Code Of Nomenclature Research Articles

Community structure and abundance of ACC deaminase containing bacteria in soils with 16S-PICRUSt2 inference or direct acdS gene sequencing

Bacteria containing the enzyme 1-aminocyclopropane-1-carboxylate deaminase (ACCD+) can reduce plant ethylene levels and increase root development and elongation resulting in increased resiliency to drought and other plant stressors. Although these bacteria are ubiquitous in the soil, non-culture-based methods for their enumeration and identification are not well developed. In this study we compare two culture-independent approaches for identifying ACCD+ bacteria. First, quantitative PCR (qPCR) and direct acdS sequencing with newly designed gene-specific primers; and second, phylogenetic construction of 16S rRNA amplicon libraries with the PICRUSt2 tool. Using soils from eastern Colorado, we showed complementary yet differing results in ACCD+ abundance and community structure responding to water availability. Across all sites, gene abundances estimated from qPCR with the acdS gene-specific primers and phylogenetic reconstruction using PICRUSt2 were significantly correlated. However, PICRUSt2 identified members of the Acidobacteria, Proteobacteria, and Bacteroidetes phyla (now known as Acidobacteriota, Pseudomonadota, and Bacteroidota according to the International Code of Nomenclature of Prokaryotes) as ACCD+ bacteria, whereas the acdS primers amplified only members of the Proteobacteria phyla. Despite these differences, both measures showed that bacterial abundance of ACCD+ decreased as soil water content decreased along a potential evapotranspiration (PET) gradient at three sites in eastern Colorado. One major advantage of using 16S sequencing and PICRUSt2 in metagenomic studies is the ability to get a potential functional profile of all known KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes within the bacterial community of a single soil sample. The 16S-PICRUSt2 method paints a broader picture of the biological and biochemical function of the soil microbiome compared to direct acdS sequencing; however, phylogenetic analysis based on 16S gene relatedness may not reflect that of the functional gene of interest.

Nomenclatural standards of raspberry cultivars bred by the Sverdlovsk Horticultural Breeding Station and Novosibirsk Zonal Gardening Station

This article is devoted to designing of nomenclatural standards of raspberry cultivars bred by the Sverdlovsk Horticultural Breeding Station (‘Alaya rossy’p’’, ‘Antares’, ‘Barxatnaya’, ‘Vanda’, ‘Vy’sokaya’, ‘Lel’’, ‘Lyubitel’skaya Sverdlovska’, ‘Muza’, ‘Rovnicza’ and ‘Fregat’) and by the Novosibirsk Zonal Gardening Station (‘Arochnaya’, ‘Persikovaya’ and ‘Prelest’’). The work has been performed according to the rules and recommendations outlined in the International Code of Nomenclature for Cultivated Plants and VIR methodology for the vegetatively propagated plants. Nomenclatural standards include two or three herbarium sheets with the simultaneously collected several parts of the same plant: the middle third of a primocane and a leaf from this part, the middle third of a floricane, and a lateral branch with fruits. Also, specimens were supplied with photos of flowers and fruits. Nomenclatural standards are preserved in the Herbarium of cultivated plants of the world, their wild relatives and weeds (WIR) of N. I. Vavilov All-Russian Institute of Plant Genetic Resources.

(258–260) Proposals to eliminate contradiction between Articles 11.7 and 11.8 and to equate non‐fossil with fossil names of dinophytes for purposes of priority

(258–260) Proposals to eliminate contradiction between Articles 11.7 and 11.8 and to equate non‐fossil with fossil names of dinophytes for purposes of priority

(261–266) Proposals to amend the Code to update regulations of the nomenclature of fossils

(261–266) Proposals to amend the <i>Code</i> to update regulations of the nomenclature of fossils

(282) Proposal to amend Article 60 Note 4 by specifying possible options of the grammatical gender and number of epithets honouring certain non‐binary persons

Article 60.8 of the International Code of Nomenclature for algae, fungi, and plants (Turland & al. in Regnum Veg. 159. 2018) explains the terminations of specific and infraspecific epithets derived from personal names; in particular, the grammatical gender-determined terminations applied depending on the gender of a person. However, the epithets mentioned in this Article refer only to persons of either the male or female gender. I consider such an approach as not covering all currently recognized gender identities. In particular, it does not take into account non-binary people whose gender identities are beyond the binary gender system (e.g. Matsuno & Budge in Curr. Sex. Health Rep. 9: 116–120. 2017; see also https://nonbinary.wiki/wiki/Main_Page, accessed 22 Mar 2023). Non-binary (also nonbinary) is an umbrella term encompassing several categories of social gender identities falling outside the traditional sociobiological binary gender framework, including persons whose gender identity falls between or outside the basic biological male and female identities, persons who experience being male or female at separate times, and persons who do not experience having a gender identity or reject having a gender identity. It is advisable to use people's preferred pronouns and grammatical gender identifiers (in addition to names and terms for gender). For example, some non-binary people use they/their/them/themselves in singular or have explicitly developed neutral pronouns (also sometimes termed neopronouns), such as xe/xyr/xem/xyrself or ze/zir/zem/zirs, rather than he/his/him/himself or she/her/her/herself (Richards & al. in Int. Rev. Psychiatry 28: 95–102. 2016; Hekanaho in Neuphilol. Mitteilungen 121: 498–509. 2020). The first person in Australia in 2003 and the first person in the United States in 2016 obtained legal recognition of their non-binary gender. Therefore, I propose to amend Art. 60 Note 4. “Note 4. If the gender and/or number of a substantival epithet derived from a personal name is/are inappropriate for the gender and/or number of the person(s) whom the name commemorates, the termination is to be corrected in conformity with Art. 60.8. However, the grammatical gender used for a person whom the epithet commemorates may be determined by the preferred gender identity of that person. Also, an epithet honouring a non-binary person in some cases may be created by adding -iorum, -iarum, or another indicator of grammatical plurality.” The proposed amendment will not affect the stability of existing nomenclature but will provide for the future an option of forming epithets of scientific names of organisms with due consideration of the gender identities and rights of non-binary people. I am grateful to Nicholas J. Turland (Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Germany) and John H. Wiersema (Smithsonian Institution, Washington, D.C., U.S.A.) for their useful comments and editing. Sergei L. Mosyakin (M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Kyiv, Ukraine) also provided his comments and advice.

Establishing the availability of the mammalian genus name Antillomys and species name Antillomys rayi (Rodentia, Cricetidae)

The rodent genus name Antillomys and the species name Antillomys rayi (Cricetidae: Sigmodontinae) are unavailable, given that the publication where it originally appears did not satisfy the requirements of the International Code of Zoological Nomenclature. The names were formally described in the supplementary information (electronic online text) in Word format, and the work itself did not contain evidence that it was registered in Zoobank, as per Article 8.5.3 (amended) of the International Code of Zoological Nomenclature. In this note we establish the availability of the names Antillomys and Antillomys rayi, by fulfilling ICZN´s requirements.

Correction of collecting number errors in the protologues of sixty-four taxon names from China

Revision and collation of Chinese type specimens from the Harvard University Herbaria and the William and Lynda Steere Herbarium of New York Botanical Garden led to the discovery of errors in the designation of type specimens in the protologues of several taxa names. Following the Article 9.2 of the International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code, 2018), the typographical errors of collecting number in the protologues of 64 taxa from China were corrected.

Epitypification of Anplectrum assamicum C.B. Clarke (Melastomataceae), with Nomenclatural Notes

The basionym Anplectrum assamicum C.B. Clarke of Pseudodissochaeta assamica (C.B. Clarke) Nayar was published in 1879. However, it was not validly published as per article 36.1 of International Code of Nomenclature, and continuous use of the invalid name in taxonomy creates more invalid names if transferred to other ranks. The name also warrants epitypification to avoid any ambiguity in the application of names. Herein I designate an epitype and discuss some issues in the lectotypification of the name.

Making Lantaneae (Verbenaceae) taxonomy useful: A phylogenetic classification

AbstractRecent phylogenetic results strongly suggest that neither Lantana nor Lippia are monophyletic. This has a direct impact on taxonomy and nomenclature in the tribe Lantaneae and it underscores the need to revise its classification. However, any generic recircumscription following the International Code of Nomenclature for algae, fungi, and plants will require substantial nomenclatural changes. As a solution, a phylogenetic classification following the PhyloCode is applied to the whole Lantaneae, and 28 rank‐free names are proposed and defined for clades. Clade /Lantaneae is defined to exclude Coelocarpum. Traditional taxon names previously recognized at the ranks of tribe, genus, and section are maintained when associated with clades. Discussion about fruit and corolla morphology, the basis of most previous classifications, within the group is presented along with a key to the clades of /Lantaneae. A useful classification of the plant diversity in tribe Lantaneae consistent with the phylogenetic relationships within the group is provided. This rank‐free system promotes name stability as new data become available and avoids name changes to well‐known species.

Phylogeny and taxonomy of three species of Blastospora (Pucciniales) from East Asia

ABSTRACT Three species of the rust fungus genus Blastospora, Bl. betulae, Bl. itoana, and Bl. smilacis, have been reported in East Asia. Although their morphological characteristics and life cycles have been investigated, their phylogenetic positions have not been clarified sufficiently. Phylogenetic analysis showed that these three species were included into Zaghouaniaceae of Pucciniales. However, Bl. betulae was phylogenetically distinct from Bl. itoana and Bl. smilacis and different from other genera. Based on this result, and applying recent International Code of Nomenclature decisions/recommendations/requirements, Botryosorus, gen. nov., and Bo. deformans,, comb. nov., were applied for Bl. betulae. Two new combinations, Bl. radiata for Bl. itoana and Bl. makinoi for Bl. smilacis, were also applied. Their host plants and distribution were described based on literature records. Zaghouania yunnanensis, comb. nov., was proposed for Cystopsora yunnanensis as a result of this analysis.

DNA sequences as types: A discussion paper from the Special‐purpose Committee established at the XIX International Botanical Congress in Shenzhen, China

AbstractA special‐purpose Committee on DNA Sequences as Types was established at the XIX International Botanical Congress (IBC) in Shenzhen, China, in 2017, with a mandate to report to the XX IBC in Madrid in 2024 with recommendations on a preferred course of action with respect to potential amendments of the International Code of Nomenclature for algae, fungi, and plants to allow DNA sequences as types. This is the first in an expected series of papers from the Special‐purpose Committee on this issue. We set out the background to the establishment of the Committee, explore key issues around typification that are pertinent to the question of DNA sequences as types, enumerate pros and cons of allowing DNA sequences as types, and foreshadow options for future discussion and potential recommendations.

A checklist of Onagraceae in the Pan-Himalaya region

This study provides a checklist of Onagraceae in the Pan-Himalayan region based on extensive specimen consultation, literature investigation, and field surveys. According to recent phylogenetic studies and taxonomic revisions, five genera of Onagraceae are recognized including a total of 56 species in the Pan-Himalayan region. The five genera are Chamaenerion, Circaea, Epilobium, Oenothera, and Ludwigia. In this checklist, we verified all the validly published names in this region and confirmed their taxonomic status. Type status of names are checked according to the International Code of Nomenclature for algae, fungi and plants (ICN). Epilobium ladakhianum is treated as a new synonym of E. williamsii and lectotypification of Chamaenerion conspersum is made, which are the taxonomic novelties in this study. In addition, we provide identification keys to all the genera and their species, descriptions of the five genera, and distribution ranges as well as taxonomic notes for the species.

Contribution to the knowledge of marsh vegetation of montane and submontane areas of Northern Apennines (Italy)

Freshwater ecosystems are crucial for biodiversity conservation. They are among the most threatened habitats in the world. However, the wetlands of southern European mountains still lack fine-scale plant community studies. Here we studied submontane and montane palustrine communities of the Tuscan-Romagna Apennines. Data from 123 vegetation plots dominated by palustrine species were analysed by means of cluster analysis. We identified 18 vegetation types that we attributed to five classes (Phragmito-Magnocaricetea, Montio-Cardaminetea, Isoëto-Nanojuncetea, Molinio-Arrhenatheretea, and Epilobietea angustifolii), and to two Natura 2000 habitats (3130 - Oligotrophic to mesotrophic standing waters with vegetation of the Littorelletea uniflorae and/or of the Isoëto-Nanojuncetea, and 6430 - Hydrophilous tall herb fringe communities of plains and of the montane to alpine levels). According the 4th edition of the International Code of Phytosociological Nomenclature we corrected the names Phragmition communis Koch 1926 nom. inept. in P. australis Koch 1926 nom. corr., Phragmitetum communisSavič 1926nom. inept. in P. australisSavič 1926nom. corr., Glycerietum plicataeKulczyński 1928nom. inept. in G. notataeKulczyński 1928nom. corr., Beruletum angustifoliaeRoll 1938nom. inept. in Beruletum erectaeRoll 1938nom. corr., and we mutated the name Scirpetum lacustrisChouard 1924nom. inept. in Schoenoplectetum lacustrisChouard 1924nom. mut. nov. Our study highlights the diversity of marsh vegetation of montane and submontane areas of Northern Apennines. Most of the palustrine communities, though important from the point of view of conservation, cannot be attributed at present to any habitat type legally protected at the European level.

Naming genera after geographical locations. Proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes.

Appendix 9, Section E of the International Code of Nomenclature of Prokaryotes provides guidelines on how to form adjectival specific and subspecific epithets that reflect the geographical location where the organism was found or studied. It does not mention ways of naming genera after geographical locations. We here propose emendation of Appendix 9 with the recommendations on how to form such names. Comments on the implementation of the current wording of Appendix 9, Section E are also made.

Unbiased analyses of ITS folding motifs in a taxonomically confusing lineage: Anagnostidinema visiae sp. nov. (CYANOBACTERIA).

Cyanobacteria are diverse prokaryotic, photosynthetic organisms present in nearly every known ecosystem. Recent investigations around the world have recovered vast amounts of novel biodiversity in seldom sampled habitats. One phylogenetically significant character, the secondary folding structures of the 16S-23S ITS rDNA region, has allowed an unprecedented capacity to erect new species. However, two questions arise: is this feature as informative as is proposed, and how do we best employ these features? Submerged sinkholes with oxygen-poor, sulfur-rich ground water in Lake Huron (USA) contain microbial mats dominated by both oxygenic and anoxygenic cyanobacteria. We sought to document some of this unique cyanobacterial diversity. Using culture-based investigations, we recovered 45 strains, of which 23 were analyzed employing 16S-23S rDNA sequences, ITS folding patterns, ecology, and morphology. With scant morphological discontinuities and nebulous 16S rDNA gene sequence divergence, ITS folding patterns were effective at articulating cryptic biodiversity. However, we would have missed these features had we not folded all the available motifs from the strains, including those with highly similar 16S rDNA gene sequences. If we had relied solely on morphological or 16S rDNA gene data, then we might well have missed the diversity of Anagnostidinema. Thus, in order to avoid conformation basis, which is potentially common when employing ITS structures, we advocate clustering strains based on ITS rDNA region patterns independently and comparing them back to 16S rDNA gene phylogenies. Using a total evidence approach, we erected a new taxon according to the International Code of Nomenclature for Algae, Fungi, and Plants: Anagnostidinema visiae.

ERATUM TO THE NOTE: ZORNIELLA, A REPLACEMENT GENUS NAME FOR ZORNIA SENOWBARI-DARYAN ET DI STEFANO, 2001 (BY BABA SENOWBARI-DARYAN AND IOAN I. BUCUR) PUBLISHED IN ACTA PALAEONTOLOGICA ROMANIAE, 17 (1), P. 49, 2021

In an e-mail from April 17, 2023 Eduardo Antonio Molinari-Novoa drew our attention to the fact that the new combination Zorniella obscura is invalid as a result of the fact that no express reference is made (cf. art. 41.5 of the International Code of Nomenclature for algae, fungi, and plants) to the original page and illustration in the article by Senowbari-Daryan and Di Stefano (2001). In order to rectify this mistake, we publish again the text of the note with the respective specification.

Resolving Confusion Surrounding d-Ala-d-Ala Ligase Catalysis in Cyanobacterial Mycosporine-Like Amino Acid (MAA) Biosynthesis.

Mycosporine-like amino acids (MAAs) are natural UV-absorbing sunscreens that evolved in cyanobacteria and algae to palliate harmful effects from obligatory exposure to solar radiation. Multiple lines of evidence prove that in cyanobacteria all MAAs are derived from mycosporine-glycine, which is typically modified by an ATP-dependent ligase encoded by the gene mysD. The function of the mysD ligase has been experimentally described but haphazardly named based solely upon sequence similarity to the d-alanine-d-alanine ligase of bacterial peptidoglycan biosynthesis. Combining phylogeny and alpha-fold tertiary protein structure prediction unambiguously distinguished mysD from d-alanine-d-alanine ligase. The renaming of mysD to mycosporine-glycine-amine ligase (MG-amine ligase) using recognised enzymology rules of nomenclature is, therefore, proposed, and considers relaxed specificity for several different amino acid substrates. The evolutionary and ecological context of MG-amine ligase catalysis merits wider appreciation especially when considering exploiting cyanobacteria for biotechnology, for example, producing mixtures of MAAs with enhanced optical or antioxidant properties.

Status of the SeqCode in the International Journal of Systematic and Evolutionary Microbiology.

The recent publication of an alternative nomenclatural code that targets prokaryotes, the Code of Nomenclature of Prokaryotes Described from DNA Sequence Data (SeqCode), raises questions about how to treat names 'validly published' under that code in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). Here, it is reiterated that the IJSEM must function in accordance with the International Code of Nomenclature of Prokaryotes (ICNP). It is also reiterated that the ICNP covers all prokaryotes and that it accordingly assigns a nomenclatural status to all names of prokaryotic taxa. This implies that the ICNP also assigns a status to names that are only 'validly published' under the SeqCode. It follows that the IJSEM must treat such names as not validly published, since 'validly published under the SeqCode' is not a nomenclatural status, under the ICNP. Such names should be marked accordingly as Candidatus names or printed in quotation marks. The same measures would need to be taken by other journals which intend to adhere to the ICNP.

Proposals to emend Rules 8, 15, 22, 25a, 30(3)(b), 30(4), 34a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes.

To complete the ongoing revision of the International Code of Nomenclature of Prokaryotes, we here propose emendation of Rules 8, 15, 22, 25a, 30(3)(b), 30(4), 34a and Appendix 7. These proposed emendations deal with: the nomenclatural type of taxa above genus; the suitability of names published in supplementary material or in papers published on e-print servers for effective publication; the number of culture collection designations to be included in an effective publication of a name of a species or subspecies to qualify for validation of the name; the kinds of restrictions that may be attached to deposits of type strains; and the question whether elevation of a subspecies to the rank of species or lowering of a species to the rank of subspecies establish new combinations. Some of these emendations change the meaning of the Code while others are mere textual clarifications.

Naming and gaming: The illicit taxonomic practice of ‘nomenclatural harvesting’ and how to avoid it

AbstractWe coin the term 'nomenclatural harvesting' to identify a distinct form of taxonomic vandalism, in which practitioners generate taxon names for operational taxonomic units (OTUs) identified in phylogenetic trees published by others, even when there is no scientifically useful or practical basis for doing so. This practice can destabilize the nomenclature of scientifically established groups by swamping them with questionable new names, and this may have broader impacts in the application of taxon names to clinical toxinology, studies of biodiversity and conservation, and it may contribute to further erode the trust placed by the public in science. A change to Article 73 of the International Code of Zoological Nomenclature and the addition of suitable language in publications presenting taxonomic decisions to authenticate research effort and specimen work would alleviate the problem.