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Gago JF, Viver T, Urdiain M, Ferreira E, Robledo P, Rossello-Mora R. Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode. Syst Appl Microbiol 2024; 47:126506. [PMID: 38640749 DOI: 10.1016/j.syapm.2024.126506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/21/2024]
Abstract
Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Elaine Ferreira
- The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain
| | - Pedro Robledo
- Unit of Geological and Mining Institute of Spain in Balearic Islands (IGME-CSIC), Palma de Mallorca, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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Rodriguez-R LM, Conrad RE, Viver T, Feistel DJ, Lindner BG, Venter SN, Orellana LH, Amann R, Rossello-Mora R, Konstantinidis KT. An ANI gap within bacterial species that advances the definitions of intra-species units. mBio 2024; 15:e0269623. [PMID: 38085031 PMCID: PMC10790751 DOI: 10.1128/mbio.02696-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/03/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings.
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Affiliation(s)
- Luis M. Rodriguez-R
- Department of Microbiology, and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Roth E. Conrad
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tomeu Viver
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Dorian J. Feistel
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Blake G. Lindner
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ramon Rossello-Mora
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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Viver T, Conrad RE, Rodriguez-R LM, Ramírez AS, Venter SN, Rocha-Cárdenas J, Llabrés M, Amann R, Konstantinidis KT, Rossello-Mora R. Towards estimating the number of strains that make up a natural bacterial population. Nat Commun 2024; 15:544. [PMID: 38228587 PMCID: PMC10791622 DOI: 10.1038/s41467-023-44622-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with four-fold lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural "gap" in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that -although our 138 isolates represented about 80% of the Sal. ruber population- the total population in one saltern pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in-situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in-situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. The methodology and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.
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Affiliation(s)
- Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Roth E Conrad
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Luis M Rodriguez-R
- Department of Microbiology, and Digital Science Center (DiSC), Universität of Innsbruck, Innsbruck, Austria
| | - Ana S Ramírez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jairo Rocha-Cárdenas
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| | - Mercè Llabrés
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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Font-Verdera F, Liébana R, Rossello-Mora R, Viver T. Impact of dilution on stochastically driven methanogenic microbial communities of hypersaline anoxic sediments. FEMS Microbiol Ecol 2023; 99:fiad146. [PMID: 37989854 PMCID: PMC10673710 DOI: 10.1093/femsec/fiad146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/02/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023] Open
Abstract
Sediments underlying the solar salterns of S'Avall are anoxic hypersaline ecosystems dominated by anaerobic prokaryotes, and with the especial relevance of putative methanogenic archaea. Slurries from salt-saturated sediments, diluted in a gradient of salinity and incubated for > 4 years revealed that salt concentration was the major selection force that deterministically structured microbial communities. The dominant archaea in the original communities showed a decrease in alpha diversity with dilution accompanied by the increase of bacterial alpha diversity, being highest at 5% salts. Correspondingly, methanogens decreased and in turn sulfate reducers increased with decreasing salt concentrations. Methanogens especially dominated at 25%. Different concentrations of litter of Posidonia oceanica seagrass added as a carbon substrate, did not promote any clear relevant effect. However, the addition of ampicillin as selection pressure exerted important effects on the assemblage probably due to the removal of competitors or enhancers. The amended antibiotic enhanced methanogenesis in the concentrations ≤ 15% of salts, whereas it was depleted at salinities ≥ 20% revealing key roles of ampicillin-sensitive bacteria.
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Affiliation(s)
- Francisca Font-Verdera
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
| | - Raquel Liébana
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
- AZTI, Basque Research Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, 48395 Sukarrieta, Bizkaia, Spain
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
| | - Tomeu Viver
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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Viver T, Ruiz A, Bertomeu E, Martorell-Barceló M, Urdiain M, Grau A, Signaroli M, Barcelo-Serra M, Aspillaga E, Pons A, Rodgers C, Gisbert E, Furones D, Alós J, Catalán IA, Rossello-Mora R. Food determines ephemerous and non-stable gut microbiome communities in juvenile wild and farmed Mediterranean fish. Sci Total Environ 2023; 889:164080. [PMID: 37201821 DOI: 10.1016/j.scitotenv.2023.164080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/30/2023] [Accepted: 05/07/2023] [Indexed: 05/20/2023]
Abstract
Novel insights were provided by contrasting the composition of wild and farmed fish gut microbiomes because the latter had essentially different environmental conditions from those in the wild. This was reflected in the gut microbiome of the wild Sparus aurata and Xyrichtys novacula studied here, which showed highly diverse microbial community structures, dominated by Proteobacteria, mostly related to an aerobic or microaerophilic metabolism, but with some common shared major species, such as Ralstonia sp. On the other hand, farmed non-fasted S. aurata individuals had a microbial structure that mirrored the microbial composition of their food source, which was most likely anaerobic, since several members of the genus Lactobacillus, probably revived from the feed and enriched in the gut, dominated the communities. The most striking observation was that after a short fasting period (86 h), farmed gilthead seabream almost lost their whole gut microbiome, and the resident community associated with the mucosa had a very much reduced diversity that was highly dominated by a single potentially aerobic species Micrococcus sp., closely related to M. flavus. The results pointed to the fact that, at least for the juvenile S. aurata studied, most of the microbes in the gut were transient and highly dependent on the feed source, and that only after fasting for at least 2 days could the resident microbiome in the intestinal mucosa be determined. Since an important role of this transient microbiome in relation to fish metabolism could not be discarded, the methodological approach needs to be well designed in order not to bias the results. The results have important implications for fish gut studies that could explain the diversity and occasional contradictory results published in relation to the stability of marine fish gut microbiomes, and might provide important information for feed formulation in the aquaculture industry.
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Affiliation(s)
- Tomeu Viver
- Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Alberto Ruiz
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentaries (IRTA), La Ràpita, Spain
| | - Edgar Bertomeu
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentaries (IRTA), La Ràpita, Spain
| | | | - Mercedes Urdiain
- Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Amalia Grau
- LIMIA (IRFAP, Balearic Government), Av. Eng. Gabriel Roca, 69, 07157 Port Andratx, Majorca, Spain
| | - Marco Signaroli
- Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | | | - Eneko Aspillaga
- Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Aina Pons
- Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Chris Rodgers
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentaries (IRTA), La Ràpita, Spain
| | - Enric Gisbert
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentaries (IRTA), La Ràpita, Spain
| | - Dolors Furones
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentaries (IRTA), La Ràpita, Spain
| | - Josep Alós
- Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Ignacio A Catalán
- Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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6
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Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R, Sutcliffe IC. International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision). Int J Syst Evol Microbiol 2023; 73. [PMID: 37219928 DOI: 10.1099/ijsem.0.005585] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Affiliation(s)
- Aharon Oren
- Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, 46100 Burjassot (Valencia), Spain
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 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
| | - Ramon Rossello-Mora
- Grup de Microbiologia Marina, IMEDEA (CSIC-UIB), C/Miquel Marques 21, 07190 Esporles, Illes Balears, Spain
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Mulet M, Gomila M, Lalucat J, Bosch R, Rossello-Mora R, García-Valdés E. Stutzerimonas decontaminans sp. nov. isolated from marine polluted sediments. Syst Appl Microbiol 2023; 46:126400. [PMID: 36706672 DOI: 10.1016/j.syapm.2023.126400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/20/2022] [Accepted: 01/12/2023] [Indexed: 01/24/2023]
Abstract
Strains 19SMN4T and ST27MN3 were isolated from marine sediments after enrichment with 2-methylnaphthalene and were classified as Pseudomonas stutzeri genomovar 4. Four other strains, BG 2, HT20, HT24, and A7, were isolated from sulphide-oxidizing bioreactors or activated sludge affiliated with the same clade in the 16S rRNA phylogenetic tree. P. stutzeri has been recently reclassified as a new genus, Stutzerimonas, and a preliminary analysis indicated that the strains in this study were distinct from any classified Stutzerimonas and are considered representatives of phylogenomic species 4 (pgs4). Strains 19SMN4T and ST27MN3 were extensively characterized with phenotypic, chemotaxonomic, genomic and phylogenomic data. Strain 19SMN4T had a well-characterized naphthalene degradative plasmid that has been compared with other plasmids, while in strain ST27MN3, the naphthalene degradative genes were detected in the chromosome sequence. Phylogenomic analysis of the core gene sequences showed that strains 19SMN4T and ST27MN3 shared 3,995 genes and were closely related to members of the species "Stutzerimonas songnenensis" and Stutzerimonas perfectomarina, as well as to the Stutzerimonas phylogenomic species, pgs9, pgs16 and pgs24. The aggregate average nucleotide identity (ANI) indicated that strains 19SMN4T and ST27MN3 belonged to the same genomic species, whereas the genomic indices with their closest-related type strains were below the accepted species threshold (95 %). We therefore conclude that strains 19SMN4T and ST27MN3 represent a novel species of Stutzerimonas, for which the name Stutzerimonas decontaminans is proposed; the type strain is 19SMN4T (=CCUG44593T = DSM6084T = LMG18521T).
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Affiliation(s)
- Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Grup Microbiologia del Medi Ambient, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Rafael Bosch
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Grup Microbiologia del Medi Ambient, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Ramon Rossello-Mora
- Grup Microbiologia del Medi Ambient, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Grup Microbiologia del Medi Ambient, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain.
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8
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Viver T, Conrad RE, Lucio M, Harir M, Urdiain M, Gago JF, Suárez-Suárez A, Bustos-Caparros E, Sanchez-Martinez R, Mayol E, Fassetta F, Pang J, Mădălin Gridan I, Venter S, Santos F, Baxter B, Llames ME, Cristea A, Banciu HL, Hedlund BP, Stott MB, Kämpfer P, Amann R, Schmitt-Kopplin P, Konstantinidis KT, Rossello-Mora R. Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov. Syst Appl Microbiol 2023; 46:126416. [PMID: 36965279 DOI: 10.1016/j.syapm.2023.126416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023]
Abstract
Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.
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Affiliation(s)
- Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Roth E Conrad
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Marianna Lucio
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Ana Suárez-Suárez
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Rodrigo Sanchez-Martinez
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Eva Mayol
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Federico Fassetta
- Laboratorio de Ecología Acuática, Instituto Tecnológico Chascomús (INTECH)-CONICET-UNSAM, Escuela de Bio y Nanotecnologías -UNSAM, Buenos Aires, Argentina
| | - Jinfeng Pang
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154-4004, USA
| | - Ionuț Mădălin Gridan
- Doctoral School of Integrative Biology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Stephanus Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Bonnie Baxter
- Great Salt Lake Institute, Westminster College, Salt Lake City, UT, 84105, USA
| | - María E Llames
- Laboratorio de Ecología Acuática, Instituto Tecnológico Chascomús (INTECH)-CONICET-UNSAM, Escuela de Bio y Nanotecnologías -UNSAM, Buenos Aires, Argentina
| | - Adorján Cristea
- Department of Taxonomy and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj‑Napoca, Romania
| | - Horia L Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj‑Napoca, Romania; Emil G. Racoviță Institute, Babeș-Bolyai University, Cluj‑Napoca, Romania
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154-4004, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig Universität Giessen, Giessen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
| | - Konstantinos T Konstantinidis
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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9
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Arahal DR, Bull CT, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, Ventosa A, Göker M. Judicial Opinion 128. Int J Syst Evol Microbiol 2023; 73. [PMID: 37000638 DOI: 10.1099/ijsem.0.005797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
Judicial Opinion 128 addresses nomenclatural issues related to the names of classes validly published under the International Code of Nomenclature of Prokaryotes. It is confirmed that the common ending -proteobacteria of some class names is not indicative of a joint taxonomic or phylogenetic placement; that the nomenclatural type of Mollicutes Edward and Freundt 1967 (Approved Lists 1980) is Mycoplasmatales Freundt 1955 (Approved Lists 1980); and that the placement of a name on the list of rejected names does not imply that another name with the same spelling but a distinct rank is also placed on that list. The names at the rank of class Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988, Archaeobacteria Murray 1988, Bacteria Haeckel 1894 (Approved Lists 1980), Firmibacteria Murray 1988, Microtatobiotes Philip 1956 (Approved Lists 1980), Oxyphotobacteria (ex Gibbons and Murray 1978) Murray 1988, Photobacteria Gibbons and Murray 1978 (Approved Lists 1980), Proteobacteria Stackebrandt et al. 1988, Schizomycetes Nägeli 1857 (Approved Lists 1980), Scotobacteria Gibbons and Murray 1978 (Approved Lists 1980) are placed on the list of rejected names. For three common nominative singular suffixes of genus names their genitive singular and nominative plural forms are confirmed: -bacter (-bacteris, -bacteres); -fex (-ficis, -fices); and -genes (-genis, -genes). The class names Aquificae Reysenbach 2002, Chrysiogenetes Garrity and Holt 2002, Chthonomonadetes Lee et al. 2011, Gemmatimonadetes Zhang et al. 2003, Opitutae Choo et al. 2007 and Verrucomicrobiae Hedlund et al. 1998 are orthographically corrected to Aquificia, Chrysiogenia, Chthonomonadia, Gemmatimonadia, Opitutia and Verrucomicrobiia, respectively.
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Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, PA 16802, USA
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, QLD 4072, Australia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | | | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Charles T Parker
- NamesforLife, LLC, East Lansing, Okemos, Michigan 48805-0769, USA
| | - Ramon Rossello-Mora
- Department of Animal and Microbial Biodiversity, Institut Mediterrani d'Estudis Avançats, CSIC-UIB, C/Miquel Marqués 21, 07190 Esporles, Illes Balears, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
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10
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Snyder C, Centlivre JP, Bhute S, Shipman G, Friel AD, Viver T, Palmer M, Konstantinidis KT, Sun HJ, Rossello-Mora R, Nadeau J, Hedlund BP. Microbial Motility at the Bottom of North America: Digital Holographic Microscopy and Genomic Motility Signatures in Badwater Spring, Death Valley National Park. Astrobiology 2023; 23:295-307. [PMID: 36625891 DOI: 10.1089/ast.2022.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Motility is widely distributed across the tree of life and can be recognized by microscopy regardless of phylogenetic affiliation, biochemical composition, or mechanism. Microscopy has thus been proposed as a potential tool for detection of biosignatures for extraterrestrial life; however, traditional light microscopy is poorly suited for this purpose, as it requires sample preparation, involves fragile moving parts, and has a limited volume of view. In this study, we deployed a field-portable digital holographic microscope (DHM) to explore microbial motility in Badwater Spring, a saline spring in Death Valley National Park, and complemented DHM imaging with 16S rRNA gene amplicon sequencing and shotgun metagenomics. The DHM identified diverse morphologies and distinguished run-reverse-flick and run-reverse types of flagellar motility. PICRUSt2- and literature-based predictions based on 16S rRNA gene amplicons were used to predict motility genotypes/phenotypes for 36.0-60.1% of identified taxa, with the predicted motile taxa being dominated by members of Burkholderiaceae and Spirochaetota. A shotgun metagenome confirmed the abundance of genes encoding flagellar motility, and a Ralstonia metagenome-assembled genome encoded a full flagellar gene cluster. This study demonstrates the potential of DHM for planetary life detection, presents the first microbial census of Badwater Spring and brine pool, and confirms the abundance of mobile microbial taxa in an extreme environment.
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Affiliation(s)
- Carl Snyder
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Jakob P Centlivre
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Shrikant Bhute
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Gözde Shipman
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Ariel D Friel
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | | | - Henry J Sun
- Desert Research Institute, Las Vegas, Nevada, USA
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Jay Nadeau
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, Las Vegas, Nevada, USA
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11
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Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, Ventosa A, Göker M. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73. [PMID: 36912622 DOI: 10.1099/ijsem.0.005782] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Abstract
In this paper the Judicial Commission provides general guidance for interpreting the International Code of Nomenclature of Prokaryotes (ICNP) and specific assistance to authors, reviewers and editors of a Request for an Opinion, or of other suggestions related to the ICNP. The role of the Judicial Commission is recapitulated, particularly with respect to the processing of such Requests. Selected kinds of nomenclature-related proposals are discussed that are unsuitable as the basis for a Request. Particular emphasis is put on Requests for placing names or epithets on the list of nomina rejicienda, and a dichotomous identification key is provided to guide potential authors of a Request that targets the name of a species or subspecies because of issues with its type strain. To this end, the criteria for the valid publication of such names under the ICNP are revisited. Aspects of other kinds of Requests are also addressed. The study is based on a comprehensive review of all Judicial Opinions issued since the publication of the Approved Lists in 1980. One goal of this paper is to assist potential authors in deciding whether their concern should be the subject of a Request, and if so, in composing it with the greatest chance of success. It is also clarified how to obtain additional help regarding nomenclature-related issues.
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Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, PA 16802, USA
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, University of Veterinary Medicine, Veterinärplatz 1, A- 1210 Wien, Austria
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, QLD 4072, Australia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | | | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Charles T Parker
- Names for Life, LLC, East Lansing, Okemos, Michigan 48805-0769, USA
| | - Ramon Rossello-Mora
- Department of Animal and Microbial Biodiversity, Institut Mediterrani d'Estudis Avançats, CSIC-UIB, C/Miquel Marqués 21, 07190 Esporles, Illes Balears, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, ES-41012 Sevilla, C/. Prof. Garcia Gonzalez 2, Spain
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
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12
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Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, Ventosa A, Göker M. Judicial Opinions 123-127. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748499 DOI: 10.1099/ijsem.0.005708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Opinion 123 places the epithet of the name Aeromonas punctata on the list of rejected epithets and clarifies the citation of authors of selected names within the genus Aeromonas. Opinion 124 denies the request to place Borreliella on the list of rejected names because the request is based on a misinterpretation of the Code, which is clarified. There are alternative ways to solve the perceived problem. Opinion 125 denies the request to place Lactobacillus fornicalis on the list of rejected names because the provided information does not yield a reason for rejection. Opinion 126 denies the request to place Prolinoborus and Prolinoborus fasciculus on the list of rejected names because a relevant type strain deposit was not examined. Opinion 127 grants the request to assign the strain deposited as ATCC 4720 as the type strain of Agrobacterium tumefaciens, thereby correcting the Approved Lists. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, PA 16802, USA
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Wien, Austria
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, QLD 4072, Australia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | | | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Charles T Parker
- NamesforLife, LLC, East Lansing, Okemos, Michigan 48805-0769, USA
| | - Ramon Rossello-Mora
- Department of Animal and Microbial Biodiversity, Institut Mediterrani d'Estudis Avançats, CSIC-UIB, C/ Miquel Marqués 21, 07190 Esporles, Illes Balears, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, C/ Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
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13
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Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R, Sutcliffe IC. 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. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748491 DOI: 10.1099/ijsem.0.005630] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
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.
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Affiliation(s)
- Aharon Oren
- Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, 46100 Burjassot (Valencia), Spain
| | - Markus Göker
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B3, 38124 15 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
| | - Ramon Rossello-Mora
- Grup de Microbiologia Marina, IMEDEA (CSIC-UIB), C/Miquel Marques 21, 07190 Esporles, Illes Balears, Spain
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14
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Hedlund BP, Chuvochina M, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe IC, Venter SN, Whitman WB. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat Microbiol 2022; 7:1702-1708. [PMID: 36123442 PMCID: PMC9519449 DOI: 10.1038/s41564-022-01214-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 07/25/2022] [Indexed: 01/03/2023]
Abstract
Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry ( https://seqco.de/ ), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.
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Affiliation(s)
- Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, 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, Las Vegas, NV, USA
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, 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, Innsbruck, Austria
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Spain
| | - Iain C Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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16
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Conrad RE, Viver T, Gago JF, Hatt JK, Venter SN, Rossello-Mora R, Konstantinidis KT. Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations. ISME J 2022; 16:1222-1234. [PMID: 34887548 PMCID: PMC9039077 DOI: 10.1038/s41396-021-01149-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 05/03/2023]
Abstract
Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological processes that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of this ecosystem. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (noncore) genes were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results provide an explanation for how this immense intrapopulation gene diversity is maintained, which has implications for the prokaryotic species concept.
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Affiliation(s)
- Roth E Conrad
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Janet K Hatt
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
| | - Konstantinos T Konstantinidis
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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17
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Ivulic D, Rossello-Mora R, Viver T, Montero DA, Vidal S, Aspee F, Hidalgo H, Vidal R. Litter Management Strategies and Their Impact on the Environmental and Respiratory Microbiome Might Influence Health in Poultry. Microorganisms 2022; 10:microorganisms10050878. [PMID: 35630323 PMCID: PMC9144224 DOI: 10.3390/microorganisms10050878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/12/2022] Open
Abstract
Aerial and respiratory tract-associated bacterial diversity has been scarcely studied in broiler production systems. This study examined the relationship between the environmental air and birds’ respiratory microbiome, considering a longitudinal sampling. Total viable bacteria and coliforms in the air were quantified, and the 16S rRNA gene was sequenced from tracheal and air samples obtained through a novelty protocol. Air results showed a decrease in coliforms over time. However, at week 3, we reported an increase in coliforms (from 143 to 474 CFUc/m3) associated with litter management. Additionally, 16S rRNA gene results indicated a distinctive air microbial community, associated primarily with Bacillota phylum particularly of the Bacilli class (>58%), under all conditions. Tracheal results indicated a predominance of Escherichia coli/Shigella at the beginning of the productive cycle, shifting toward the middle and end of the cycle to Gallibacterium. However, at week 3, the dominance of Escherichia coli/Shigella (>99.5%) associated with litter aeration by tumbling stood out. Tracheal and air samples displayed a statistically different community structure, but shared differentially abundant features through time: Enterococcus, Gallibacterium, and Romboutsia ilealis. These results indicate the impact of production management protocols on the birds’ respiratory system that should be considered a breakpoint in poultry farm health.
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Affiliation(s)
- Dinka Ivulic
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile;
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), 07190 Esporles, Illes Balears, Spain; (R.R.-M.); (T.V.)
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), 07190 Esporles, Illes Balears, Spain; (R.R.-M.); (T.V.)
| | - David A. Montero
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile;
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago 8370993, Chile
| | - Sonia Vidal
- Laboratory of Veterinary Vaccines, Department of Animal Biology, Faculty of Veterinary and Animal Science, Universidad de Chile, Santiago 8820808, Chile;
| | | | - Héctor Hidalgo
- Laboratory of Avian Pathology, Faculty of Veterinary and Animal Sciences, Universidad de Chile, Santiago 8820808, Chile
- Correspondence: (H.H.); (R.V.); Tel.: +56-998-477-740 (H.H.); +56-998-496-363 (R.V.)
| | - Roberto Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile;
- ANID—Millennium Science Initiative Program—Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago 8320000, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
- Correspondence: (H.H.); (R.V.); Tel.: +56-998-477-740 (H.H.); +56-998-496-363 (R.V.)
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18
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Alejandre-Colomo C, Francis B, Viver T, Harder J, Fuchs BM, Rossello-Mora R, Amann R. Cultivable Winogradskyella species are genomically distinct from the sympatric abundant candidate species. ISME Commun 2021; 1:51. [PMID: 36747039 PMCID: PMC9723794 DOI: 10.1038/s43705-021-00052-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 02/08/2023]
Abstract
Winogradskyella is a genus within the phylum Bacteroidetes with a clear marine origin. Most members of this genus have been found associated with marine animals and algae, but also with inorganic surfaces such as sand. In this study, we analyzed genomes of eleven species recently isolated from surface seawater samples from the North Sea during a single spring algae bloom. Corresponding metagenomes yielded a single Candidatus species for this genus. All species in culture, with the exception of W. ursingii, affiliated with a Winogradskyella lineage characterized by large genomes (~4.3 ± 0.4 Mb), with high complexity in their carbohydrate and protein degradation genes. Specifically, the polysaccharide utilization loci (PULs) were diverse within each individual strain, indicating large substrate versatility. Although present in the North Sea, the abundances of these strains were at, or below, the detection limit of the metagenomes. In contrast, the single species, classified as Candidatus W. atlantica, to which all North Sea MAGs belonged, affiliated with a lineage in which the cultivated representatives showed small genomes of ~3.0-3.5 Mb, with the MAGs having ~2.3 Mb. In Ca. W. atlantica, genome streamlining has apparently resulted in the loss of biosynthesis pathways for several amino acids including arginine, methionine, leucine and valine, and the PUL loci were reduced to a single one for utilizing laminarin. This as-yet uncultivated species seems to capitalize on sporadically abundant substrates that are released by algae blooms, mainly laminarin. We also suggest that this streamlined genome might be responsible for the lack of growth on plates for this Candidatus species, in contrast to growth of the less abundant but coexisting members of the genus.
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Affiliation(s)
- Carlota Alejandre-Colomo
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Ben Francis
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain.
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.
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19
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Konstantinidis KT, Viver T, Conrad RE, Venter SN, Rossello-Mora R. Solar salterns as model systems to study the units of bacterial diversity that matter for ecosystem functioning. Curr Opin Biotechnol 2021; 73:151-157. [PMID: 34438234 DOI: 10.1016/j.copbio.2021.07.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/03/2022]
Abstract
Microbial communities often harbor overwhelming species and gene diversity, making it challenging to determine the important units to study this diversity. We argue that the reduced, and thus tractable, microbial diversity of manmade salterns provides an ideal system to advance this cornerstone issue. We review recent time-series genomic and metagenomic studies of the saltern-dominating bacterial and archaeal taxa to show that these taxa form persistent, sequence-discrete, species-like populations. While these populations harbor extensive intra-population gene diversity, even within a single saltern site, only a small minority of these genes appear to be functionally important during environmental perturbations. We outline an approach to detect and track such populations and their ecologically important genes that should be broadly applicable.
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Affiliation(s)
- Konstantinos T Konstantinidis
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Roth E Conrad
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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20
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Gago JF, Viver T, Urdiain M, Pastor S, Kämpfer P, Ferreira E, Rossello-Mora R. Description of three new Alteromonas species Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. isolated from marine environments, and proposal for reclassification of the genus Salinimonas as Alteromonas. Syst Appl Microbiol 2021; 44:126226. [PMID: 34171620 DOI: 10.1016/j.syapm.2021.126226] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 11/26/2022]
Abstract
In the course of a bioprospective study of marine prokaryotes for cosmetic purposes, four strains, MD_567T, MD_652T, MD_674 and PS_109T, were isolated that 16S rRNA gene affiliation indicated could represent three new species within the family Alteromonadaceae. A thorough phylogenetic, genomic and phenotypic taxonomic study confirmed that the isolates could be classified as three new taxa for which we propose the names Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. In addition, the consistent monophyletic nature of the members of the genera Alteromonas and Salinimonas showed that both taxa should be unified, and therefore we also propose the reclassification of the genus Salinimonas within Alteromonas, as well as new combinations for the species of the former. As the specific epithets profundi and sediminis are already used for Alteromonas species, we created the nomina nova "Alteromonas alteriprofundi" nom. nov. and Alteromonas alterisediminis nom. nov. to accommodate the new names for "Salinimonas profundi" and Salinimonas sediminis. Whole genome comparisons also allowed us to detect the unexpected codification of aromatic hydrocarbon biodegradative compounds, such as benzoate and catechol, whose activity was then demonstrated phenotypically. Finally, the high genomic identity between the type strains of Alteromonas stellipolaris and Alteromonas addita indicated that the latter is a junior heterotypic synonym of Alteromonas stellipolaris.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Lipotrue S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | | | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig Universität Giessen, Giessen, Germany
| | | | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
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21
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Ludwig W, Viver T, Westram R, Francisco Gago J, Bustos-Caparros E, Knittel K, Amann R, Rossello-Mora R. Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains. Syst Appl Microbiol 2021; 44:126218. [PMID: 34111737 DOI: 10.1016/j.syapm.2021.126218] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/27/2021] [Accepted: 05/14/2021] [Indexed: 01/29/2023]
Abstract
The new release of the All-Species Living Tree Project (LTP) represents an important step forward in the reconstruction of 16S rRNA gene phylogenies, since we not only provide an updated set of type strain sequences until December 2020, but also a series of improvements that increase the quality of the database. An improved universal alignment has been introduced that is implemented in the ARB format. In addition, all low-quality sequences present in the previous releases have been substituted by new entries with higher quality, many of them as a result of whole genome sequencing. Altogether, the improvements in the dataset and 16S rRNA sequence alignment allowed us to reconstruct robust phylogenies. The trees made available through this current LTP release feature the best topologies currently achievable. The given nomenclature and taxonomic hierarchy reflect all the changes available up to December 2020. The aim is to regularly update the validly published nomenclatural classification changes and new taxa proposals. The new release can be found at the following URL: https://imedea.uib-csic.es/mmg/ltp/.
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Affiliation(s)
- Wolfgang Ludwig
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Spain
| | - Ralf Westram
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany; Ribocon GmbH, Fahrenheitstraße. 1, D-28359 Bremen, Germany
| | - Juan Francisco Gago
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Spain
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Spain.
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22
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 6:136. [PMID: 33184503 PMCID: PMC7752755 DOI: 10.1038/s41564-020-00827-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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23
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Armengaud J, Delaunay-Moisan A, Thuret JY, van Anken E, Acosta-Alvear D, Aragón T, Arias C, Blondel M, Braakman I, Collet JF, Courcol R, Danchin A, Deleuze JF, Lavigne JP, Lucas S, Michiels T, Moore ERB, Nixon-Abell J, Rossello-Mora R, Shi ZL, Siccardi AG, Sitia R, Tillett D, Timmis KN, Toledano MB, van der Sluijs P, Vicenzi E. The importance of naturally attenuated SARS-CoV-2in the fight against COVID-19. Environ Microbiol 2020; 22:1997-2000. [PMID: 32342578 PMCID: PMC7267670 DOI: 10.1111/1462-2920.15039] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 11/26/2022]
Abstract
The current SARS‐CoV‐2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID‐19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS‐CoV‐2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS‐CoV‐2 would offer significant relief, although vaccine developers have warned that design, testing and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (i), but the earliest vaccines were based on the live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS‐CoV‐2 will mutate and may naturally attenuate over time (ii). What makes the current pandemic unique is that, thanks to state‐of‐the‐art nucleic acid sequencing technologies, we can follow in detail how SARS‐CoV‐2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS‐CoV‐2 variants across the globe should be of key interest in our fight against the pandemic.
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Affiliation(s)
- Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Agnès Delaunay-Moisan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Jean-Yves Thuret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Eelco van Anken
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Università Vita-Salute San Raffaele, Via Olgettina 58, Milan, 20132, Italy
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Tomás Aragón
- Center for Applied Medical Research, Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Street, Pamplona, 31008, Spain
| | - Carolina Arias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Marc Blondel
- Institut National de la Santé et de la Recherche Médicale UMR1078, 22 Avenue Camille Desmoulins, Brest, F-29200, France.,Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, 22 Avenue Camille Desmoulins, Brest, F-29200, France.,Etablissement Français du Sang (EFS) Bretagne, Brest, F-29200, France.,CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, Brest, F-29200, France
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Science, Science for Life, Utrecht University, The Netherlands
| | - Jean-François Collet
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium.,WELBIO, Wallonia, Belgium
| | - René Courcol
- Expertise France, 73 Avenue de Vaugirard, Paris, 75006, France
| | - Antoine Danchin
- Stellate Therapeutics/Kodikos, Institut Cochin, Paris, 75014, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, 91057, France
| | - Jean-Philippe Lavigne
- U1047, Institut National de la Santé et de la Recherche Médicale, Université Montpellier, Montpellier, France.,Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Sophie Lucas
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium.,WELBIO, Wallonia, Belgium
| | - Thomas Michiels
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Edward R B Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, SE-41346, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, SE-41346, Sweden
| | - Jonathon Nixon-Abell
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Bacterial Diversity, IMEDEA (CSIC-UIB), Esporles, Balearic Islands, 07190, Spain
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Antonio G Siccardi
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Università Vita-Salute San Raffaele, Via Olgettina 58, Milan, 20132, Italy
| | - Roberto Sitia
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Università Vita-Salute San Raffaele, Via Olgettina 58, Milan, 20132, Italy
| | - Daniel Tillett
- Nucleics Pty Ltd, 29 John Street, Woollahra, New South Wales, 2025, Australia
| | - Kenneth N Timmis
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Michel B Toledano
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Peter van der Sluijs
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Science, Science for Life, Utrecht University, The Netherlands
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, Milan, 20132, Italy
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24
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 5:987-994. [PMID: 32514073 PMCID: PMC7381421 DOI: 10.1038/s41564-020-0733-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 05/01/2020] [Indexed: 11/09/2022]
Abstract
The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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25
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Rossello-Mora R, Konstantinidis KT, Sutcliffe I, Whitman W. Opinion: Response to concerns about the use of DNA sequences as types in the nomenclature of prokaryotes. Syst Appl Microbiol 2020; 43:126070. [PMID: 32081606 DOI: 10.1016/j.syapm.2020.126070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022]
Abstract
In the current Opinion we respond to the major concerns by Bisgaard et al. (2019) and Overmann et al. (2019) and conclude that the adoption of sequences as types for the names of prokaryotes will allow for improvements of the taxonomic framework, increased stability of names derived from robust phylogenomic methods, and enable a full circumscription of the microbial world rather than just the cultivated minority.
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Affiliation(s)
- Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Bacterial Diversity, IMEDEA (CSIC-UIB), 07190 Esporles, Balearic Islands, Spain.
| | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Iain Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - William Whitman
- Department of Microbiology, University of Georgia, Athens, GA, USA
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26
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Whitman WB, Sutcliffe IC, Rossello-Mora R. Proposal for changes in the International Code of Nomenclature of Prokaryotes: granting priority to Candidatus names. Int J Syst Evol Microbiol 2019; 69:2174-2175. [DOI: 10.1099/ijsem.0.003419] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- William B. Whitman
- 1Department of Microbiology, University of Georgia, Athens GA 30602-2605, USA
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27
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Ramírez AS, Vega-Orellana OM, Viver T, Poveda JB, Rosales RS, Poveda CG, Spergser J, Szostak MP, Caballero MJ, Ressel L, Bradbury JM, Mar Tavío M, Karthikeyan S, Amann R, Konstantinidis KT, Rossello-Mora R. First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov. Syst Appl Microbiol 2019; 42:457-467. [PMID: 31072660 DOI: 10.1016/j.syapm.2019.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/05/2019] [Accepted: 04/05/2019] [Indexed: 11/29/2022]
Abstract
Two moderately halophilic and psychrotolerant new Mycoplasma species were isolated from common cephalopods. Three strains were isolated in pure culture from two individual European flying squid (Todarodes sagittatus), and two individual octopuses (Octopus vulgaris). The strains showed optimal growth at 25 °C and a salinity of 3% (w/v) NaCl. Molecular analyses revealed that the isolates belonged to two new, but phylogenetically related species, divergent from all previously described Mollicutes, representing the first marine isolates of the class, and also the first Mycoplasma strains for which NaCl requirement has been demonstrated. A genome search against all available marine metagenomes and 16S rRNA gene databases indicated that these two species represent a novel non-free-living marine lineage of Mollicutes, specifically associated with marine animals. Morphology and physiology were compatible with other members of this group, and genomic and phenotypic analyses demonstrated that these organisms represent two novel species of the genus Mycoplasma, for which the names Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov. are proposed; the type strains are PET (DSM 105487T, CIP 111404T) and 5HT (DSM 105,488T, CIP 111405T), respectively.
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Affiliation(s)
- Ana S Ramírez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Orestes M Vega-Orellana
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), 07190, Esporles, Spain
| | - José B Poveda
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain.
| | - Rubén S Rosales
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Carlos G Poveda
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Joachim Spergser
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Michael P Szostak
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Mª José Caballero
- Unidad de Histología y Patología Animal, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Lorenzo Ressel
- University of Liverpool, Institute of Veterinary Science, Leahurst Campus, Neston CH64 7TE, UK
| | - Janet M Bradbury
- University of Liverpool, Institute of Veterinary Science, Leahurst Campus, Neston CH64 7TE, UK
| | - Mª Mar Tavío
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Smruthi Karthikeyan
- School of Civil & Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rudolf Amann
- Department of Molecular Ecology, Max-Planck-Institut für Marine Mikrobiologie, Bremen D-28359, Germany
| | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), 07190, Esporles, Spain
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28
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Affiliation(s)
- Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC-UIB), Esporles, Spain
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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29
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Affiliation(s)
- Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Balearic Islands, Spain.
| | - Iain C Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
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30
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Bai X, Lu S, Yang J, Jin D, Pu J, Díaz Moyá S, Xiong Y, Rossello-Mora R, Xu J. Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau. Front Microbiol 2018; 9:2321. [PMID: 30323800 PMCID: PMC6172336 DOI: 10.3389/fmicb.2018.02321] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/11/2018] [Indexed: 01/16/2023] Open
Abstract
The metataxonomic approach combining 16S rRNA gene amplicon sequencing using the PacBio Technology with the application of the operational phylogenetic unit (OPU) approach, has been used to analyze the fecal microbial composition of the high-altitude and herbivorous Tibetan antelopes. The fecal samples of the antelope were collected in Hoh Xil National Nature Reserve, at an altitude over 4500 m, the largest depopulated zone in Qinghai-Tibetan Plateau, China, where non-native animals or humans may experience life-threatening acute mountain sickness. In total, 104 antelope fecal samples were enrolled in this study, and were clustered into 61,258 operational taxonomic units (OTUs) at an identity of 98.7% and affiliated with 757 OPUs, including 144 known species, 256 potentially new species, 103 potentially higher taxa within known lineages. In addition, 254 comprised sequences not affiliating with any known family, and the closest relatives were unclassified lineages of existing orders or classes. A total of 42 out of 757 OPUs conformed to the core fecal microbiome, of which four major lineages, namely, un-cultured Ruminococcaceae, Lachnospiraceae, Akkermansia, and Christensenellaceae were associated with human health or longevity. The current study reveals that the fecal core microbiome of antelope is mainly composited of uncultured bacteria. The most abundant core taxa, namely, uncultured Ruminococcaceae, uncultured Akkermansia, uncultured Bacteroides, uncultured Christensenellaceae, uncultured Mollicutes, and uncultured Lachnospiraceae, may represent new bacterial candidates at high taxa levels, and several may have beneficial roles in health promotion or anti-intestinal dysbiosis. These organisms should be further isolated and evaluated for potential effect on human health and longevity.
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Affiliation(s)
- Xiangning Bai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ji Pu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Sara Díaz Moyá
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB), Esporles, Spain
| | - Yanwen Xiong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB), Esporles, Spain
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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31
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Leon CG, Moraga R, Valenzuela C, Gugliandolo C, Lo Giudice A, Papale M, Vilo C, Dong Q, Smith CT, Rossello-Mora R, Yañez J, Campos VL. Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile). PLoS One 2018; 13:e0195080. [PMID: 29715297 PMCID: PMC5929503 DOI: 10.1371/journal.pone.0195080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 03/17/2018] [Indexed: 12/20/2022] Open
Abstract
Arsenic (As), a highly toxic metalloid, naturally present in Camarones River (Atacama Desert, Chile) is a great health concern for the local population and authorities. In this study, the taxonomic and functional characterization of bacterial communities associated to metal-rich sediments from three sites of the river (sites M1, M2 and M3), showing different arsenic concentrations, were evaluated using a combination of approaches. Diversity of bacterial communities was evaluated by Illumina sequencing. Strains resistant to arsenic concentrations varying from 0.5 to 100 mM arsenite or arsenate were isolated and the presence of genes coding for enzymes involved in arsenic oxidation (aio) or reduction (arsC) investigated. Bacterial communities showed a moderate diversity which increased as arsenic concentrations decreased along the river. Sequences of the dominant taxonomic groups (abundances ≥1%) present in all three sites were affiliated to Proteobacteria (range 40.3–47.2%), Firmicutes (8.4–24.8%), Acidobacteria (10.4–17.1%), Actinobacteria (5.4–8.1%), Chloroflexi (3.9–7.5%), Planctomycetes (1.2–5.3%), Gemmatimonadetes (1.2–1.5%), and Nitrospirae (1.1–1.2%). Bacterial communities from sites M2 and M3 showed no significant differences in diversity between each other (p = 0.9753) but they were significantly more diverse than M1 (p<0.001 and p<0.001, respectively). Sequences affiliated with Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi and Actinobacteria at M1 accounted for more than 89% of the total classified bacterial sequences present but these phyla were present in lesser proportions in M2 and M3 sites. Strains isolated from the sediment of sample M1, having the greatest arsenic concentration (498 mg kg-1), showed the largest percentages of arsenic oxidation and reduction. Genes aio were more frequently detected in isolates from M1 (54%), whereas arsC genes were present in almost all isolates from all three sediments, suggesting that bacterial communities play an important role in the arsenic biogeochemical cycle and detoxification of arsenical compounds. Overall, results provide further knowledge on the microbial diversity of arsenic contaminated fresh-water sediments.
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Affiliation(s)
- Carla G. Leon
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Ruben Moraga
- Microbiology Laboratory, Faculty of Renewable Natural Resources, Arturo Prat University, Iquique, Chile
| | - Cristian Valenzuela
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Concetta Gugliandolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Angelina Lo Giudice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Messina, Italy
| | - Maria Papale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Claudia Vilo
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Qunfeng Dong
- Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Carlos T. Smith
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Institut Mediterrani d’Estudis Avancats (CSIC-UIB), Esporles, Spain
| | - Jorge Yañez
- Department of Analytical and Inorganic Chemistry, Faculty of Chemical Sciences, University of Concepcion, Concepcion, Chile
| | - Victor L. Campos
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
- * E-mail:
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32
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Whitman WB, Oren A, Chuvochina M, da Costa MS, Garrity GM, Rainey FA, Rossello-Mora R, Schink B, Sutcliffe I, Trujillo ME, Ventura S. Proposal of the suffix -ota to denote phyla. Addendum to 'Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes'. Int J Syst Evol Microbiol 2018; 68:967-969. [PMID: 29458499 DOI: 10.1099/ijsem.0.002593] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As an addendum to the earlier proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes (Oren et al., Int J Syst Evol Microbiol 2015;65:4284-4287) we propose the suffix -ota to denote phyla, replacing the somewhat awkward -aeota. We therefore present a new draft modified version of Rule 8 of the International Code of Nomenclature of Prokaryotes and a corrected list of names of phyla to be considered for validation after approval of the proposal to include the rank of phylum in the Code.
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Affiliation(s)
- William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Maria Chuvochina
- Australian Centre for Ergogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Milton S da Costa
- Microbiology Unit, BIOCANT Biotechnological Park, Cantanhede 3060-197, Portugal
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | - Fred A Rainey
- Department of Biological Sciences, University of Alaska, Anchorage, AK 99508, USA
| | - Ramon Rossello-Mora
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles 07190, Spain
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Konstanz D-78457, Germany
| | - Iain Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca 37007, Spain
| | - Stefano Ventura
- National Research Council of Italy, Institute of Ecosystem Study, Sesto Fiorentino I-50019, Italy
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Federhen S, Rossello-Mora R, Klenk HP, Tindall BJ, Konstantinidis KT, Whitman WB, Brown D, Labeda D, Ussery D, Garrity GM, Colwell RR, Hasan N, Graf J, Parte A, Yarza P, Goldberg B, Sichtig H, Karsch-Mizrachi I, Clark K, McVeigh R, Pruitt KD, Tatusova T, Falk R, Turner S, Madden T, Kitts P, Kimchi A, Klimke W, Agarwala R, DiCuccio M, Ostell J. Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015). Stand Genomic Sci 2016. [PMCID: PMC4748488 DOI: 10.1186/s40793-016-0134-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes from type. A workshop was organized with broad representation from the bacterial taxonomic community to review the proposal, the GenBank Microbial Genomic Taxonomy Workshop, Bethesda MD, May 12–13, 2015.
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Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PSG, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, MA J, Markowitz V, Moore ERB, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki KI, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 2014; 12:e1001920. [PMID: 25093819 PMCID: PMC4122341 DOI: 10.1371/journal.pbio.1001920] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This manuscript calls for an international effort to generate a comprehensive catalog from genome sequences of all the archaeal and bacterial type strains. Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
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Affiliation(s)
- Nikos C. Kyrpides
- DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (NCK); (HPK)
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics Research, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Jonathan A. Eisen
- University of California, Davis, Davis, California, United States of America
| | - Tanja Woyke
- DOE-Joint Genome Institute, Walnut Creek, California, United States of America
| | - Markus Göker
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | | | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Brian J. Beck
- American Type Culture Collection (ATCC), Manassas, Virginia, United States of America
| | - Patrick S. G. Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, United States of America
| | - Jongsik Chun
- School of Biological Sciences and Chunlab Inc., Seoul National University, Seoul, Korea
| | - Rita R. Colwell
- University of Maryland, College Park, College Park, Maryland, United States of America
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | - Peter Dawyndt
- Ghent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium
| | - Tom Dedeurwaerdere
- Centre for Philosophy of Law, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Edward F. DeLong
- Department of Civil and Environmental Engineering and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, United States of America
| | - Paul De Vos
- Ghent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium
- Ghent University, BCCM/LMG Bacteria collection, Laboratory of Microbiology, Ghent, Belgium
| | - Timothy J. Donohue
- University of Wisconsin-Madison, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America
| | - Xiu-Zhu Dong
- Bioresource Center (BRC) of Institute of Microbiology, Chinese Academy of Sciences, P. R. China
| | - Dusko S. Ehrlich
- Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Claire Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jack Gilbert
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Paul Gilna
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Knoxville, Tennessee, United States of America
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen gGmbH, Bremen, Germany
| | - Janet K. Jansson
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jay D. Keasling
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Joint BioEnergy Institute (JBEI), Berkeley, California, United States of America
| | - Rob Knight
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America
| | - David Labeda
- ARS, USDA, National Center for Agricultural Utilization Research, Peoria, Illinois, United States of America
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon, Korea
| | - Wen-Jun Li
- The Key Laboratory for Microbial Resources of the Ministry of Education, Kunming, People's Republic of China
| | - Juncai MA
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Victor Markowitz
- DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Edward R. B. Moore
- CCUG - Culture Collection University of Gothenburg, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Mark Morrison
- Diamantina Institute, The University of Queensland, St Lucia, Queensland, Australia
| | - Folker Meyer
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Karen E. Nelson
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Moriya Ohkuma
- Riken Bioresource Center, Japan Collection of Microorganisms, Hirosawa, Wako, Saitama, Japan
| | - Christos A. Ouzounis
- Chemical Process & Energy Resources Institute, Centre for Research & Technology, Thessalonica, Greece
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Norman Pace
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Julian Parkhill
- The Pathogen Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Nan Qin
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ramon Rossello-Mora
- Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Illes Balears, Spain
| | - Johannes Sikorski
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - David Smith
- CABI, Bakeham Lane, Egham, Surrey, United Kingdom
| | - Mitch Sogin
- Josephine Bay Paul Center for Comparative Evolution and Molecular Biology, MBL, Woods Hole, Massachusetts, United States of America
| | - Rick Stevens
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Uli Stingl
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | | | - Dorothea Taylor
- NamesforLife, LLC, East Lansing, Michigan, United States of America
| | - Jim M. Tiedje
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Brian Tindall
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Michael Wagner
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
| | - George Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Jean Weissenbach
- Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, France
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jun Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lixin Zhang
- Bioresource Center (BRC) of Institute of Microbiology, Chinese Academy of Sciences, P. R. China
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Dawn Field
- U.K. Natural Environment Research Council (NERC), Environmental Bioinformatics Centre, Oxford, United Kingdom
| | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - George M. Garrity
- NamesforLife, LLC, East Lansing, Michigan, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Hans-Peter Klenk
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
- * E-mail: (NCK); (HPK)
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Schmitt-Kopplin P, Englmann M, Rossello-Mora R, Schiewek R, Brockmann KJ, Benter T, Schmitz OJ. Combining chip-ESI with APLI (cESILI) as a multimode source for analysis of complex mixtures with ultrahigh-resolution mass spectrometry. Anal Bioanal Chem 2008; 391:2803-9. [PMID: 18566804 DOI: 10.1007/s00216-008-2211-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 05/19/2008] [Accepted: 05/27/2008] [Indexed: 11/30/2022]
Abstract
Recently we have established atmospheric-pressure laser ionisation (APLI) as a method for coupling time-of-flight mass spectrometric detectors (TOF MS) with chromatographic systems (HPLC and GC) to allow two-photon ionisation of non-polar aromatic compounds. Here we demonstrate that APLI can be combined with chip-electrospray ionisation (cESI) coupled to Fourier-transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) for ultrahigh-resolution analysis of complex samples. With the laser turned off, the analytes are ionised only by ESI, whereas when the laser is switched on non-polar aromatic substances also are ionised. In combination with the extremely high mass resolution of an FT-ICR MS, simultaneous qualitative analysis of polar and non-polar analytes is possible in both positive and negative modes, as is exemplified with a crude oil sample. Nevertheless, ion suppression was observed (up to ca. 70% for D(10)-pyrene) and thus sample preparation with chromatographic or electrophoretic pre-separation is necessary for quantitative analysis of targets. In addition, for the first time, the dopant-assisted APLI method in combination with cESI (DA-cESILI) was used for determination of 1-nitrocoronene.
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Affiliation(s)
- Philippe Schmitt-Kopplin
- German Research Center for Environmental Health, Institute for Ecological Chemistry, Helmholtz Zentrum München, Ingoldstaedter Landstrasse 1, 85764, Neuherberg, Germany
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Nogales B, Moore ER, Llobet-Brossa E, Rossello-Mora R, Amann R, Timmis KN. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 2001; 67:1874-84. [PMID: 11282645 PMCID: PMC92809 DOI: 10.1128/aem.67.4.1874-1884.2001] [Citation(s) in RCA: 236] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2000] [Accepted: 01/09/2001] [Indexed: 11/20/2022] Open
Abstract
The bacterial diversity assessed from clone libraries prepared from rRNA (two libraries) and ribosomal DNA (rDNA) (one library) from polychlorinated biphenyl (PCB)-polluted soil has been analyzed. A good correspondence of the community composition found in the two types of library was observed. Nearly 29% of the cloned sequences in the rDNA library were identical to sequences in the rRNA libraries. More than 60% of the total cloned sequence types analyzed were grouped in phylogenetic groups (a clone group with sequence similarity higher than 97% [98% for Burkholderia and Pseudomonas-type clones]) represented in both types of libraries. Some of those phylogenetic groups, mostly represented by a single (or pair) of cloned sequence type(s), were observed in only one of the types of library. An important difference between the libraries was the lack of clones representative of the Actinobacteria in the rDNA library. The PCB-polluted soil exhibited a high bacterial diversity which included representatives of two novel lineages. The apparent abundance of bacteria affiliated to the beta-subclass of the Proteobacteria, and to the genus Burkholderia in particular, was confirmed by fluorescence in situ hybridization analysis. The possible influence on apparent diversity of low template concentrations was assessed by dilution of the RNA template prior to amplification by reverse transcription-PCR. Although differences in the composition of the two rRNA libraries obtained from high and low RNA concentrations were observed, the main components of the bacterial community were represented in both libraries, and therefore their detection was not compromised by the lower concentrations of template used in this study.
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Affiliation(s)
- B Nogales
- Division of Microbiology, GBF-National Research Centre for Biotechnology, Braunschweig, Germany.
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