralnomenclature. When naming new taxa at the rank of genus or higher, names that are alreadyregulated by the International Code of Zoological Nomenclature, the International Code of
Nomenclature for algae, fungi and plants and the International Code of Virus Classification and
Nomenclature must not be used.
The names formed under the SeqCode are not independent of the names regulated by theInternational Code of Nomenclature of Prokaryotes (ICNP) and formed before January 1, 2022.
Before that date, legitimate names formed under the ICNP have priority. After that date, the rulesof priority of the SeqCode are used to determine priority of names formed under the ICNP
compared with names formed under the SeqCode.
Principle 3
The scientific names of all taxa are Latin or Latinized words treated as Latin.
Principle 4
The primary purpose of giving a name to a taxon is to supply a means of referring to it. A secondary
consideration is that names should aid memorability.
Principle 5
Names of taxa are tied to their nomenclatural types, referred to as types in the SeqCode. Typesshould serve as a reference point that allow the unambiguous identification of taxa.
Principle 6
The correct name of a taxon is based upon valid publication, legitimacy, taxonomic position, andpriority of publication.
Principle 7
A name only has standing in nomenclature if it is validly published under the rules of the SeqCode.
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Principle 8
Each taxon 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 the SeqCode. The circumscription of a taxon isan indication of its limits or the set of biological entities it contains. The position of a taxon or rank
is an indication of its relationship to a parent taxon within a taxonomy.
Principle 9
To promote stability, the name of a taxon should not be changed or replaced without sufficientreason based on either further taxonomic studies or the need to rectify a name that is contrary to
the rules of SeqCode.
Principle 10
Names created should be clear enough to avoid errors, confusion, or misunderstandings.

CHAPTER 3. RULES OF NOMENCLATURE WITH RECOMMENDATIONS
Section 1. General
Rule 1The Code on the Nomenclature of Prokaryotes Described from Sequence Data, or SeqCode, willtake effect on January 1, 2022.
Rule 2The SeqCode Legislative Commission has been established as the legislative branch of the
SeqCode Committee in accordance with its statutes. The SeqCode Legislative Commission is the
only body authorized to amend the SeqCode.
Rule 3The SeqCode Reconciliation Commission has been established as the judicial branch of the
SeqCode Committee to make decisions pertaining to the application of the SeqCode in accordancewith its statutes. Examples of cases for the Reconciliation Commission may include: (a) cases inwhich the consequences or interpretation of a rule are uncertain, (b) cases in which the applicationof a name is likely to endanger health or have serious economic consequences, or (c) cases where
the application of a rule is likely to lead to confusion. When the opinion of the SeqCode
Reconciliation Commission is sought, a summary of pertinent facts should be submitted to theReconciliation Commission. The SeqCode Reconciliation Commission is the only body authorized
to render decisions on the application of the SeqCode.
Rule 4The SeqCode Registry has been established to record and maintain names that are formed orrecognized under the SeqCode in accordance with its statutes. Registration of names constitutes
valid publication and is required for naming under the SeqCode.
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Rule 5
The rules of the SeqCode are retroactive except where specified.
Rule 6
Names contrary to a rule may not be maintained in the SeqCode Registry.
Section 2. Ranks of Taxa
Rule 7a
The taxonomic categories covered by these rules are given below in descending taxonomic rank.
PhylumClass
Order
FamilyGenus
Species
Subspecies
Rule 7b
The relative order of these categories may not be altered in any classification even thoughdefinitions of taxonomic categories may vary with individual opinion.
Rule 7c
The use of the taxonomic category of subspecies is optional.
Rule 7dIntermediate or informal ranks or categories not mentioned in Rule 7a are not covered by the
SeqCode.
Recommendation 7: An author who describes and names a new taxon should indicate the rank of
the taxon and where possible the rank and name of the parent taxon. If the parent taxon is not
currently named, the author should name it.
Section 3. Naming of Taxa
GeneralRule 8The scientific names of all taxa must be treated as Latin and spelled only with the Latin alphabet.
A species name is a binary combination of a genus name and a specific epithet; names of taxa
above the rank of species are single words. Typographical signs, numbers, and additional
characters cannot be used.
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Rule 9a
A name at any taxonomic rank can only refer to a single type.
Rule 9b
A later homonym of a name formed under the nomenclatural codes listed in Principle 2 cannot
be used.
Recommendation 9
To form new prokaryotic names, authors are advised as follows:
Names that are very long or difficult to pronounce should be avoided.
Names should differ by at least three characters from existing names of genera or species within
the same genus.
Languages other than Latin should be avoided when Latin equivalents exist or can be constructedby combining Latin word elements. Exceptions include names derived from local items such as
foods, drinks, geographic localities, and other names for which no Latin words exist.
Authors should not name organisms after themselves. If names are formed from personal names,
they should contain only the name of one person. They may contain the untruncated family and/or
first names.
All personal genus names should be feminine regardless of the gender identity of the person theycommemorate.
Names should not be deliberately contentious or abusive of any person, gender or sexual identity,
race, religion, political belief, or ideology.
Names that include mnemonic cues are preferred because they promote learning and memory.
Names of Genera
Rule 10The name of a genus is a noun or adjective used as a noun, in the singular number and written withan initial capital letter.
Recommendation 10
Authors should attend to the following Recommendation and those of Recommendation 9 whenforming genus names.
1. Names that have the same suffixes as those used for the higher taxonomic ranks should be
avoided: -aceae, -ales, -ia, and -ota (see Table 1).
Names of Species
Rule 11
The name of a species is a binary combination consisting of the name of the genus followed by asingle word known as a species epithet. The genus part of the name must begin with an initial
capital letter, and the species epithet must begin with a lowercase letter.
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Rule 12A species epithet must be related to the genus name in one of three ways.
1. As an adjective. Example: aureus in Staphylococcus aureus.
2. As a substantive (noun) in apposition in the nominative case. Example: Desulfovibrio
gigashttps://doi.org/10.1601/nm.3486 or other names cited in Trüper and De’Clari (1997).
3. As a noun in the genitive case. Example: coli in Escherichia coli.
Recommendation 12
Authors should attend to the following recommendations and those of Recommendation 9 whenforming species names.
1. When a species epithet is chosen to indicate a property or source of the species, epithets should
not express a character common to all, or nearly all, the species of a genus.
2. When the species epithet is an adjective, it should agree in gender with the genus name.
Names of Subspecies
Rule 13a
The name of a subspecies is a ternary combination consisting of three names: the genus name, thespecies epithet, the abbreviation “subsp.” (subspecies), and the subspecies epithet that begins witha lower-case letter.
Rule 13b
A subspecies epithet is formed in the same way as a species epithet.
Rule 13c
A subspecies that includes the type of the species must bear the same epithet as the species.
Names of Taxa above the Rank of Genus (Family, Order, Class, Phylum)
Rule 14
The name of a taxon above the rank of genus is a Latinized word. Names of families and orders
are in the feminine gender, the plural number, and written with an initial capital letter. Names ofclasses and phyla are in the neuter gender, the plural number, and written with an initial capitalletter.
Rule 15
The name of a family, order, class, or phylum is formed by the addition of the appropriate suffix
to the stem of the type genus name (see Section 4). These suffixes are presented in Table 1.

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Table 1. Suffixes for Taxonomic Ranks
Example for the genus Hadarchaeuma
Hadarchaeota
Hadarchaeia
Hadarchaeales
Hadarchaeaceae

Rank
Suffix
Phylum
-ota
Class
-ia
Order
-ales
Family-aceaea
From Chuvochina et al., 2019

Section 4. Nomenclatural Types and Their Designation
GeneralRule 16
Each named taxon must have a designated nomenclatural type. The nomenclatural type, referred
to in the SeqCode as “type”, for a species or subspecies is the evidence for that taxon (DNAsequence, see Rule 18a) with which the name is permanently associated. For taxa above the rankof species, the type is one of the subordinate taxa, with which the name is permanently associated.
Formation of names of the taxa above the level of genus is based on the names of the types,
allowing tracing which biological entity is included in the taxon. The nomenclatural type is notnecessarily the most typical or representative element of the taxon.
Types of the various taxonomic categories are presented in Table 2.
Table 2. Nomenclatural types of taxonomic ranks
Taxonomic category
Nomenclatural type
Subspecies
Designated DNA sequence
Species
Designated DNA sequence
Genus
Designated species
FamilyDesignated genus
Order
Designated genus
Class
Designated genus
PhylumDesignated genus
Rule 17
The type of a taxon must be designated for the name to be validly published (see Section 5).
Type of a Species or Subspecies
Rule 18a
The type of a species or subspecies is a designated DNA sequence that is compliant with theminimum standards designated by the SeqCode Committee for genome, metagenome-assembled
genome, or single-amplified genome sequences. The sequence must be available in theInternational Nucleotide Sequence Database Collaboration (INSDC). Upon recommendations of
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the SeqCode Committee or subcommittees on the taxonomy of specific groups, the SeqCode
Committee may approve other minimal standards as suitable types for specific groups.
Rule 18b
The type of a species or subspecies must allow the unambiguous identification of the taxon. Names
based on types that later prove to be ambiguous are not legitimate unless a neotype is proposed.
Rule 18c
If the type of a name is lost or demonstrated to be ambiguous, a neotype sequence may be proposedto the SeqCode Reconciliation Commission. If approved, the SeqCode Registry will be amended
to reflect the new type.
Rule 19
Unless designated under the rules of this code, a reference DNA sequence is not a type but asequence used in comparative studies. A reference sequence has no standing in nomenclature.
Recommendation 19
When a strain belonging to a taxon named under the SeqCode is isolated, a reference strain should
be designated and submitted to two culture collections in different countries. Reference strains
have no standing in nomenclature.
Types of higher taxa
Rule 20
Only taxa with legitimate names may serve as types for taxa higher than the rank of species.
Rule 21a
The nomenclatural type of a genus is the type species that was designated when the genus namewas originally validly published.
Rule 21b
The valid publication of a new genus name as a deliberate substitute for an earlier name found tobe illegitimate does not change the type species of the genus.
Rule 22
When more than one subordinate taxa are available to serve as type, the earliest legitimately named
taxon available at the time must be chosen, except where the type is neither a strain nor sequence
data (i.e., taxa described from illustrations under the ICNP).
Section 5. Priority and Valid Publication of Names
Rule 23a
Any taxon with a given circumscription, position, and rank can bear only one correct name, theearliest name that is in accordance with the rules of SeqCode.
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Note 1. In the case of a species epithet, Rule 23a must be applied independently of the genus name.
Under most circumstances, the species epithet remains the same on transfer of a species from one
genus to another. However, if the species epithet is currently in use in the name of another species
or subspecies in the genus to which the species is to be transferred, a new name must be proposed
for the transferred species.
Note 2. In the case of a subspecies, Rule 23a must be applied independently of the genus nameand species epithet. The subspecies epithet remains the same on transfer of a subspecies from one
species to another unless the subspecies epithet has been previously used as the name of anotherspecies or subspecies in the genus to which the subspecies is to be transferred.
Rule 23b
The priority of a genus, species, or subspecies name is determined by the time and date of its valid
publication, i.e., when the registration of the name is completed. For purposes of priority, only
legitimate names are taken into consideration.
Rule 23c
The priority of species and subspecies names will compete for priority with names in any othercode after January 1, 2022. If two names validly published after 1 January 2022 compete forpriority, priority is determined by the time and date of valid publication, either under the rules of
the SeqCode or other nomenclatural codes. If both names are published at the same time and date,priority will be decided by the SeqCode Reconciliation Committee.
Rule 23d
The priority date of names of taxa of rank higher than genus proposed after 1 January 2022 is thesame as the priority date of the corresponding type genus name. The priority date for names
published before 1 January 2022 is the same as their priority under the ICNP.
Rule 23eLegitimate names validly published under the ICNP remain legitimate in the SeqCode even if there
are differences in type designations.
Effective publication
Rule 24a
Effective publication under the SeqCode means that the name and evidence for the taxon havebeen published in a peer-reviewed journal or book.
Rule 24b
When a name of a new taxon is published in a work written in a language other than English, theauthor(s) should include a description in English in the publication.

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Rule 24c
The following are not accepted as forms of effective publication.
1. Communication of new names at a meeting, minutes of a meeting, or abstracts of papers
presented at meetings.
2. Placing of names in listings or catalogues of collections.
3. Reports in ephemeral publications, newsletters, white papers, self-published papers, or
non-scientific periodicals.
4. A published patent application or issued patent including the name.
5. A database containing names associated with a sequence or metadata.
6. Electronic material available in advance of publication (e.g., papers in press or preprints).
Valid and Invalid Publication and Registration of Names
Rule 25
The time and date of validation is the time and date of completion of the registration in the SeqCode
Registry.
Rule 26
A name of a new taxon, or a new combination for an existing taxon, is not validly published unlessthe following criteria are met:
1. The name is effectively published under the rules of the SeqCode.
2. The name is registered in the SeqCode Registry, along with mandatory data fields listed
below.
3. The type of the taxon is clearly designated. In the case of species or subspecies, the typesequence is deposited according to Rule 18a and the accession number cited.
4. The taxonomic rank is designated.
5. The derivation (etymology) of a new name (and if necessary of a new combination) is
given, wherein one or more distinguishable roots are identified. Roots can originate fromany language in use or extinct (see also Recommendation 9).
Note 1. When a new species or a new combination results in the proposal of a new genus, both the
new genus name and the new species name or the new combination must be validly published.
Publication of the new species epithet or new combination alone does not constitute valid
publication of the new genus name.
Note 2. When possible, authors are recommended to include the SeqCode Registry identifier inthe effective publication.
Note 3. If the information provided in the registration and the effective publication differ, theregistration is considered definitive.
Recommendation 26
It is recommended that the name, etymology, type information, and diagnosis of the novel taxon
should be clearly identifiable in a designated section of the effective publication (i.e., the section
termed the ‘protologue’ by some microbial taxonomists). Authors are encouraged to provide
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information describing the taxon, such as predicted or known physiological characteristics,
ecological data, location, and additional metadata. Authors are also encouraged to submit metadata
with the type sequence in one of the INSDC databases.
Rule 27
Placement of a species or subspecies epithet into a genus or species that is illegitimate does notpreclude the legitimacy of the species or subspecies epithet.
Section 6. Citation of Authors and Names
Proposal and Subsequent Citation of the Name of a New Taxon
Recommendation 28
The effective publication should be cited with the name of a previously proposed taxon. Correct
citation of a name enables the date of publication, the description, and the circumscription of thetaxon to be found. For names published under the SeqCode, the validly published name and dateof valid publication should be determined from the SeqCode Registry.
Proposal of a New Combination
Rule 29
When an author proposes transfer of a species to another genus, or a subspecies to another species,
then the author who makes the proposal should indicate the formation of the new combination by
the addition of the abbreviation ‘‘comb. nov.’’ (combinatio nova). This convention should be used
when the author retains the original species epithet in the new combination. However, if an author
is obliged to substitute a new species epithet as a result of homonymy, the abbreviation ‘‘nom.
nov.’’ (nomen novum) should be used. The original name is referred to as the basonym and should
be given, along with the citation of the effective publication, in the description of the novel
combination.
Citation of the Name of a Taxon whose Circumscription Has Been Emended
Recommendation 30
If an alteration of a taxon modifies its circumscription, the author responsible may be indicated by
the addition to the author citation of the abbreviation ‘‘emend.’’ (emendavit) followed by the nameof the author responsible for the change. Only alterations that cause significant changes in thecircumscription warrant description as an emendation.
Section 7. Changes in Names of Taxa as a Result of Transference, Union, or Change in Rank
Rule 31
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If the type of a taxon is excluded, a type must be designated for the remaining members of theoriginal taxon (see Rule 17), which must be given a new name.
Rule 32
A change in the name of a taxon is not warranted by an alteration of the diagnostic characters or
the circumscription.
Rule 33
If a genus is divided into two or more genera, the genus name must be retained for the genus thatretains the type species.
Division of Species and Subspecies
Rule 34a
When a species is divided into two or more species, the species epithet of the original species must
be retained for the taxon that includes the type.
Rule 34b
When a species is divided into two or more subspecies, the species epithet of the original species
must be retained for the subspecies that includes the type.
Note. Although the species and subspecies epithets in the name of a type subspecies are the same,
they do not contravene Rule 9 because they are based on the same type.
Rule 34c
When a subspecies is divided into two or more subspecies, the subspecies epithet of the original
subspecies must be retained for the subspecies that includes the type.
Transfer of a Species to Another Genus
Rule 35a
When a species is transferred to another genus without any change of rank, the species epithet
must be retained unless it is already in use in the new genus. In that case, a new species epithet
must be chosen for the transferred species. This rule avoids creation of a later homonym.
Rule 35b
Regardless of its priority, the transfer of species that is not the type of another genus does not affectthe type species or priority of the receiving genus even if it involves union of the incoming species
with the type species of the receiving genus.
Rule 35c
When the name of a genus is changed, the epithets of the species within it must be retained unlessalready in use (see Rule 29).
14

585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630

Note 1: Modification of the gender of the species epithet to accommodate the gender of the new
genus name is a minor orthographic variant and encouraged.
Union of Taxa of Equal Rank
Rule 36
When two or more taxa of the same rank are united, then the name and type of the taxon isdetermined by following the rules of priority (see Section 5). In cases of species and subspecies,
if the names or epithets are of the same time and date, the author who first unites the taxa has theright to choose one of them, and their choice must be followed.
Rule 37
When several species are united under one species as subspecies, the subspecies that includes thetype of the species under whose name they are united must be designated by the same epithet as
the species name (see Rule 13c).
Rule 38
If two or more species of different genera are united to form a single genus, and if those species
include the type species of one or more genera, the genus name must be the earliest validly
published, legitimate name. If no type species is placed in the genus, a new genus name must be
proposed, and a type species must be specified.
Rule 39
When two or more taxa of the same rank from family to class are brought together under a taxonof higher rank, the higher-ranking taxon should derive its name from the name of the earliest
legitimate type genus among the lower-ranking taxa.
Rule 40
If no type genera were placed in the taxon, a new name based on the selected type must be
proposed. (see Rule 22)
Change in Rank
Rule 41a
When the rank of a taxon of genus or above is changed, the stem of the name must be retained andonly the suffix altered (see Rule 15).
Rule 41b
When a subspecies is elevated in rank to a species, the subspecies epithet must be used as the
species epithet unless the resulting combination is illegitimate.
Rule 41c
When a species is lowered in rank to a subspecies, the species epithet must be used as thesubspecies epithet unless the resulting combination is illegitimate.
15

631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675

Section 8. Illegitimate Names and Epithets: Replacement, Rejection, and Conservation ofNames and Epithets
Illegitimate Names
Rule 42
A name contrary to a rule is illegitimate and must not be used. However, a name of a taxon that isillegitimate when the taxon is in one taxonomic position is not necessarily illegitimate when thetaxon is in another taxonomic position.
Note: Some common reasons for which a name may be illegitimate are the following.
1. If the taxon to which the name was applied, as circumscribed by the author, included thenomenclatural type of a name which the author ought to have adopted under one or moreof the rules.
2. If the author did not adopt for a binary or ternary combination the earliest legitimate genus
name, species epithet, or subspecies epithet available for the taxon with its particular
circumscription, position, and rank.
3. A species or subspecies epithet is illegitimate if it duplicates a species or subspecies epithet
previously validly published for the same genus but whose name is based upon another
type.
Replacement of Names
Rule 43
An illegitimate name or epithet should be replaced by the earliest legitimate name or epithet in abinary or ternary combination which in the new position will be in accordance with the rules. If nolegitimate name or epithet exists, one must be chosen. Since a species epithet is not renderedillegitimate by publication in a species name in which the generic name is illegitimate, authors
may use such an epithet if they wish provided that there is no obstacle to its employment in the
new position or sense; the resultant combination is treated as a new name (nom. nov.) and isascribed to the author. The epithet is, however, ascribed to the original author.
Rule 44
A legitimate name or epithet may not be replaced.
Rule 45
Names contrary to the General Considerations or Principles of the code may be rejected by the
SeqCode Reconciliation Commission.
Section 9. Orthography
Rule 46
16

676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721

All names comprise only the 26 letters of the ISO basic Latin alphabet. Diacritic signs are not to
be used.
Rule 47
Any name or epithet should be written in conformity with the spelling of the word from which itis derived and in accordance with the rules of Latin grammar. Exceptions are provided for
typographic and orthographic errors and orthographic variants.
Notes:
1. Consult Appendix 9 of the ICNP for recommendations on forming properly Latinized names.
2. In the SeqCode an orthographic variant is a name (or epithet) applied to the same type thatdiffers from another name only in transliteration into Latin of the same word from a language otherthan Latin or in its grammatical correctness. Changes in suffixes for consistency with the namesof higher taxa are orthographic variants. Names transliterated from the same word and based on
different types are not orthographic variants.
Typographic and Orthographic Errors
Rule 48
The original spelling of a name or epithet must be retained, except for typographical or
orthographic errors.
An unintentional typographical or orthographic error later corrected by the author is to be accepted
in its corrected form without affecting the status and date of valid publication. It can also becorrected by a subsequent author who may or may not mention that the spelling is corrected.
However, the abbreviation ‘‘corrig.’’ (corrigendum) may be appended to the name if an author
wishes to draw attention to the correction. Succeeding authors may be unaware that the originalusage was incorrect and use the spelling of the original author(s). Other succeeding authors may
follow the correction of a previous author or may independently correct the spelling themselves,
but in no case is the use of corrig. regarded as obligatory. None of these corrections affects thestatus and date of validation.
Note. The liberty of correcting a name or epithet must be used with reserve, especially if the change
affects the first syllable and above all the first letter of the name or epithet.
Personal Names
Rule 49
The genitive and adjectival forms of a personal name are treated as different epithets and not as
orthographic variants unless they are so similar as to cause confusion.

17

722
723
724
725
7261.
727
728
7292.
730
7313.
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767

Gender of Names
Rule 50
The gender of genus names is governed by the following.
A Latin or Latinized genus name retains the gender of its language of origin. Authors must givethe gender of any proposed genus name. In cases where the classical gender varies, the author has
the right of choice between the alternatives.
Genus names that are compounds from two or more Latin words take the gender of the lastcomponent of the compound word.
Arbitrarily formed genus names or vernacular names used as genus names take the gender assigned
to them by their authors.

CHAPTER FOUR. RECOMMENDATIONS FOR AUTHORS AND PUBLISHERS
When it is desirable to distinguish the nature of the type of a name, the following convention isrecommended. When the type for a species or subspecies is determined by the ICNP, thesuperscript “T” will be used immediately following the name or strain identifier. If the type isdetermined by the SeqCode, the superscript “Ts” or “TS” will be used. When the type is a taxon
at the rank of genus or higher, the superscript is determined by the nature of the type of the species.
If superscripts are not possible, they may be replaced by the symbols in parentheses, i.e., (T), (Ts)or (TS).
For the purpose of identification in the text, names of taxa at all ranks should be italicized.

REFERENCES
Chuvochina M, Rinke C, Parks DH, Rappé MS, Tyson GW, Yilmaz P, Whitman, WB, Hugenholtz
P (2019) The importance of designating type material for uncultured taxa. Syst Appl Microbiol 42(2019) 15–21
Trüper HG, de’Clari L (1997) Taxonomic note: necessary correction of specific epithets formed
as substantives (nouns) "in Apposition". Int J Syst Bacteriol 47:908–909.

18

768
769
770
771
772
773
774
775

APPENDIX 1
Data quality and reporting requirements and recommendations for an isolate genome, metagenome
assembled genome (MAG), or single amplified genome (SAG) to serve as the nomenclatural typefor a species named under the SeqCode. Requirements will be checked as part of the validation
process on the SeqCode Registry. Recommendations are suggested best practices to guide authors
and peer reviewers to ensure high quality data supporting species to be named.
To be included in publication proposing new species names under SeqCode
RequiredName
Recommended
Etymology
Name formed with mnemonic cues
Interpretation of biological properties inferred or demonstrated physiologicaltraits and ecological information, such as habitat, in the manuscript bodyand/or protologue.
Designated genome assembly (e.g., INSDC accession) and access to raw data
(e.g., SRA accession).
Include as much metadata as possible (see Field et al., 2008).
Provide evidence of the species, taxonomic rank, and position including theuniqueness of the species with respect to existing named species andjustify the taxonomic rank and position (e.g., Jain et al., 2018,
Karthikeyan et al., 2019; Parks et al., 2020; Rodriguez-R et al., 2018).
For MAGs and SAGs, compare multiple high-quality genomes representing thespecies in more than one sample (e.g., Supplemental Information).a
Rationale: Initial requirements encourage wide participation from many
microbiological disciplines and enable validation of names published prior
to the SeqCode. Critical data will be captured in the SeqCode Registry in
any case. Some recommendations could become requirements in the
future.
Data quality necessary for completion of SeqCode Registryb
Required
Type genome assembly quality for MAGs and SAGs: >90% complete and <5%contaminated; (modified from Bowers et al., 2017).
For isolates, read coverage ≥10x (Field et al., 2008).
Recommended
16S rRNA genes >75% complete and passes chimera checks
Agreement between genome and 16S rRNA taxonomic assignments>80% of tRNAs present (modified from Bowers et al., 2017).
High genome integrity (contig # <100; N50 >25 kb; max. contig >100 kb).
MAG/SAG read coverage ≥10x.
Data availability required for SeqCode Registry
Assembly available in INSDC databases
19

776
777
778
779
780
781
782
783
784
785

Raw data available in INSDC databases (e.g., Sequence Read Archive)c
Rationale: Registry queries the INSDC databases to perform automatic checks ofdata quality
a. Comparison of multiple high-quality genomic assemblies from multiple samples can support
the non-chimeric nature of MAGs and provide confidence of the assembly for both MAGs andSAGs.
b. Data quality will be assessed by automated pipelines or other approaches. Exceptions forlower data quality should be justified by authors in the effective publication.
c. Not required for names effectively published before January 1, 2023, to allow for existing
published names (e.g., existing Candidatus names) and names currently undergoing peer review
to be validated under the SeqCode.

20

786

Glossary

787
788

Basonym: The original or earliest validly published name of a taxon on which a new combination
is based when this taxon has been changed, typically as a result of reclassification.

789
790
791

comb. nov. (combinatio nova): Abbreviation to denote transfer of a species to a new genus.
Because the species name includes both the genus name and species epithet, the new name is acombination of the new genus name and the original species epithet. See Rule 29.

792
793
794
795
796

Correct: Validly published names or epithets that must be adopted for a taxon under the rules in
the proposed taxonomy (i.e., circumscription, position and rank). Note that validly publishednames may be legitimate but not correct, depending on the taxonomy. For instance, a given
taxonomy may merge two species. While both names are validly published and legitimate, only
the name of the earlier synonym is correct in this taxonomy.

797

Diagnosis: A statement of the characters that allows one to distinguish the taxon from other taxa.

798
799

Earlier synonym: The first validly published synonym [in some taxonomic literature, this isreferred to as senior synonym].

800
801

Epithet: An adjective or descriptive phrase expressing a quality characteristic of the person orthing mentioned. The species name is an epithet of the genus name.

802
803
804

Effectively published: Names and epithets that have appeared in print and/or electronic matterthat is peer reviewed and made generally available to the scientific community. Under the
SeqCode, preprints are not eligible as an effective publication. See Rule 24 for more explanation.

805
806

Effective publication: The peer-reviewed publication in which a name first appears. Under the
SeqCode, preprints are not eligible as an effective publication. See Rule 24 for more explanation.

807
808

Homotypic synonyms: Two or more names associated with the same type [in some taxonomic
literature, these are referred to as objective synonyms].

809
810
811

Heterotypic synonyms: Two or more names associated with different types that in the opinion of
the microbiologist concerned belong to the same taxon [in some taxonomic literature, these arereferred to as subjective synonyms].

812
813
814
815

Homonymy: A situation in which two names are the same but have different types, often due touniting two genera each of which contains species with the same species epithet or when a nameis chosen that is already in use by another taxon, including taxa named under other international
codes of nomenclature.

816

Illegitimate: Names or epithets that are contrary to the rules of the SeqCode.

817
818

Later synonym: A subsequently validly published synonym [in some taxonomic literature, this isreferred to as junior synonym].
21

819

Legitimate (names and epithets): In accordance with the rules of the SeqCode.

820
821

Name: The label applied to an object. A word or set of words by which a taxon is known,addressed, or referred to. A term used for identification.

822
823

nom. nov. (nomen novum): A name that is created to replace another scientific name in cases
where an earlier name cannot be used for technical, nomenclatural reasons. See Rules 29 and 43.

824

Nomenclature: The body or system of names in a particular field.

825
826
827
828
829

Nomenclatural type (or just type): For a species, it is the evidence for the taxon, such as genome
sequence, with which the name is permanently associated. In the ICNP, the type is a viable strain
deposited in and available from two culture collections in different countries. For higher taxa, thetype is a lower taxon. The nomenclatural type is not necessarily the most typical or representative
element of the taxon.

830

Orthography: Formation of words or names.

831
832
833

Orthographic variant: Names or epithets that are variant spellings of the same name. Under the
SeqCode, orthographic errors may be corrected without affecting the priority of the name. See
Rules 46 and 47.

834

Position: The higher taxon in which a taxon is placed when there may be alternatives.

835
836
837
838
839

Principle of Priority: A principle that states that the correct name of a taxon is the oldest
legitimate, validly published name applied to it. It is the fundamental guiding precept that
preserves the stability of biological nomenclature. It was first formulated in 1842 by a committee
appointed by the British Association to consider the rules of zoological nomenclature. The
committee's report was written by Hugh Edwin Strickland.

840
841

Rank: A level within a taxonomic hierarchy. In the SeqCode, ranks are restricted to phylum, class,order, family, genus, species, and subspecies. See Rule 7.

842
843

Species name: A binomial combination of the genus name and species epithet. See Rules 11 and
12.

844

Taxon: Any group of organisms treated as a named group in a formal taxonomy.

845
846
847

Validation (of a name or epithet): The process by which a name becomes “official” under aparticular code of nomenclature. Under the SeqCode, validation is completed when the registration
process is complete on the SeqCode Registry. See Rule 26.

848
849

Validly published: Names and epithets that are effectively published and registered according to
the rules of the code. See Rule 26.

850

22

851

Examples of application of the SeqCode852

Example of path 1: Wolframiiraptoraceae and child taxa

853
854
855
856
857
858
859
860
861
862
863
864
865
866
867

Overview. As an example case for Path 1, several authors of the SeqCode (Palmer, Reysenbach,Hedlund) recently completed a combined cultivation/metagenomics study of a novel group ofarchaea in the GTDB family designated as NZ13-MGT within the GTDB order “Caldarchaeales”,
class Nitrososphaeria, and phylum Thermoproteota. The study initially focused on anaerobic
enrichment cultures from sediments of Great Boiling Spring, Nevada, USA, with a single memberof the taxon that requires tungsten for growth on corn stover or a sugar mix. The taxon was shown
to prefer xylose by combining fluorescence in situ hybridization (FISH) with nanometer-scalesecondary ion mass spectrometry (nanoSIMS). It is currently represented by a single high-quality
MAG, although that MAG formed a >99.5% average nucleotide identity (ANI) cluster with MAGsof lower quality from separate samples of the same enrichment culture and sediments from which
the enrichment culture was derived (Buessecker et al., 2022). Analysis of the MAG revealed aputative TupA tungstate transporter and six annotated tungsten-dependent ferredoxin
oxidoreductases. To expand the study, 77 additional high-quality MAGs assigned to the GTDB
family NZ13-MGT by GTDB-tk (Chaumeil et al., 2020) were assembled from metagenomes fromterrestrial and marine hydrothermal systems globally.

868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891

Importance of multiple genomes per species. It is recommended (main text Table 2) that species
or subspecies named under the SeqCode include more than one genome. This parallels the generalrecommendation under the ICNP to characterize multiple strains for proposals of new taxonomic
names and is especially important for MAGs and SAGs because of challenges associated withaccurately binning metagenomic data and the low completeness of most SAGs. Here, FastANI wasused to dereplicate the 78 high-quality MAGs into 11 >95% ANI clusters (i.e., species clusters),
and phylogenetic analyses of concatenated marker gene sets confirmed that each ANI cluster wasmonophyletic. In total, nine of the species clusters were represented by multiple high-quality
MAGs derived from metagenomes from different sampling dates and/or geothermal springs,
ranging from two to 16 MAGs. Comparison of the multiple MAGs per species cluster allowed us
to assess: (1) monophyly of the species by using a multiple marker gene set; (2) the true presenceof multiple copies of normally single-copy, conserved marker genes and true absence of conserved
marker genes used to assess genome completeness and contamination; (3) the existence ofhomologs of genes encoding important functions (in this case, tungstate transporters,
tungstoenzymes, and genes related to energy conservation) to support the association of thosegenes/pathways with the species; (4) shared gene content in general; and (5) similar genome sizes
for the genomes within a species. These comparisons strengthened our conclusions about the
proposed mode of energy conservation and evolution of the organisms and allowed us to identify
and reject problematic MAGs. Briefly, various bioinformatic pipelines were used for generationof MAGs, but metagenomic assembly was typically performed with metaSPAdes (Nurk et al.,2017), followed by binning of contigs > 2.5 kbp in length with the MetaBAT (Kang et al., 2015)
or MetaBAT2 (Kang et al., 2019), and/or MaxBin2 (Wu et al., 2016), and/or CONCOCT v.1.1.0(Alneberg et al., 2014) algorithms. In some cases, the “bin_refinement” module of MetaWRAP
was also used to identify the highest quality MAGs among the three binning strategies, and quality
23

892
893
894
895
896
897
898
899

of all genomes was assessed based on CheckM v.1.1.39 estimates of completeness andcontamination. Only those MAGs exhibiting > 90 % estimated completeness and < 5 % estimatedcontamination are reported here. Here, we rejected all MAGs generated by MaxBin2 (Wu et al.,2016) because all were massively contaminated, as evidenced by reproducibly larger and morevariable genome sizes than MAGs generated with other pipelines, but without any additional
conserved marker genes. These MAGs were therefore not flagged as contaminated by automatedcontamination detection software such as CheckM (Parks et al., 2018), so comparison of the MAGs
within each species was critical.

900
901
902
903
904
905
906
907
908

In this study, we named two species based on single high-quality MAGs. In one case,Terraquivivens tikiterensis, we justified this decision based on the very high quality of the MAG(99.0 % completeness with 0.49 % estimated contamination; 75x coverage including sequences
for 5S, 16S and 23S rRNAs and tRNAs coding for 19 amino acids) and the availability of 24
MAGs from other species of the genus for comparison. In the other case, Benthortus lauensis, wejustified this decision again on the high quality of the MAG (94.0 % completeness with 2.91 %estimated contamination; 34x coverage including sequences or 5S, 16S and 23S rRNAs and tRNAs
coding for 20 amino acids) and on the difficulty of obtaining additional samples from the only
known habitat of this genus, the Lau Hydrothermal Field.

909
910
911
912
913
914
915
916

Data quality under the SeqCode. Only MAGs exhibiting estimated completeness > 90 % andestimated contamination < 5 % were considered possible candidates for naming under the
SeqCode. We furthermore accounted for rRNAs and tRNAs and selected the best MAG
representing each species cluster as type genome, ensuring that we adhered to data quality
standards (Table 3 of the main text). We note that several GTDB species representatives did notcontain any high-quality MAGs; those MAGs were analyzed phylogenetically in our study, butthey could not be named under the SeqCode. Nevertheless, they can be identified using GTDB
placeholder names.

917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932

Nomenclature under the SeqCode. We decided to propose names for all 11 species clusters under
the SeqCode as well as the parent taxa as prescribed under the SeqCode. Names were formed under
the rules of Latin following general recommendations of Appendix 9 in the ICNP and werechecked by the nomenclature expert Aharon Oren. To follow Rules 18a and 26 in the SeqCode,the publication includes the following for each taxonomic name that is proposed: (i) clear
designation of their nomenclatural type; (ii) designation of the taxonomic rank; and (iii) the
etymology of the new name (Buessecker et al., 2022). We also followed Recommendation 26 in
the SeqCode by clearly separating the nomenclature proposals in the manuscript within aprotologue. An annotated example protologue (with annotations [in brackets in italics]) for eachtaxonomic rank is shown below, preceded by a brief discussion of the elements of the protologue.
To be clear, standardized protologues are not required under the SeqCode as long as the rules of
the SeqCode are applied, particularly Rule 18a and Rule 26 for new taxon names that don’t require
unions or divisions of existing taxa. Authors of publications proposing many new taxa may choose
to summarize the required elements as a table, for example. A summary of the key elements
required by the SeqCode are listed in Supplementary Table S1 for these same three taxonomic
names as an example.
24

933
934
935
936

Example protologue for a new family. The protologue below describes the new family
Wolframiiraptoraceae. Note that for a family or higher taxon, the nomenclatural type is a genus.
Here, that genus is Wolframiiraptor from which the name of the family must be derived under
Rule 15 of the SeqCode.

937

Description of the family Wolframiiraptoraceae

938
939
940
941
942

Wolframiiraptoraceae (Wolf.ra.mi.i.rap.to.ra'ce.ae. N.L. masc. n. Wolframiiraptor, type genus of
the family; L. fem. pl. suff. -aceae, ending to denote a family; N.L. fem. pl. n.
Wolframiiraptoraceae, family of the genus Wolframiiraptor). [This text designates the taxonomic
rank (family) and the etymology under Rule 26.4 and 26.5. Both will also be captured in defined
fields in the SeqCode Registry.]

943
944
945
946
947
948
949
950
951
952
953
954
955
956
957

Members of this family are associated with thermal aquatic environments and have been identified
from geothermal springs in China, New Zealand and the USA and a marine hydrothermal vent in
the Western Pacific. Phylogenomic inference robustly recovers the genomes of these organisms asa well-supported monophyletic lineage within the order Caldarchaeales, and delineation of thesetaxa as a family is supported by Relative Evolutionary Divergence (RED) and Average Amino
Acid Identity (AAI). AAI values among designated type genomes for species in this family range
between 65 and 85 % within proposed genera, and between 49 and 57 % among members ofdifferent genera. The distribution of genes required for oxidative phosphorylation indicate thatmembers of the family may either be strict or facultative anaerobes. Sulfide-dependent respiration
may also occur in some members of the family, but this trait is not conserved for all genera. Several
putative tungsten-dependent ferredoxin oxidoreductases, specifically aldehyde ferredoxin
oxidoreductases (AORs), formaldehyde ferredoxin oxidoreductases (FORs), and glyceraldehyde3-phosphate ferredoxin oxidoreductases (GAPORs) are encoded by genomes belonging to thisfamily. [This text includes a description of the taxon, following Recommendation 26. Such text is
recommended but not required under the SeqCode.]

958
959
960
961
962
963
964
965
966

The nomenclatural type for the family is the genus Wolframiiraptor. [This text designates thenomenclatural type under Rule 26.3. Note that the nomenclatural type for ranks of class, order,and family is the first legitimately named genus in the taxon. These dates are clearly shown in the
SeqCode Registry. Rule 26.3 embodies Principle 5 and serves to unambiguously identify the taxon.
See Rule 16, especially Table 2, Rule 18, and Rule 22. Under the SeqCode, the name of newly
proposed higher taxon must be derived from the root of the type genus Wolframiiraptor(Wolframi(-um)) plus a connecting vowel (i), raptor (genitive case –oris, dropping the ending of
genitive case gives us the root raptor-) followed by the appropriate suffix to denote the rank (aceae). See Rule 15 and Table 1.]

967
968

Example protologue for a new genus. The protologue below describes the new genus
Wolframiiraptor. Note that for a genus, the nomenclatural type is a species.

969
25

970

Description of the genus Wolframiiraptor

971
972
973

Wolframiiraptor (Wolf.ra.mi.i.rap’tor N.L. neut. n. wolframium, tungsten; L. masc. n. raptor,
snatcher or thief; N.L. masc. n. Wolframiiraptor, snatcher of tungsten). [This text designates thetaxonomic rank (genus) and the etymology under Rule 26.4 and 26.5.]

974
975
976
977
978
979
980
981
982
983
984
985

Members of this genus have been identified from geothermal springs from the Great Basin,
Yellowstone National Park, USA, and the Rehai Geothermal Field and the town of Dientan,
Tengchong, China. AAI values among genomes representing separate species within the genus
range between 81 and 90 %. Based on ancestral state reconstruction analysis, likely losses of thegenes encoding cytochrome c oxidase subunits, the aerobic carbon-monoxide dehydrogenase large
subunit, and sulfide:quinone oxidoreductase (Sqr), indicate that members of this genus are likely
strict anaerobes and are incapable of sulfide oxidation. Genomes of this genus encode a tupA
subunit of the tungstate (Tup) ABC transporter and contain multiple genes encoding tungstendependent oxidoreductases, including three putative AOR-like, one FOR-like and one GAPORlike proteins. This taxon is supported as a genus-level group by phylogenomics, AAI and RED.
[This text includes a description of the taxon, following Recommendation 26. Such text is
recommended but not required under the SeqCode.]

986
987
988
989
990
991
992
993

The nomenclatural type of the genus is Wolframiraptor gerlachensisTs. [This text designates thenomenclatural type under Rule 26.3. Note that the nomenclatural type for rank of genus is a
species, typically the first legitimate species in the genus. These dates are clearly shown in the
SeqCode Registry. Rule 26.3 embodies Principle 5 and serves to unambiguously identify the taxon.
See Rule 16, especially Table 2, and Rule 22. Note that genus names do not need to have a standard
suffix like family, order and above, but they should avoid suffixes used for other taxonomic ranks
to prevent confusion. See Rule 15 and Table 1. Under Chapter 4, the superscript Ts can be added
when this species is a nomenclatural type under the SeqCode.]

994
995
996
997

Example protologue for a new species. The protologue below describes the new species
Wolframiiraptor gerlachensis. Note that for a species, the nomenclatural type is a DNA sequence,
typically a genome assembly (Table 2).

998

Description of Wolframiiraptor gerlachensisTs

999
1000
1001
1002
1003

Wolframiiraptor gerlachensis (ger.lach.en'sis N.L. masc. adj. gerlachensis, of Gerlach, the region
where Great Boiling Spring is located in Nevada, and where the samples containing this organism
were obtained). [This text designates the taxonomic rank (species) and the etymology under Rule26.4 and 26.5. Under Chapter 4, the superscript Ts can be added to denote that this species is thetype for the genus.]

1004
1005
1006

A MAG representing this species was recovered from metagenomic sequencing of a stableenrichment culture, established from an in-situ corn stover enrichment from Great Boiling Spring,
Nevada, USA. Enrichment and maintenance of this species within the mixed-culture community
26

1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020

was optimal at an incubation temperature of 80 °C with lignocellulose and sugars, at circumneutral
pH. This species is dependent on tungsten for growth, with significant decline in its abundance
within the community without tungsten added to the growth medium. Additionally, several
tungstoenzymes conserved within the genus were expressed at a higher rate during growth on cornstover, suggesting direct involvement of tungstoenzymes in complex carbohydrate metabolism.
Cells of this organism showed significant isotope enrichment when grown on isotopically labeled
xylose-amended medium, with limited isotope enrichment during growth on medium amended
with amino acids, glucose, ribose, and starch, indicating preferential assimilation of xylose. The
genome sequence for the type of this species is 1,277,965 bp, consists of 27 contigs, and has a
G+C content of 52 %. Completeness is estimated at 98.06 % with 0.49 % contamination, as
estimated with CheckM. ANI comparisons among this genome and those of closely related species
were below 86 %, supporting the delineation of this taxon as unique and distinct to other species
in the genus. [This text includes a description of the taxon, following Recommendation 26. Suchtext is recommended but not required under the SeqCode.]

1021
1022
1023
1024
1025
1026
1027
1028
1029

The genome Wger_A8Ts, available under the GenBank assembly accession number(GCA_021323375.2Ts), is the designated nomenclatural type for the species, and was recoveredfrom an enrichment culture, established from an in-situ enrichment from Great Boiling Spring,
Nevada, USA. [This text designates the nomenclatural type under Rule 26.3. Note that thenomenclatural type for rank of species or subspecies is a DNA sequence, typically a genomic
assembly (Table 1). Rule 26.3 embodies Principle 5 and serves to unambiguously identify thetaxon. Metadata for this sequence is included in the GenBank entry. Under Chapter 4, thesuperscript Ts can be added to denote that this genomic assembly is the nomenclatural type of thespecies.]

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27

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Supplementary Table S1. Example spreadsheet format for nomenclature proposals. Example
proposals for family, genus, and species ranks. Such tables are simple alternatives to protologues
and may be especially valuable when many names are proposed.
Proposed taxon
Etymology
FamilyWolf.ra.mi.i.rap.to.ra'ce.ae N.L. masc.
Wolframiiraptoraceae n. Wolframiiraptor, type genus of thefamily; L. fem. pl. suff. -aceae, ending
to denote a family; N.L. fem. pl. n.
Wolframiiraptoraceae, family of thegenus Wolframiiraptor
Genus
Wolf.ra.mi.i.rap’tor N.L. neut. n.
Wolframiiraptor
wolframium, tungsten; L. masc. n.
raptor, snatcher or thief; N.L. masc. n.
Wolframiiraptor, snatcher of tungsten
Speciesger.lach.en'sis
N.L.
masc.
adj.
Wolframiiraptor
gerlachensis, of Gerlach, the regionTsgerlachensis
where Great Boiling Spring is located in
Nevada, and this organism was obtained
from

Nomenclatural type
Genus Wolframiiraptor

SpeciesWolframiiraptor
gerlachensisTs

Genomic
assembly:
GCA_021323375.2Ts

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1036
1037
1038

SeqCode Pre-registration: registration of path 1 names in the expert mode of the SeqCode
Registry

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1048
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1050
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1054

Names may currently be entered into the SeqCode Registry (https://seqco.de/) using the expert
mode. Guided submission modes are also under development to assist users with the registration
process. Within expert mode, a profile is created in the SeqCode Registry (https://seqco.de/) andthen contributor privileges are requested. Once approved, a “Contributor” dashboard will become
available. The “Create a name” option for name registration is selected. Then the proposed nameis provided in the textbox and “Register” is selected (e.g., Wolframiiraptor gerlachensis as an
example). This will only reserve the name and does not entail validation. During this registration
step, automated quality checks will be performed, and red and orange flags will be generated withdescriptions of what is required or recommended, respectively, and how each relates to Rules andRecommendations of the SeqCode. Red flags need to be addressed before progressing further. For“Missing rank” red flags, “Define rank” is selected, and then the appropriate rank is selected (e.g.,
species), and “Submit” is selected. For addressing the “Missing type” red flags, select “Edit type”,
and under material, select the appropriate description of the type genome sequence and provide its
accession number (e.g., GenBank assembly; GCA_021323375.2). Here additional orange flags
relating to the genome serving as nomenclatural type can also be addressed. For the “Missing
genome kind” the type of genome can be selected (e.g., Metagenome-assembled genome (MAG))
28

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1080
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and the sequencing depth can be indicated (e.g., 12 in the case of GCA_021323375.2). If available,
provide the source information under the “Missing genome source” orange flag (e.g., INSDC
Sequence Read Archive (SRA) with the run accessions SRX13128468 and SRX13128467,
comma-separated for multiple run accessions). Additionally, to assist in genome quality
assessments of genomes by curators, indicate the quality metrics in this section (e.g., G+C content(%), estimated completeness and contamination, the completeness fraction of the 16S and 23S
rRNA genes, and how many rRNA fragments and predicted tRNA elements are present in the
genome). To add the etymology, select “Edit etymology” under the “Missing etymology” red flag.
Provide the syllabication and grammar information of components of the name (e.g.,ger.lach.en'sis N.L. masc. adj. gerlachensis, of Gerlach, the town where Great Boiling Spring islocated in Nevada, and where the samples containing this organism were obtained). To address
additional orange flags, the same process can be followed, although these flags are not obligatory
for registration. Orange flags can include, but are not limited to, “Missing description”, “Missing
parent”, and “Missing effective publication” flags. If a description for the taxon is available, add
this to the “Missing description” flag (e.g., the description from the protologue included for
publication). If possible, link a parent taxon to the name, even if the parent taxon is also a newly
proposed name to be registered (e.g., Wolframiiraptor). As the pre-registration of the names is
occurring before effective publication, the “Missing effective publication” flag remains. If
additional names or parent taxon names are proposed, complete this process for all proposed taxa.
This can be accessed and/or evaluated under the “My names” list in the “Contributor” dashboard.
Once all required information for review is provided for each entry, the “Propose name” option
under “Contributor Actions” can be selected for each entry. This allows the addition of the nameto a new register list or, as part of larger projects with a single intended effective publication, allproposed taxa can be added to the same register list for curator review. Select “Register name” togenerate a draft register list. This draft register list is assigned an accession URL that should be
included in the effective publication (e.g., seqco.de/r:slp2ijs4). Submit the draft register list for
curator review. Once a curator provisionally accepts the names, this completes pre-registration. At
this point, the proposed names are hidden from the public but can be accessed via the URL,
allowing reviewers and editors to review the proposed names.

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Finally, authors are required to complete the registration/validation process by entering the DOI
and submitting the published article, at which point the names become valid and visible to the
public. Minor edits/corrections can be made at any time following validation by registeredcontributors as long as they are validated by curators. While curators will currently ensure the data
quality while guiding users through the naming process; contingent upon community support andfunding, automated checks will be implemented for evaluation of genome sequence quality andnames.

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29

1093

Example of path 2: Macondimonas diazotrophicaTs

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Path 2 (main text Figure 1) should be used to register and validate names under the SeqCode after
the effective publication is already published. This could be done by the authors or by otherscientists, although we recommend working with authors to register their names wheneverfeasible. The names of the taxa must appear in the effective publication including online
supplementary material, although minor orthographic variants are allowable.

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1101
1102
1103
1104
1105
1106
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1108
1109
1110
1111
1112
1113

Overview. Several authors of the SeqCode (Konstantinidis, Rodriguez-R, Rosselló-Móra) wereco-authors on a publication on the metagenome-guided isolation of a crude-oil degrading
bacterium, abundant in oil-contaminated sediments of coastal marine ecosystems but largely
absent from pristine environments, recovered specifically from the oiled sands of Pensacola Beachafter the oil spill in April of 2010 in the Gulf of Mexico. The initial metagenomic datasets fromthe oiled sands (Rodriguez-R et al 2015) were used to identify a high-quality MAG throughtargeted genome reconstruction on the basis of dominant nifH gene alleles. The reconstructed
MAG was used to reconstruct the metabolic potential of this species, identify auxotrophies, andultimately isolate this organism (Karthikeyan et al 2019). The resulting isolate genome has a 99.8%
ANI with the MAG, but the fastidious nature of the microorganism prevents its deposition in
culture collections. In the publication (Karthikeyan et al 2019), the microorganism is identified asa novel genus in the order Chromatiales, designated Macondimonas. The only species andnomenclatural type of the genus is Macondimonas diazotrophica. The publication designates strain
KTK01 as type material of the species, which we emend here to specify instead the genome
sequence.

1114
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Best practices for cooperativity for Path 2. We consider it best practice to communicate withkey authors before registering and validating effectively published names under the SeqCode. In
this case, three of the authors of the original publication including the corresponding author*(Konstantinidis*, Rodriguez-R, Rosselló-Móra) registered the names in the SeqCode Registry.

1118
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Deposition of type DNA sequences for species and subspecies into an INSDC database. The
genome designated as the nomenclatural type for the proposed species is publicly available froman INSDC database under the GenBank Assembly accession number GCA_004684205.1, in
accordance with Rule 18a. This rule states that type DNA sequences must be available from
INSDC databases, a decision made to promote stable access to the data.

1123

Protologues and descriptions (Karthikeyan et al., 2019)1124

Description of Macondimonas gen. nov

1125
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Macondimonas (Ma.con.di.mo’nas. L. fem. n. monas, a unit, a monad; N.L. fem. n.
Macondimonas, a monad from Macondo Prospect, the site of DWH oil spill. Additionally,
Macondo is a fictional town in A Hundred Years of Solitude by G. G. Márquez. In the book, thetown of Macondo has a rapid population growth, a period of economic prosperity, and then a rapid
30

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population fall, which is reminiscent of the ecologic pattern observed for this group upon crudeoil exposure)

1131
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Members of this genus exhibit a coccobacilli morphology and a heterotrophic aerobic metabolism.
No phototrophic, nor chemoautotrophic growth, or their corresponding genes in the genome wereobserved. The type species is Macondimonas diazotrophica.

1134

Description of Macondimonas diazotrophica sp. nov.

1135
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1137
1138

Macondimonas diazotrophica (di.a.zo.tro’phi.ca. Gr. pref. di, in two; N.L. neut. n. azotum,
nitrogen; N.L. pref. diazo-, pertaining to dinitrogen; Gr. adj. trophikos -ê -on, feeding, tending;
N.L. fem. adj. diazotrophica, one that feeds on dinitrogen, named after its ability to fix atmosphericnitrogen)

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Cells grown on solidified mineral artificial seawater media using hexadecane as substrate show a
coccobacillus morphology, of about 0.6 μm in length and 0.35 μm in width, and formed circularcolonies. Members of the species are aerobes, growing at a pH range of 6.5–8.5 with a pH optimumof 7.5, and a salinity range of 250–500 mM of NaCl, with an optimum concentration of 330 mM.
The temperature range for optimal growth is 22–30 °C, with no growth observed at 4 °C and above
34 °C. Cells can grow with hexadecane and pyruvate as a sole carbon sources and fix nitrogen.
Genome size is ~2.8 Mbp with a G+C% content of 61.56. The designated type material is strain
KTK01, and its genome sequence can be found under NCBI BioSample accession number
SAMN11302943.

1148

Emendation of the species Macondimonas diazotrophicaTs

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The properties of the species are as given by Karthikeyan et al 2019, and the designatednomenclatural type is the genome of strain KTK01, deposited in the NCBI databases withaccession number GCF_004684205.1.

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1162
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1165

Registration of effectively published names in the SeqCode Registry. Registration of names in
the SeqCode Registry can occur after effective publication. This example outlines the registrationof a name after effective publication through the expert registration mode in the Registry. Registeras “Contributor”. Select the “Create a name” option from the “Contributor” dashboard and provide
the effectively published name in the textbox and select register (e.g., Macondimonas
diazotrophica). Similar as described before, automatic checks are performed, and red and orange
flags related to Rules and Recommendations in the SeqCode are generated. In addition toaddressing all flags described before, the orange “Missing effective publication” flag needs to beaddressed. Select the “Register publication” option under this flag, provide the DOI to the effective
publication (10.1038/s41396-019-0400-5) in the provided space, and select “Register”. From here,
the linked publication shows which names are linked to the specific publication. Select the taxon
name being edited (e.g., Macondimonas diaozotrophica). This publication will appear in the“Publications” section of the entry (end of page). Several publications proposing, emending,
31

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correcting, or citing the taxon in question can be linked to the name in this fashion. Under the“Actions” associated with the publication, select “Proposed this name” for publications proposing
the name, “Corrigendum” for publication correcting names or “Emended this name” for publishedemendations. Repeat this process for any higher-level taxonomic names and link the associatedeffective publication with these names. Notify the SeqCode curators by submitting these names(typically with all associated names in a single Register List) as a draft register list for curator
review (e.g., seqco.de/r:6ns_rdob) and click “Validate Published Names” to submit the manuscript
PDF and (if relevant) supplementary material. If proposed names satisfy all criteria for validation
under the SeqCode, proposals will be reviewed, and contributors will be notified of validation
under the SeqCode or further recommendations on corrections to the submission.

1176
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Example of combination of path 1 and path 2 for validation: class Kryptonia and child taxa

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In some cases, some names are published in an effective publication, but additional names are also
warranted, such as a case where one or more new higher ranks for a proposed taxon are notpublished. This would require a combination of path 1 (registration of new names) and path 2(registration of effectively published names).

1182
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Overview. As an example for a combination of Path 1 and Path 2, Eloe-Fadrosh et al. (2016)
proposed the new genus and species Candidatus Kryptonium thompsoni based on 13 SAGs and asingle MAG from geothermal springs in British Columbia Canada, Yunnan Province China, andNevada USA. In addition, Candidatus Kryptonium thompsoni was visualized by FISH in cells
collected from Dewar Creek, British Columbia. Candidatus Kryptonium thompsoni was proposed
as one of four Candidatus genera, each with a single species, belonging to a new candidate phylum
named Kryptonia. None of the ranks between genus and phylum were named. In Supplementary
Table 4 of that paper, the proposed candidate taxa were named, and the etymology described.
Ranks were described in the manuscript. However, no nomenclatural type was designated because
there was no path to validate the names under the ICNP or any other authority at the time the paper
was published. Many problems like this exist in the past literature because the community hadn’t
come together to develop standards or best practices, and this is part of the impetus for the
SeqCode. The SeqCode is deliberately designed to allow critical information to be captured in the
SeqCode Registry, allowing most previous Candidatus names to be named under the SeqCode,provided the names appear in an effective publication. However, substantial changes to publishednames will need to be described separately in a peer-reviewed paper, which then becomes theeffective publication. This test case is a good example, as described below.

1199
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1201
1202
1203

Taxonomic decisions and example of taxonomic freedom. Per Principle 1, the SeqCode does
not endorse any particular taxonomy. This is true of all major codes of nomenclature except theInternational Code of Virus Classification and Nomenclature. The taxonomic decisions describedin this section were made by one of the authors of the original publication describing thesegenomes (Hedlund) and Palmer in collaboration with the first author (Eloe-Fadrosh) and
32

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corresponding author (Ivanova). Again, we consider it best practice to communicate with key
authors before registering and validating names under the SeqCode. It is our position that the four
genera proposed in the effective publication should be combined into one genus based on (i)monophyly with strong support in phylogenetic analyses using conserved marker genes; (ii) RED
values consistent with a single genus as implemented within GTDB; and (iii) average amino acid
identity (AAI) values consistent with a single genus (>65% (Konstaninidis et al., 2017)). In thiscase, we will retain the genus and species name Kryptonium thompsonii for the largest group of
genomes described from Dewar Creek. This is the largest species cluster, and it was also visualized
by FISH. This MAG is of high quality per Genome Standards Consortium recommendations(Bowers et al., 2018) (18 contigs, 95.61 % completeness with 1.91 % estimated contamination;
68x coverage and sequences of the 5S, 16S and 23S rRNAs and tRNAs coding for 20 amino acids).
Below is the original etymology from Supplemental Table 4 from the effective publication, butwith the Candidatus prefix removed (Supplementary Table S2). This etymology with or without
the Candidatus prefix and information contained in the paper is sufficient to satisfy Rules 26.1,
26.4, and 26.5 to name both the genus and species. Rules 26.2 and 26.3 will be satisfied when thename is registered with the SeqCode Registry. In this case, the nomenclatural type for the species
will be the highest quality genome in the species cluster, which is the MAG JGI-4. The superscriptTsis added after the species epithet to denote that this is the type species of the genus, following
Chapter 4. We also note that the species name has been corrected to thompsonii, as the second “i”
is the correct suffix to denote a genitive masculine noun, in this case for a species named after amale (David Thompson). “Perfect” Latin is recommended under the SeqCode but not required.
We consider this to be a minor orthographic variant on the original name. Also, the etymology is
modified from the original to remove the definition of ‘bios’ because the root ‘bios’ does notappear in the name. We note here that the GTDB species representative (JGI-8) is actually amedium-quality MAG. We speculate that the GTDB used this species representative, a SAG, as it
was erroneously labeled an “isolate” in NCBI, which was apparently carried over to GTDB. Thus,
we recommend caution and care at all levels when designating nomenclatural types to ensure thatthe highest quality genomic data are used.

1232
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Modified etymology and typification of Kryptonium thompsoniiTs. Eloe-Fadrosh et al., 2016
remains the effective publication.

1235

Description of the genus Kryptonium

1236

Kryptonium (Kryp.to’ni.um. Gr. adj. krypton, hidden; N.L. neut. n. Kryptonium a hidden life form).

1237

The nomenclature type of the genus is Kryptonium thompsoniiTs.

1238

Description of the species Kryptonium thompsonii

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Kryptonium thompsonii (thomp.son’i.i. N.L. gen. masc. n. after David Thompson, explorer of theregion around Dewar Creek).
33

1241

The nomenclatural type is GCA_001442925.1Ts.

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Following Recommendation 7, the ranks above the genus Kryptonium should be named until anexisting name of a parent taxon exists. All available phylogenetic analyses of this genus indicatethat it is very distant from the closest relatives named under the ICNP. However, there isdisagreement between the original publication describing the SAGs and MAGs and the GDTB
taxonomy as to whether the monophyletic lineage containing Kryptonium should be considered aphylum or a class. As a matter of conservatism, we choose to only propose names up to the rankof class as suggested by the GTDB taxonomy and ascribe that class to the phylum Bacteroidota.
The GTDB has suggested the following names at ranks of family, order, and class: Kryptoniaceae,
Kryptoniales, and Kryptoniia. Those names follow the rules of the SeqCode, particularly Rule 15,
which states that the “The name of a family, order, class, or phylum is formed by the addition of
the appropriate suffix to the stem of the type genus name”. Thus, we will use the GTDB names
but require an etymology, which is provided in the table below. The current manuscript thenbecomes the effective publication for those names (Path 1).

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Table S2. Etymology and typification of higher taxa for Kryptonium thompsoniiTs
Proposed taxon
Etymology
Family Kryptoniaceae Kryp.to.ni.a’ce.ae N.L. neut. n.
Kryptonium, type genus of the family;
L. fem. pl. suff. -aceae, ending todenote a family; N.L. fem. pl. n.
Kryptoniaceae, family of the genus
Kryptonium
Order Kryptoniales
Kryp.to.ni.a’les
N.L.
neut.
n.
Kryptonium, type genus of the order;
N.L. fem. pl. suff. -ales, ending
denoting an order; N.L. fem. pl. n.
Kryptoniales, order of the genus
Kryptonium
Class Kryptoniia
Kryp.to’ni.i.a N.L. neut. n. Kryptonium,
type genus of the class; N.L. neut. n.
suff. -ia, ending to denote a class; N.L.
neut. pl. n. Kryptoniia, class of thegenus Kryptonium

Nomenclatural type
Genus Kryptonium

Genus Kryptonium

Genus Kryptonium

1257
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Additional species of the genus Kryptonium. As described above, we have chosen to merge four
genera originally proposed into the single genus Kryptonium. In the GTDB, these genomes are
instead divided into six species clusters based on circumscription radii determined from ANI
34

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clustering, splitting the original taxon Candidatus Kryptobacter tengchongensis into three species.
However, these two additional species clusters likely represent artificial clusters with very highsequence similarity because these clusters are based on three replicate MAG assemblies each.
Regardless, only one other species cluster has a high-quality genome representative that could
serve as a type under minimal standards described in Table 2 (main text). Thus, we will only namea single additional species for the cluster originally proposed as Candidatus Kryptothermus
mobilis, from Great Boiling Spring, Nevada, USA. This taxon was enriched in situ in Great Boiling
Spring sediments following the addition of corn stover, consistent with many annotated glycosidehydrolases in the genome. The original publication has only one MAG; the GTDB cluster again
has three MAGs, although all are publicly available replicate assemblies from the same
metagenomic sequencing run. We nevertheless choose to name this species based on the highquality of the MAG (97.25 % completeness with 2.73 % estimated contamination; 44x coverageand sequences of 5S, 16S and 23S rRNAs and tRNAs coding for 20 amino acids) and based on
recruitment of the genome at high identity in two different cellulolytic enrichments in Great
Boiling Spring that were incubated at 77 °C and 85 °C, providing clear evidence of growth at insitu temperature and consistent with a role in consortial degradation of plant biomass. In addition,
21 MAGs and SAGs from different samples representing the genus are available for comparison,providing confidence of genome size, assembly fidelity, and the presence/conservation of key
genes.

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In the case of the union of the genus Kryoptonium and Candidatus Kryptothermus, we retain thegenus name Kryoptonium, as justified above. However, we consider this a nom. nov. because not
only is a different genus name used, but also the species name should be changed.

1283

Etymology and typification of Kryptonium mobile nom. nov.

1284

Kryptonium mobile (mo’bi.le. L. neut. adj. mobile, motile, moving).

1285

Synonym: Candidatus Kryptothermus mobilis (Eloe-Fadrosh et al., 2016)

1286

The nomenclatural type is NCBI Assembly GCA_900070205.1.

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Pre-registration of names in the SeqCode Registry. To register names for taxa that encompass
names for a lineage where some were proposed in the effective publication and others that are new(and have been effectively published), register as a “Contributor” to the SeqCode Registry. Select“Create a name” option on the “Contributor” dashboard and register all names associated with thelineage as described above in the Wolframiiraptoraceae example (e.g., Kryptoniia, Kryptoniales,
Kryptoniaceae, Kryptonium, Kryptonium thompsonii, and Kryptonium mobile). Link effective
publications for the taxon names proposed previously (e.g., Kryptonium thompsonii proposed by
Eloe-Fadrosh et al., (2016) [10.1038/ncomms10476], corrected by Oren et al., (2020)[10.1099/ijsem.0.003789]) and create new names for those that have not been proposed before(e.g., Kryptoniia, Kryptoniales, Kryptoniaceae, and Kryptonium mobile). As these taxa would havedifferent effective publications associated with the taxon names, separate register lists need to be
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created and associated with the appropriate effective publications. Add all of the taxa associatedwith the previously published effective publication to a single register list for approval by a curator(e.g., seqco.de/r:jvapsuy2) and all newly proposed names to a separate register list (e.g.,
seqco.de/r:rgrmqbgb). The provided register list accession URL for the newly proposed names
should be included in the effective publication to allow automated checks and validation upon
publication if approval was given by the curator. In this case, this manuscript serves as the effective
publication for Kryptoniia, Kryptoniales, Kryptoniaceae, and Kryptonium mobile, and should be
provided for validation under “Validate Published Names” in PDF along with supplementarymaterial (if relevant).

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References
1. Alneberg, J., et al. Binning metagenomic contigs by coverage and composition. Nature

Methods 11, 1144–1146 (2014).
2. Beussecker S, Palmer M, Lai D, Dimapilis J, Mayali X, Mosier D, Jiao J-Y, Colman DR,
Keller LM, St. John E, Miranda M, Gonzalez C, Gonzalez L, Sam C, Villa C, Zou M,
Bodman N, Robles F, Boyd ES, Cox AD, St. Clair B, Hua Z-S, Li W-J, Reysenbach A-L,
Stott MB, Weber PK, Pett-Ridge J, Dekas AE, Hedlund BP, Dodsworth JA. Tungsten isessential for carbohydrate metabolism in members of a novel family of anaerobic,
thermophilic Caldarchaeales (Aigarchaeota). Nature Communications, in press (2022).
3. Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit toclassify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925-1927(2020).
4. Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Dekas AE, Grasby
SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmstrom R, Pati A, Pett-Ridge
J, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN. Global metagenomic survey reveals a
new bacterial candidate phylum in geothermal springs. Nature Communications. 7:10476.
(2016). https://doi.org/10.1038/ncomms10476
5. Hua ZS, Wang YL, Evans PN, Qu YN, Goh KM, Rao YZ, Qi YL, Li YX, Huang MJ, Jiao
JY, Chen YT, Mao YP, Shu WS, Hozzein W, Hedlund BP, Tyson GW, Zhang T, Li WJ.
Insights into the ecological roles and evolution of methyl-coenzyme M reductasecontaining hot spring archaea. Nature Communications 10:4574. (2019).
6. Kang, D. D, Froula, J., Egan, R., & Wang, Z. MetaBAT, an efficient tool for accurately
reconstructing single genomes from complex microbial communities. PeerJ 3, e1165(2015).
7. Kang, D. D., et al. MetaBAT 2: an adaptive binning algorithm for robust and efficientgenome reconstruction from metagenome assemblies. PeerJ 7,e7359 (2019).
8. Karthikeyan,
S.,
Rodriguez-R,
L.M.,
Heritier-Robbins,
P. etal. “Candidatus Macondimonas diazotrophica”, a novel gammaproteobacterial genus
dominating crude-oil-contaminated coastal sediments. ISME J 13, 2129–2134 (2019).
https://doi.org/10.1038/s41396-019-0400-5
36

1339
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1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355

9. Li, D., Liu, C. M., Luo, R., Sadakane, K., & Lam, T. W. MEGAHIT: an ultra-fast single-

node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
Bioinformatics 31, 1674-1676 (2015).
10. Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. metaSPAdes: a new versatile
metagenomic assembler. Genome Research 27, 824-834 (2017).
11. Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM:
assessing the quality of microbial genomes recovered from isolates, single cells, andmetagenomes. Genome Research 25, 1043–1055 (2015).
12. Rodriguez-R, L., Overholt, W., Hagan, C. et al. Microbial community successional
patterns in beach sands impacted by the Deepwater Horizon oil spill. ISME J 9, 1928–1940(2015). https://doi.org/10.1038/ismej.2015.5
13. Wu, Y.-W., Simmons, B. A., & Singer, S. W. MaxBin 2.0: an automated binning algorithm
to recover genomes from multiple metagenomic datasets, Bioinformatics 32, 605–607(2016).
14. Uritskiy, G. V., DiRuggiero, J., & Taylor, J. MetaWRAP-a flexible pipeline for genomeresolved metagenomic data analysis. Microbiome 6, 158 (2018).

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