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Rosselló-Móra R, Konstantinidis KT, Amann R. How Systematic and Applied Microbiology will deal with two nomenclature codes (ICNP and SeqCode) for prokaryotes, and which classification standards are recommended for new taxa descriptions. Syst Appl Microbiol 2023; 46:126371. [PMID: 36428164 DOI: 10.1016/j.syapm.2022.126371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/15/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022]
Affiliation(s)
- Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (CSIC-UIB), 070190 Esporles, Spain.
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
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2
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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: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [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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Viver T, Orellana L, González-Torres P, Díaz S, Urdiain M, Farías ME, Benes V, Kaempfer P, Shahinpei A, Ali Amoozegar M, Amann R, Antón J, Konstantinidis KT, Rosselló-Móra R. Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano. Syst Appl Microbiol 2018; 41:198-212. [DOI: 10.1016/j.syapm.2017.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/22/2017] [Accepted: 12/23/2017] [Indexed: 01/08/2023]
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Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016; 39:281-96. [PMID: 27287844 DOI: 10.1016/j.syapm.2016.04.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/01/2016] [Accepted: 04/05/2016] [Indexed: 11/21/2022]
Abstract
Members of the phylum Bacteroidetes, which was originally defined as a monophyletic branch encompassing the genera Cytophaga, Flavobacterium and Bacteroides (CFB), are widely studied due to their importance in environmental and gut microbiology. As a consequence, the number of species names with standing in nomenclature has doubled in the past five years. In this study, a revision of an earlier phylogeny of Bacteroidetes has been performed using the 16S rRNA gene as a backbone in combination with the 23S rRNA gene, as well as multilocus sequence analysis (MLSA) of 29 orthologous protein sequences, and indels in the sequences of the beta subunit of the F-type ATPase and the alanyl-tRNA synthetase. In addition, taxonomic data for Bacteroidetes has been updated by considering the orphan species list, signature nucleotides in the 16S rRNA sequence, the list of outlier species, and discrepancies with the current taxonomy at the genus rank level. As a result, seven new taxa are proposed within Bacteroidetes (Chitinophagia classis nov., Chitinophagales ord. nov., Crocinitomicaceae fam. nov., Odoribacteraceae fam. nov., Hymenobacteraceae fam. nov., Thermonemataceae fam. nov. and Persicobacteraceae fam. nov.), as well as one new phylum Rhodothermaeota phyl. nov. that contains two classes, two orders, four families and a new genus with two new combinations.
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Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015; 38:209-16. [PMID: 25747618 DOI: 10.1016/j.syapm.2015.02.001] [Citation(s) in RCA: 355] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 12/22/2022]
Abstract
Species is the basic unit of biological diversity. However, among the different microbiological disciplines there is an important degree of disagreement as to what this unit may be. In this minireview, we argue that the main point of disagreement is the definition (i.e. the way species are circumscribed by means of observable characters) rather than the concept (i.e. the idea of what a species may be as a unit of biodiversity, the meaning of the patterns of recurrence observed in nature, and the why of their existence). Taxonomists have defined species by means of genetic and expressed characters that ensure the members of the unit are monophyletic, and exhibit a large degree of genomic and phenotypic coherence. The new technologies allowing high-throughput data acquisition are expected to improve future classifications significantly and will lead to database-based taxonomy centered on portable and interactive data. Future species descriptions of Bacteria and Archaea should include a high quality genome sequence of at least the type strain as an obligatory requirement, just as today an almost full-length 16S rRNA gene sequence must be provided. Serious efforts are needed in order to re-evaluate the major guidelines for standard descriptions.
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Affiliation(s)
- Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), E-07190 Esporles, Illes Balears, Spain.
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
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Vollmers J, Voget S, Dietrich S, Gollnow K, Smits M, Meyer K, Brinkhoff T, Simon M, Daniel R. Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin. PLoS One 2013; 8:e63422. [PMID: 23671678 PMCID: PMC3646047 DOI: 10.1371/journal.pone.0063422] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/03/2013] [Indexed: 12/11/2022] Open
Abstract
The genus Octadecabacter is a member of the ubiquitous marine Roseobacter clade. The two described species of this genus, Octadecabacter arcticus and Octadecabacter antarcticus, are psychrophilic and display a bipolar distribution. Here we provide the manually annotated and finished genome sequences of the type strains O. arcticus 238 and O. antarcticus 307, isolated from sea ice of the Arctic and Antarctic, respectively. Both genomes exhibit a high genome plasticity caused by an unusually high density and diversity of transposable elements. This could explain the discrepancy between the low genome synteny and high 16S rRNA gene sequence similarity between both strains. Numerous characteristic features were identified in the Octadecabacter genomes, which show indications of horizontal gene transfer and may represent specific adaptations to the habitats of the strains. These include a gene cluster encoding the synthesis and degradation of cyanophycin in O. arcticus 238, which is absent in O. antarcticus 307 and unique among the Roseobacter clade. Furthermore, genes representing a new subgroup of xanthorhodopsins as an adaptation to icy environments are present in both Octadecabacter strains. This new xanthorhodopsin subgroup differs from the previously characterized xanthorhodopsins of Salinibacter ruber and Gloeobacter violaceus in phylogeny, biogeography and the potential to bind 4-keto-carotenoids. Biochemical characterization of the Octadecabacter xanthorhodopsins revealed that they function as light-driven proton pumps.
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Affiliation(s)
- John Vollmers
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Sascha Dietrich
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Kathleen Gollnow
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Maike Smits
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Katja Meyer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- * E-mail:
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Oren A. Salinibacter: an extremely halophilic bacterium with archaeal properties. FEMS Microbiol Lett 2013; 342:1-9. [PMID: 23373661 DOI: 10.1111/1574-6968.12094] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 01/29/2013] [Accepted: 01/29/2013] [Indexed: 12/17/2022] Open
Abstract
The existence of large number of a member of the Bacteroidetes in NaCl-saturated brines in saltern crystallizer ponds was first documented in 1999 based on fluorescence in situ hybridization studies. Isolation of the organism and its description as Salinibacter ruber followed soon. It is a rod-shaped, red-orange pigmented, extreme halophile that grows optimally at 20-30% salt. The genus is distributed worldwide in hypersaline environments. Today, the genus Salinibacter includes three species, and a somewhat less halophilic relative, Salisaeta longa, has also been documented. Although belonging to the Bacteria, Salinibacter shares many features with the Archaea of the family Halobacteriaceae that live in the same habitat. Both groups use KCl for osmotic adjustment of their cytoplasm, both mainly possess salt-requiring enzymes with a large excess of acidic amino acids, and both contain different retinal pigments: light-driven proton pumps, chloride pumps, and light sensors. Salinibacter produces an unusual carotenoid, salinixanthin that forms a light antenna and transfers energy to the retinal group of xanthorhodopsin, a light-driven proton pump. Other unusual features of Salinibacter and Salisaeta include the presence of novel sulfonolipids (halocapnine derivatives). Salinibacter has become an excellent model for metagenomic, biogeographic, ecological, and evolutionary studies.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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8
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Molecular signatures for the phylum Synergistetes and some of its subclades. Antonie Van Leeuwenhoek 2012; 102:517-40. [DOI: 10.1007/s10482-012-9759-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
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Rosselló-Móra R. Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories. Environ Microbiol 2012; 14:318-34. [PMID: 21958017 DOI: 10.1111/j.1462-2920.2011.02599.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Taxonomy in the second decade of the 21st century is benefiting from technological advances in molecular microbiology, especially those related to genomics. Gene and genome databases are significantly increasing due to intense research activities in the field of molecular ecology and genomics. Taxa, and especially species, are tailored by means of the recognition of a phylogenetic, genomic and phenotypic coherence that reveal their uniqueness in the classification schema. Phylogenetic coherence is mainly revealed by means of 16S rRNA gene analyses for which curated databases such as EzTaxon and LTP provide a valuable tool for tree reconstruction to taxonomy users. On the other hand, in silico full or partial genomic sequence comparisons are called on to substitute cumbersome techniques such as DNA-DNA hybridization (DDH) to genomically circumscribe species. DDH similarity values around 70% would be equivalent to ANI values of 96%. Finally, finding an exclusive phenotypic property for the taxa to be classified is of paramount relevance to producing an operative and predictive classification system. The current methods used for taxonomic classification require significant laboratory experimentation, and generally will not produce interactive databases. The new high-throughput metabolomic technologies, such as ICR-FT and MALDI-TOF mass spectrometry methods, open the door to the construction of metabolic databases for taxonomic purposes. It is to be foreseen that, in the future, taxonomists will benefit significantly from public databases speeding up the classification process. However, serious effort will be needed to harmonize them and to prevent inaccurate material.
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Affiliation(s)
- Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), C/Miquel Marqués 21, Esporles, Illes Balears, Spain.
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Talavera G, Vila R. What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny. BMC Evol Biol 2011; 11:315. [PMID: 22032248 PMCID: PMC3213125 DOI: 10.1186/1471-2148-11-315] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 10/27/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Efforts to solve higher-level evolutionary relationships within the class Insecta by using mitochondrial genomic data are hindered due to fast sequence evolution of several groups, most notably Hymenoptera, Strepsiptera, Phthiraptera, Hemiptera and Thysanoptera. Accelerated rates of substitution on their sequences have been shown to have negative consequences in phylogenetic inference. In this study, we tested several methodological approaches to recover phylogenetic signal from whole mitochondrial genomes. As a model, we used two classical problems in insect phylogenetics: The relationships within Paraneoptera and within Holometabola. Moreover, we assessed the mitochondrial phylogenetic signal limits in the deeper Eumetabola dataset, and we studied the contribution of individual genes. RESULTS Long-branch attraction (LBA) artefacts were detected in all the datasets. Methods using Bayesian inference outperformed maximum likelihood approaches, and LBA was avoided in Paraneoptera and Holometabola when using protein sequences and the site-heterogeneous mixture model CAT. The better performance of this method was evidenced by resulting topologies matching generally accepted hypotheses based on nuclear and/or morphological data, and was confirmed by cross-validation and simulation analyses. Using the CAT model, the order Strepsiptera was recovered as sister to Coleoptera for the first time using mitochondrial sequences, in agreement with recent results based on large nuclear and morphological datasets. Also the Hymenoptera-Mecopterida association was obtained, leaving Coleoptera and Strepsiptera as the basal groups of the holometabolan insects, which coincides with one of the two main competing hypotheses. For the Paraneroptera, the currently accepted non-monophyly of Homoptera was documented as a phylogenetic novelty for mitochondrial data. However, results were not satisfactory when exploring the entire Eumetabola, revealing the limits of the phylogenetic signal that can be extracted from Insecta mitogenomes. Based on the combined use of the five best topology-performing genes we obtained comparable results to whole mitogenomes, highlighting the important role of data quality. CONCLUSION We show for the first time that mitogenomic data agrees with nuclear and morphological data for several of the most controversial insect evolutionary relationships, adding a new independent source of evidence to study relationships among insect orders. We propose that deeper divergences cannot be inferred with the current available methods due to sequence saturation and compositional bias inconsistencies. Our exploratory analysis indicates that the CAT model is the best dealing with LBA and it could be useful for other groups and datasets with similar phylogenetic difficulties.
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Affiliation(s)
- Gerard Talavera
- Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003 Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Edifici C, 08193 Bellaterra, Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003 Barcelona, Spain
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Campos VL, Valenzuela C, Yarza P, Kämpfer P, Vidal R, Zaror C, Mondaca MA, Lopez-Lopez A, Rosselló-Móra R. Pseudomonas arsenicoxydans sp nov., an arsenite-oxidizing strain isolated from the Atacama desert. Syst Appl Microbiol 2010; 33:193-7. [DOI: 10.1016/j.syapm.2010.02.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 11/16/2022]
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Serrano W, Amann R, Rosselló-Mora R, Fischer U. Evaluation of the use of multilocus sequence analysis (MLSA) to resolve taxonomic conflicts within the genus Marichromatium. Syst Appl Microbiol 2010; 33:116-21. [DOI: 10.1016/j.syapm.2009.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 12/15/2009] [Accepted: 12/18/2009] [Indexed: 10/19/2022]
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Schleifer KH. Classification of Bacteria and Archaea: Past, present and future. Syst Appl Microbiol 2009; 32:533-42. [DOI: 10.1016/j.syapm.2009.09.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 09/08/2009] [Indexed: 11/25/2022]
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14
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Occurrence of Halococcus spp. in the nostrils salt glands of the seabird Calonectris diomedea. Extremophiles 2009; 13:557-65. [PMID: 19363644 DOI: 10.1007/s00792-009-0238-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 03/06/2009] [Indexed: 10/20/2022]
Abstract
The nostrils of the seabird Calonectris diomedea are endowed with a salt-excreting gland that could produce a suitable environment for the colonization of extreme halophilic prokaryotes. We have studied in this organ the presence of extreme halophiles by means of culturing techniques. We could easily cultivate members of haloarchaea, and all cultures studied were identified as members of one of the two species Halococcus morrhuae and Hcc. dombrowskii. In order to reveal the diversity of these colonizers, we undertook a taxonomic study. Altogether, the results indicated that members of the genus Halococcus may constitute a part of the natural epizootic microbiota of C. diomedea, and that they exhibit such an important degree of taxonomic variability that appeals for a pragmatic species definition. This seabird nests in the west Mediterranean coasts, but its migratory habits, reaching locations as distant from the Mediterranean as the South Atlantic, may help in the dispersal mechanisms of haloarchaea through the Earth's surface.
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Lin GN, Cai Z, Lin G, Chakraborty S, Xu D. ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets. BMC Bioinformatics 2009; 10 Suppl 1:S5. [PMID: 19208152 PMCID: PMC2648732 DOI: 10.1186/1471-2105-10-s1-s5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background With the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. We developed a new tool ComPhy, 'Composite Distance Phylogeny', based on a composite distance matrix calculated from the comparison of complete gene sets between genome pairs to produce a prokaryotic phylogeny. Results The composite distance between two genomes is defined by three components: Gene Dispersion Distance (GDD), Genome Breakpoint Distance (GBD) and Gene Content Distance (GCD). GDD quantifies the dispersion of orthologous genes along the genomic coordinates from one genome to another; GBD measures the shared breakpoints between two genomes; GCD measures the level of shared orthologs between two genomes. The phylogenetic tree is constructed from the composite distance matrix using a neighbor joining method. We tested our method on 9 datasets from 398 completely sequenced prokaryotic genomes. We have achieved above 90% agreement in quartet topologies between the tree created by our method and the tree from the Bergey's taxonomy. In comparison to several other phylogenetic analysis methods, our method showed consistently better performance. Conclusion ComPhy is a fast and robust tool for genome-wide inference of evolutionary relationship among genomes. It can be downloaded from .
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Affiliation(s)
- Guan Ning Lin
- Digital Biology Laboratory, Informatics Institute, Computer Science Department and Christopher S, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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Antón J, Peña A, Santos F, Martínez-García M, Schmitt-Kopplin P, Rosselló-Mora R. Distribution, abundance and diversity of the extremely halophilic bacterium Salinibacter ruber. SALINE SYSTEMS 2008; 4:15. [PMID: 18957079 PMCID: PMC2596770 DOI: 10.1186/1746-1448-4-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 10/28/2008] [Indexed: 11/10/2022]
Abstract
Since its discovery in 1998, representatives of the extremely halophilic bacterium Salinibacter ruber have been found in many hypersaline environments across the world, including coastal and solar salterns and solar lakes. Here, we review the available information about the distribution, abundance and diversity of this member of the Bacteroidetes.
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Affiliation(s)
- Josefa Antón
- División de Microbiología, Universidad de Alicante, Alicante, Spain.
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17
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Urdiain M, López-López A, Gonzalo C, Busse HJ, Langer S, Kämpfer P, Rosselló-Móra R. Reclassification of Rhodobium marinum and Rhodobium pfennigii as Afifella marina gen. nov. comb. nov. and Afifella pfennigii comb. nov., a new genus of photoheterotrophic Alphaproteobacteria and emended descriptions of Rhodobium, Rhodobium orientis and Rhodobium gokarnense. Syst Appl Microbiol 2008; 31:339-51. [DOI: 10.1016/j.syapm.2008.07.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241-50. [DOI: 10.1016/j.syapm.2008.07.001] [Citation(s) in RCA: 663] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Soria-Carrasco V, Castresana J. Estimation of Phylogenetic Inconsistencies in the Three Domains of Life. Mol Biol Evol 2008; 25:2319-29. [DOI: 10.1093/molbev/msn176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Abstract
A large-scale phylogenetic study of the human lineage dramatically points up the problems of using single genes to build phylogenetic trees. A recent large-scale phylogenomic study has shown the great degree of topological variation that can be found among eukaryotic phylogenetic trees constructed from single genes, highlighting the problems that can be associated with gene sampling in phylogenetic studies.
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Affiliation(s)
- Jose Castresana
- Department of Physiology and Molecular Biodiversity, Institute of Molecular Biology of Barcelona, CSIC, 08034 Barcelona, Spain.
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21
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Rosselló-Mora R, Lucio M, Peña A, Brito-Echeverría J, López-López A, Valens-Vadell M, Frommberger M, Antón J, Schmitt-Kopplin P. Metabolic evidence for biogeographic isolation of the extremophilic bacterium Salinibacter ruber. ISME JOURNAL 2008; 2:242-53. [PMID: 18239610 DOI: 10.1038/ismej.2007.93] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The biogeography of prokaryotes and the effect of geographical barriers as evolutionary constraints are currently subjected to great debate. Some clear-cut evidence for geographic isolation has been obtained by genetic methods but, in many cases, the markers used are too coarse to reveal subtle biogeographical trends. Contrary to eukaryotic microorganisms, phenotypic evidence for allopatric segregation in prokaryotes has never been found. Here we present, for the first time, a metabolomic approach based on ultrahigh resolution mass spectrometry to reveal phenotypic biogeographical discrimination. We demonstrate that strains of the cosmopolitan extremophilic bacterium Salinibacter ruber, isolated from different sites in the world, can be distinguished by means of characteristic metabolites, and that these differences can be correlated to their geographical isolation site distances. The approach allows distinct degrees of discrimination for isolates at different geographical scales. In all cases, the discriminative metabolite patterns were quantitative rather than qualitative, which may be an indication of geographically distinct transcriptional or posttranscriptional regulations.
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Affiliation(s)
- Ramon Rosselló-Mora
- Marine Microbiology Group, Institut Mediterrani d'Estudis Avançats, Esporles, Spain.
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Hamana K, Itoh T, Benno Y, Hayashi H. Polyamine distribution profiles of new members of the phylum Bacteroidetes. J GEN APPL MICROBIOL 2008; 54:229-36. [DOI: 10.2323/jgam.54.229] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Gupta RS, Mok A. Phylogenomics and signature proteins for the alpha proteobacteria and its main groups. BMC Microbiol 2007; 7:106. [PMID: 18045498 PMCID: PMC2241609 DOI: 10.1186/1471-2180-7-106] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Accepted: 11/28/2007] [Indexed: 01/11/2023] Open
Abstract
Background Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales), very few or no distinctive molecular or biochemical characteristics are known. Results We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI-Blast searches on the open reading frames in the genomes of several α-proteobacteria (viz. Bradyrhizobium japonicum, Brucella suis, Caulobacter crescentus, Gluconobacter oxydans, Mesorhizobium loti, Nitrobacter winogradskyi, Novosphingobium aromaticivorans, Rhodobacter sphaeroides 2.4.1, Silicibacter sp. TM1040, Rhodospirillum rubrum and Wolbachia (Drosophila) endosymbiont). These studies have identified several proteins that are distinctive characteristics of all α-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and many families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae). Many other proteins that are present at different phylogenetic depths in α-proteobacteria provide important information regarding their evolution. The evolutionary relationships among α-proteobacteria as deduced from these studies are in excellent agreement with their branching pattern in the phylogenetic trees and character compatibility cliques based on concatenated sequences for many conserved proteins. These studies provide evidence that the major groups within α-proteobacteria have diverged in the following order: (Rickettsiales(Rhodospirillales (Sphingomonadales (Rhodobacterales (Caulobacterales-Parvularculales (Rhizobiales)))))). We also describe two conserved inserts in DNA Gyrase B and RNA polymerase beta subunit that are distinctive characteristics of the Sphingomonadales and Rhodosprilllales species, respectively. The results presented here also provide support for the grouping of Hyphomonadaceae and Parvularcula species with the Caulobacterales and the placement of Stappia aggregata with the Rhizobiaceae group. Conclusion The α-proteobacteria-specific proteins and indels described here provide novel and powerful means for the taxonomic, biochemical and molecular biological studies on these bacteria. Their functional studies should prove helpful in identifying novel biochemical and physiological characteristics that are unique to these bacteria.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton L8N3Z5, Canada.
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