1
|
Arahal D, Bisgaard M, Christensen H, Clermont D, Dijkshoorn L, Duim B, Emler S, Figge M, Göker M, Moore ERB, Nemec A, Nørskov-Lauritsen N, Nübel U, On SLW, Vandamme P, Ventosa A. The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38180015 DOI: 10.1099/ijsem.0.006188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the 'Code of Nomenclature of Prokaryotes Described from DNA Sequence Data' ('SeqCode'), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.
Collapse
Affiliation(s)
- David Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | | | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, CRBIP, CIP-Collection of Institut Pasteur, F-75015 Paris, France
| | - Lenie Dijkshoorn
- Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, Leiden / Torensteelaan 68, 3281 MA Numansdorp, Netherlands
| | - Birgitta Duim
- Department Biomolecular Health Sciences, Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CS Utrecht, Netherlands
| | - Stefan Emler
- SmartGene Services SARL, EPFL Innovation Park, PSE-C, CH-1015 Lausanne, Switzerland
| | - Marian Figge
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8 3584 CT, Utrecht, Netherlands
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Edward R B Moore
- Department of Infectious Disease and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-402 34 Gothenburg, Sweden
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, National Institute of Public Health, Srobarova 48, 100 00 Prague 10, Czech Republic
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, V Úvalu 84, 150 06 Prague 5, Czechia
| | | | - Ulrich Nübel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
- Technical University Braunschweig, Institute of Microbiology, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
| | - Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Faculty of Agricultural Science, Lincoln University, Lincoln 7647, Christchurch, New Zealand
| | - Peter Vandamme
- BCCM/LMG, Laboratorium voor Microbiologie, Universiteit Gent (UGent) K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| |
Collapse
|
2
|
Chen SQ, Wang HF, Li YJ, Gao R, Xu TJ, Ping XR, Song JQ, Li CP, Xiao M, Li QL, Li WJ. Luteimonas suaedae sp. nov., a novel bacterium isolated from rhizosphere of Suaeda aralocaspica (Bunge) Freitag & Schütze. Int J Syst Evol Microbiol 2023; 73. [PMID: 37831063 DOI: 10.1099/ijsem.0.006088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Light yellowish-white colonies of a bacterial strain, designated LNNU 24178T, were isolated from the rhizosphere soil of halophyte Suaeda aralocaspica (Bunge) Freitag and Schütze grown at Shihezi district, Xinjiang, PR China. Cells were Gram-stain-negative, non-flagellum-forming, rod-shaped and non-motile. The results of phylogenetic analysis based on the 16S rRNA gene sequence indicated that LNNU 24178T represented a member of the genus Luteimonas and shared the highest sequence similarity with Luteimonas yindakuii CGMCC 1.13927T (97.1 %) and lower sequence similarity (< 97.0 %) to other known species. The genomic DNA G+C content of LNNU 24178T was 68.8 %. The average nucleotide identity (ANI) values between LNNU 24178T and Luteimonas yindakuii CGMCC 1.13927T, Luteimonas mephitis DSM 12574T, Luteimonas arsenica 26-35T and Luteimonas huabeiensis HB2T were 78.7, 78.6, 78.4 and 80.0 %, respectively. The digital DNA-DNA hybridisation (dDDH) values between LNNU 24178T and L. yindakuii CGMCC 1.13927T, L. mephitis DSM 12574T, L. arsenica 26-35T and L. huabeiensis HB2T were 22.0, 22.3, 22.2 and 23.5 %, respectively. The respiratory quinone detected in LNNU 24178T was ubiquinone-8 (Q-8). The major fatty acids (> 5.0 %) of LNNU 24178T were identified as iso-C15 : 0 (33.9 %), iso-C17 : 0 (8.7 %), iso-C11 : 0 (6.2 %), iso-C16 : 0 (5.7 %), C16 : 0 (5.3 %) and summed feature 9 (iso-C17 : 1ω9c/10-methyl C16 : 0) (21.1 %). The major polar lipids of LNNU 24178T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), one unidentified phospholipid (PL), one unidentified glycolipid (GL) and three unidentified lipids. According to the data obtained from phenotypic, chemotaxonomic and phylogenetic analyses, strain LNNU 24178T represents a novel species of the genus Luteimonas, for which the name Luteimonas suaedae sp. nov. is proposed, with LNNU 24178T (= CGMCC 1.17331T= KCTC 62251T) as the type strain.
Collapse
Affiliation(s)
- Shao-Qi Chen
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian, 650081, PR China
| | - Hong-Fei Wang
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian, 650081, PR China
| | - Yong-Jia Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian, 650081, PR China
| | - Rui Gao
- Dandong Forestry and Grassland Development Service Center, Dandong 118000, PR China
| | - Tian-Jiao Xu
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian, 650081, PR China
| | - Xiao-Rui Ping
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian, 650081, PR China
| | - Jie-Qiong Song
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian, 650081, PR China
| | - Chang-Ping Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian, 650081, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qiu-Li Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian, 650081, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| |
Collapse
|
3
|
Kałużna M, Prokić A, Obradović A, Weldon WA, Stockwell VO, Pothier JF. Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1254107. [PMID: 37780515 PMCID: PMC10535005 DOI: 10.3389/fpls.2023.1254107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023]
Abstract
Xanthomonas arboricola pv. corylina (Xac; formerly Xanthomonas campestris pv. corylina) is the causal agent of the bacterial blight of hazelnuts, a devastating disease of trees in plant nurseries and young orchards. Currently, there are no PCR assays to distinguish Xac from all other pathovars of X. arboricola. A comparative genomics approach with publicly available genomes of Xac was used to identify unique sequences, conserved across the genomes of the pathogen. We identified a 2,440 bp genomic region that was unique to Xac and designed identification and detection systems for conventional PCR, qPCR (SYBR® Green and TaqMan™), and loop-mediated isothermal amplification (LAMP). All PCR assays performed on genomic DNA isolated from eight X. arboricola pathovars and closely related bacterial species confirmed the specificity of designed primers. These new multi-platform molecular diagnostic tools may be used by plant clinics and researchers to detect and identify Xac in pure cultures and hazelnut tissues rapidly and accurately.
Collapse
Affiliation(s)
- Monika Kałużna
- The National Institute of Horticultural Research, Skierniewice, Poland
| | - Andjelka Prokić
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Aleksa Obradović
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | | | - Virginia O. Stockwell
- United States Department of Agriculture, Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, United States
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| |
Collapse
|
4
|
Göker M. Filling the gaps: missing taxon names at the ranks of class, order and family. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748602 DOI: 10.1099/ijsem.0.005638] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) recently underwent some major modifications regarding the higher taxonomic ranks. On the one hand, the phylum category was introduced into the ICNP, which rapidly led to the valid publication of more than forty names of phyla. On the other hand, a decision on the retroactivity of Rule 8 regarding the names of classes was made, which removed most of the nomenclatural uncertainty that had affected those names during the last decade. However, it turned out that a number of names at the ranks of class, order and family are either not validly published or are validly published but illegitimate, although these names occur in the literature and are based on the type genus of a phylum with a validly published name. A closer examination of the literature for these and similar cases indicates that the names are unavailable under the ICNP either because of minor formal errors in the original descriptions, because another name should have been adopted for the taxon when the name was proposed, because of taxonomic uncertainties that were settled in the meantime, or because the names were placed on the list of rejected names. The purpose of this article is to fill the gaps by providing the missing formal descriptions and to ensure that the resulting taxon names are attributed to the original authors who did the taxonomic work.
Collapse
Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| |
Collapse
|
5
|
Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe I, Venter SN. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Syst Appl Microbiol 2022; 45:126305. [PMID: 36049255 PMCID: PMC9489671 DOI: 10.1016/j.syapm.2022.126305] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 11/15/2022]
Abstract
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.
Collapse
Affiliation(s)
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | | | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Alexander J Probst
- 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
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innrain 15 / 01-05, Innsbruck 6020, Austria
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Iain Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| |
Collapse
|
6
|
Heins A, Amann RI, Harder J. Cultivation of particle-associated heterotrophic bacteria during a spring phytoplankton bloom in the North Sea. Syst Appl Microbiol 2021; 44:126232. [PMID: 34399113 DOI: 10.1016/j.syapm.2021.126232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022]
Abstract
Seawater contains free-living and particle-attached bacteria. Only a small fraction is cultivable on plates. As free-living and particle-associated bacteria differ in their physiological traits, their cultivability on plates may coincide with particle association. Using filtration and Imhoff sedimentation cones, particles were collected during a spring phytoplankton bloom off Helgoland (North Sea) in order to obtain particle-associated bacteria as inocula. Direct dilution plating resulted in 526 strains from 3 µm filtration retentates and 597 strains from settled particles. Motile Gammaproteobacteria from the genera Pseudoalteromonas, Shewanella, Psychrobacter, Vibrio and Colwellia, as well as particle-attached Flavobacteriia affiliating with the genera Tenacibaculum and Gramella, were frequently isolated. As a result, a diverse collection comprised of 266 strains was deposited. Two strains were most likely to represent novel genera and 78 strains were probably novel species. Recently, a high-throughput cultivation study from the same site using seawater as an inoculum had retrieved 271 operational phylogenetic units (OPUs) that represented 88% of the 4136 characterized strains at the species level. A comparison of 16S rRNA gene sequences revealed that the collection obtained matched 104 of the 271 seawater OPUs at the species level and an additional 113 at the genus level. This large overlap indicated a significant contribution of particle-associated bacteria to the cultivable microbiome from seawater. The presence of 49 genera not identified in the larger seawater study suggested that sample fractionation was an efficient strategy to cultivate rare members of the planktonic microbiome. The diverse collection of heterotrophic bacteria retrieved in this study will be a rich source for future studies on the biology of particle-associated bacteria.
Collapse
Affiliation(s)
- Anneke Heins
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| |
Collapse
|
7
|
Lysobacter segetis sp. nov., Isolated from Soil. Curr Microbiol 2019; 77:166-172. [PMID: 31728699 DOI: 10.1007/s00284-019-01801-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 10/22/2019] [Indexed: 10/25/2022]
Abstract
A Gram-negative, aerobic, motile by gliding, rod-shaped bacterium, strain 17J68-2T, was isolated from a soil sample taken from Jeju Island, Republic of Korea. The isolate displayed high 16S rRNA gene sequence similarity to the members of the genus Lysobacter in the family Lysobacteraceae, with Lysobacter humi FJY8T (98.4% similarity), Lysobacter xinjiangensis RCML-52T (98.3%), and Lysobacter mobilis 9NM-14T (98.1%) as closest phylogenetic neighbors. Growth of strain 17J68-2T occurred at 15-42 °C, pH 7-8, and in the presence of 0-1.0% NaCl. Draft genome was 2.94 Mb in size with G+C content of 70.5 mol%. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine. Ubiquinone Q-8 was the predominant respiratory quinone and the major fatty acids were C16:0 iso (39.4%), summed feature 3 (C16:1ω7c/C16:1ω6c) (6.6%), C11:0 iso 3-OH (6.4%), C15:0 iso (6.4%), and C16:1 iso H (6.2%). The DNA-DNA relatedness between strain 17J68-2T and L. humi, L. xinjiangensis, and L. mobilis were 39.9, 39.4, and 25.3%, respectively. From these results, it is concluded that the novel isolate possesses sufficient characteristics to differentiate it from the most closely affiliated Lysobacter species, and strain 17J68-2T represents a novel species of the genus Lysobacter, for which the name Lysobacter segetis sp. nov. (=KCTC 62237T = JCM 33058T) is proposed.
Collapse
|
8
|
Tindall BJ. When treated as heterotypic synonyms the names Caryophanaceae Peshkoff 1939 (Approved Lists 1980) and Caryophanales Peshkoff 1939 (Approved Lists 1980) have priority over the names Planococcaceae Krasil'nikov 1949 (Approved Lists 1980) and Bacillales Prévot 1953 (Approved Lists 1980), respectively. Int J Syst Evol Microbiol 2019; 69:2187-2195. [PMID: 30896383 DOI: 10.1099/ijsem.0.003354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The International Code of Nomenclature of Prokaryotes provides rules that govern the way names are to be selected based on priority of valid publication when two or more alternatives (synonyms) are available. However, these rules are not always followed. In the case of the name CaryophanaceaePeshkoff 1939 (Approved Lists 1980), when its nomenclatural type CaryophanonPeshkoff 1939 (Approved Lists 1980) is placed in the same taxon as PlanococcusMigula 1894 (Approved Lists 1980), the nomenclatural type of PlanococcaceaeKrasil'nikov 1949 (Approved Lists 1980), then the two are considered to be heterotypic synonyms and the name which has priority is CaryophanaceaePeshkoff 1939 (Approved Lists 1980). Similarly in the case of the name CaryophanalesPeshkoff 1939 (Approved Lists 1980) when its nomenclatural type CaryophanonPeshkoff 1939 (Approved Lists 1980) is placed in the same taxon as Bacillus Cohn 1872 (Approved Lists 1980), the nomenclatural type of BacillalesPrévot 1953 (Approved Lists 1980), then the two are considered to be heterotypic synonyms and the name which has priority is CaryophanalesPeshkoff 1939 (Approved Lists 1980) While the rules of the International Code of Nomenclature of Prokaryotes are unambiguous in determining the correct names despite the fact that the names CaryophanaceaePeshkoff 1939 (Approved Lists 1980) and CaryophanalesPeshkoff 1939 (Approved Lists 1980) are rarely used.
Collapse
Affiliation(s)
- B J Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B 38124 Braunschweig, Germany
| |
Collapse
|
9
|
Liu Q, Liu HC, Zhou YG, Xin YH. Stenotrophobium rhamnosiphilum gen. nov., sp. nov., isolated from a glacier, proposal of Steroidobacteraceae fam. nov. in Nevskiales and emended description of the family Nevskiaceae. Int J Syst Evol Microbiol 2019; 69:1404-1410. [PMID: 30821681 DOI: 10.1099/ijsem.0.003327] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative strain, designated GT1R17T, was isolated from an ervoconite sample collected from Gawalong glacier in the Tibet Autonomous Region, PR China. Strain GT1R17T was catalase- and oxidase-positive, and grew optimally at 20-25°C and pH 7.0. The highest level of 16S rRNA gene sequence similarities were found to members of the genera Nevskia(92.27-93.15 %) and Hydrocarboniphaga(91.92-92.96 %). Phylogenetic analyses based on 16S rRNA gene sequences and genomic data revealed that the strain GT1R17T belonged to the family Nevskiaceae, but could not be assigned to any known genera. The genomic DNA G+C content was 54.4 mol%. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1ω6c), C16 : 0, iso-C16 : 0 and summed feature 2 (C14 : 0 3OH and/or iso-C16 : 1 I). The polar lipids were phosphatidylglycerol, phosphatidylethanolamine and one unidentified lipid. The ubiquinone was Q-8. On the basis of the phenotypic, chemotaxonomic, genotypic and phylogenetic data, a novel species of a new genus,Stenotrophobiumrhamnosiphilum gen. nov., sp. nov. within the family Nevskiaceae, is proposed, with GT1R17T (=CGMCC 1.16137T=NBRC 113346T) as the type strain. In addition, phylogenetic analyses revealed that Steroidobacter and Povalibacter formed an independent clade in the order Nevskiales and were away from the families Nevskiaceae, Algiphilaceae and Salinisphaeraceae. Therefore, we propose to remove Steroidobacter and Povalibacter from the family Nevskiaceae and propose a new family Steroidobacteraceae in the order Nevskiales.
Collapse
Affiliation(s)
- Qing Liu
- 1China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- 1China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- 2State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,1China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Hua Xin
- 1China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| |
Collapse
|
10
|
Busse HJ, Huptas C, Baumgardt S, Loncaric I, Spergser J, Scherer S, Wenning M, Kämpfer P. Proposal of Lysobacter pythonis sp. nov. isolated from royal pythons (Python regius). Syst Appl Microbiol 2019; 42:326-333. [PMID: 30826139 DOI: 10.1016/j.syapm.2019.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/31/2019] [Accepted: 02/08/2019] [Indexed: 11/29/2022]
Abstract
The bacterial strains 4284/11T and 812/17 isolated from the respiratory tract of two royal pythons in 2011 and 2017, respectively were subjected to taxonomic characterization. The 16S rRNA gene sequences of the two strains were identical and showed highest sequence similarities to Lysobacter tolerans UM1T (97.2%) and Luteimonas aestuarii DSM 19680T (96.7 %). The two strains were identical in the sequences of the 16S-23S rRNA internal transcribed spacer (ITS) and partial groEL gene sequences and almost identical in genomic fingerprints. In the ITS sequence Ly. tolerans DSM 28473T and in the groEL nucleotide sequence Luteimonas mephitis DSM 12574T showed the highest similarity. In silico DDH analyses using genome sequence based ANIb and gANI similarity coefficients demonstrated that strain 4284/11T represents a novel species and revealed Ly. tolerans UM1T as the next relative (ANIb = 76.2 %, gANI = 78.0 %). Based on the topology of a core gene phylogeny strain 4284/11T could be assigned to the genus Lysobacter. Chemotaxonomic characteristics including polyamine pattern, quinone system, polar lipid profile and fatty acid profile were in accordance with the characteristics of the genera Lysobacter and Luteimonas. Strains 4284/11T and 812/17 could be differentiated from the type strains of the most closely related species by several physiological tests. In conclusion we are here proposing the novel species Lysobacter pythonis sp. nov. The type strain is 4284/11T (= CCM 8829T = CCUG 72164T = LMG 30630T) and strain 812/17 (CCM 8830) is a second strain of this species.
Collapse
Affiliation(s)
- Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria.
| | - Christopher Huptas
- Lehrstuhl für Mikrobielle Ökologie, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, D-85354 Freising, Germany
| | - Sandra Baumgardt
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Igor Loncaric
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Joachim Spergser
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Siegfried Scherer
- Lehrstuhl für Mikrobielle Ökologie, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, D-85354 Freising, Germany
| | - Mareike Wenning
- Lehrstuhl für Mikrobielle Ökologie, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, D-85354 Freising, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| |
Collapse
|
11
|
Dialogue on the nomenclature and classification of prokaryotes. Syst Appl Microbiol 2019; 42:5-14. [DOI: 10.1016/j.syapm.2018.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/08/2018] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
|
12
|
Tindall BJ. The nomenclatural type of the genus Methanocorpusculum Zellner et al. 1988 and the selection of the correct name. Int J Syst Evol Microbiol 2016; 66:4900-4904. [PMID: 27499051 DOI: 10.1099/ijsem.0.001385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A recent Request for an Opinion has raised the issue of the inter-relationship between Methanocorpusculum parvum Zellner et al. 1988, the type species of the genus Methanocorpusculum Zellner et al. 1988 as defined at the time of valid publication of the genus name and the subsequent recognition of Methanocorpusculum aggregans (Ollivier et al., 1985) Xun et al.1989 as an earlier heterotypic synonym. Examination of the relevant literature indicates that there are a number of misunderstandings that have arisen. In particular misinterpretation of Rule 15 of the International Code of Nomenclature of Prokaryotes continues to be a source of confusion. Additional problems centre on whether the nomenclatural type of a taxon continues to be the nomenclatural type even if that name is not treated as the correct name and would not appear in a list of names in a given classification. It would be appropriate to clarify these issues.
Collapse
Affiliation(s)
- B J Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| |
Collapse
|
13
|
Tindall BJ. Priority of the genus name Clostridium Prazmowski 1880 (Approved Lists 1980) vs Sarcina Goodsir 1842 (Approved Lists 1980) and the creation of the illegitimate combinations Clostridium maximum (Lindner 1888) Lawson and Rainey 2016 and Clostridium ventriculi (Goodsir 1842) Lawson and Rainey 2016 that may not be used. Int J Syst Evol Microbiol 2016; 66:4890-4894. [PMID: 27488356 DOI: 10.1099/ijsem.0.001361] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a recent publication that attempts to deal with the growing problem of taxa being added to the genus Clostridium that are outside of Clostridium (16S rRNA) group I, a solution is proposed that seeks to limit the genus Clostridium Prazmowski 1880 (Approved Lists 1980) to a small number of species 'related' to the type species, Clostridium butyricum Prazmowski 1880 (Approved Lists 1980). It has been proposed that this genus should also include members of the genus Sarcina Goodsir 1842 (Approved Lists 1980), Sarcinamaxima Lindner 1888 (Approved Lists 1980) and Sarcinaventriculi Goodsir 1842 (Approved Lists 1980), the latter being the nomenclatural type of the genus Sarcina Goodsir 1842 (Approved Lists 1980). In making proposals to treat the genus name Sarcina Goodsir 1842 (Approved Lists 1980) as a synonym of ClostridiumPrazmowski 1880 (Approved Lists 1980), reference is made to the wording of the International Code of Nomenclature of Bacteria. However, while that wording is factually correct, other parts of the Code are relevant to this issue and clearly indicate that the proposed course of action is not sanctioned by texts that have not been directly made reference to. Rather than avoiding confusion it has been contributed to, and it is necessary to document where the problems lie.
Collapse
Affiliation(s)
- B J Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| |
Collapse
|
14
|
Description of Luteimonas pelagia sp. nov., isolated from marine sediment, and emended descriptions of Luteimonas aquatica, Luteimonas composti, Luteimonas mephitis, Lysobacter enzymogenes and Lysobacter panaciterrae. Int J Syst Evol Microbiol 2016; 66:645-651. [DOI: 10.1099/ijsem.0.000769] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
15
|
Monophyletic group of unclassified γ- Proteobacteria dominates in mixed culture biofilm of high-performing oxygen reducing biocathode. Bioelectrochemistry 2015; 106:167-76. [DOI: 10.1016/j.bioelechem.2015.04.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/01/2015] [Accepted: 04/05/2015] [Indexed: 12/31/2022]
|
16
|
Zhang XQ, Sun C, Wang CS, Zhang X, Zhou X, Wu YH, Xu XW, Wu M. Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:3541-3546. [DOI: 10.1099/ijsem.0.000452] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two aerobic, rod-shaped, non-motile, non-sporulating and Gram-staining-negative bacterial strains, namely NH6-24T and Za3-11, were isolated from the surface seawater of the South China Sea and the estuary of the Yangtze River, respectively. The two isolates grew at 14–44 °C (optimum 37–40 °C) and pH 6.0–8.5 (optimum pH 7.0–7.5). The sea salt ranges for growth were 0.5–10 % (w/v) (optimum 1–2.5 %) for strain NH6-24T and 0–12 % (w/v) (optimum 0.5–4.5 %) for strain Za3-11.Both strains could grow in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates showed closest affinity to the genera Fontimonas (96.0 %) and Solimonas (94.1–95.1 %) and formed a single lineage in the cluster of the family Solimonadaceae. The predominant isoprenoid quinone was ubiquinone-8.The major fatty acids were C18 : 1ω7c, iso-C16 : 0 and C16 : 0.The dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 65 mol%. Based on the polyphasic taxonomic characterization, strains NH6-24T and Za3-11 are considered to represent a novel species of a novel genus, for which the name Sinimarinibacterium flocculans gen. nov., sp. nov. is proposed. The type strain of the type species is NH6-24T ( = CGMCC 1.10815T = JCM 17607T) and an additional strain is Za3-11 ( = CGMCC 1.10816 = JCM 17606).
Collapse
Affiliation(s)
- Xin-Qi Zhang
- College of Forestry and Biotechnology, Zhejiang Agricultural and Forestry University, Lin'an 311300, PR China
| | - Cong Sun
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Chun-Sheng Wang
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xin Zhang
- College of Forestry and Biotechnology, Zhejiang Agricultural and Forestry University, Lin'an 311300, PR China
| | - Xiang Zhou
- College of Forestry and Biotechnology, Zhejiang Agricultural and Forestry University, Lin'an 311300, PR China
| | - Yue-Hong Wu
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| |
Collapse
|
17
|
Tindall BJ. A commentary on the interpretation of the International Code of Nomenclature of Bacteria. Int J Syst Evol Microbiol 2015; 65:2334-2336. [DOI: 10.1099/ijs.0.000355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Brian J. Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH., Inhoffenstraße 7B, 38124 Braunschweig, Germany
| |
Collapse
|
18
|
Whitman WB, Lawson PA, Losey NA. Response to Tindall (2014) on the legitimacy of the names Solimonadaceae Losey et al. 2013, Xanthomonadaceae Saddler and Bradbury 2005 and Xanthomonadales Saddler and Bradbury 2005. Int J Syst Evol Microbiol 2015; 65:1086-1087. [DOI: 10.1099/ijs.0.000061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- William B. Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Paul A. Lawson
- Deparment of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019, USA
| | - Nathaniel A. Losey
- Deparment of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019, USA
| |
Collapse
|
19
|
Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE, Gupta RS. A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie van Leeuwenhoek 2014; 107:467-85. [DOI: 10.1007/s10482-014-0344-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/28/2014] [Indexed: 01/10/2023]
|
20
|
Tindall BJ. Names at the rank of class, subclass and order, their typification and current status: Supplementary information to Opinion 79. Judicial Commission of the International Committee on Systematics of Prokaryotes. Int J Syst Evol Microbiol 2014; 64:3599-3602. [DOI: 10.1099/ijs.0.069310-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The attention of the Judicial Commission was drawn to issues relating to the use of names at the rank of class, subclass and order and the nomenclatural type of names at the rank of class and subclass that were not covered by Opinion 79. The Judicial Commission ruled that names at the rank of class and order proposed by Cavalier-Smith (Int. J. Syst. Evol. Microbiol., 52, 7–76, 2002) are to be placed on the List of Rejected Names (nomina rejicienda) and the use of names proposed in that publication above the rank of class is to be actively discouraged. In addition a list of names at the rank of class, subclass and order is given where the nomenclatural type, description or circumscription is unclear or where they otherwise appear to be not in accordance with the Rules of the International Code of Nomenclature of Bacteria.
Collapse
Affiliation(s)
- B. J. Tindall
- Leibniz Institute-DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
| |
Collapse
|