[Show abstract][Hide abstract] ABSTRACT: Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.
Full-text · Article · Aug 2014 · Nature Reviews Microbiology
[Show abstract][Hide abstract] ABSTRACT: Nitrite oxidizing bacteria are an integral part of the nitrogen cycle in marine waters, but the knowledge about their diversity is limited. Recently, a high abundance of Nitrospina-like 16S rRNA gene sequences has been detected in oceanic habitats with low oxygen content by molecular methods. Here, we describe a new strain of Nitrospina, which was sampled in 100m depth from the Black Sea. It coexisted with a not-yet cultivated chemoorganotrophic gammaproteobacterium and could be purified by classical isolation methods including Percoll density gradient centrifugation. The new Nitrospina-like bacterium grew lithoautotrophically at 28°C in diluted seawater supplemented with inorganic salts and nitrite. Gram-negative rods were characterized morphologically, physiologically and partly biochemically. The 16S rRNA gene of the new strain of Nitrospina is 97.9% similar to the described species N. gracilis and DNA/DNA hybridization experiments revealed a relatedness of 30.0%. The data from both Nitrospina species and environmental clones were used for an extensive 16S rRNA based phylogenetic study applying high quality filtering. Treeing analyses confirm the newly defined phylum status for "Nitrospinae" . The results of phylogenetic and genotypic analyses support the proposal of a novel species Nitrospina watsonii sp. nov. (type strain 347(T), LMG 27401(T), NCIMB 14887(T)).
No preview · Article · Feb 2014 · Systematic and Applied Microbiology
[Show abstract][Hide abstract] ABSTRACT: The All-Species Living Tree Project (LTP) is an international initiative for the creation and maintenance of highly curated 16SrRNA and 23SrRNA gene sequence databases, alignments, and phylogenetic trees for all the type strains of Bacteria and Archaea.
[Show abstract][Hide abstract] ABSTRACT: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.
Full-text · Article · Nov 2013 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 "orphan" species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these "orphan" species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.
Full-text · Article · Feb 2013 · Systematic and Applied Microbiology
[Show abstract][Hide abstract] ABSTRACT: This revised road map and the resulting taxonomic outline update the previous versions of Garrity and Holt (2001) and Garrity et al. (2005) with the description of additional taxa and new phylogenetic analyses. While the road map seeks to be complete for all taxa validly named prior to 1 January 2008, some taxa described after that date are included.
[Show abstract][Hide abstract] ABSTRACT: All taxa recognized within this volume of the rank of genus and above are listed below. Within each classification, the nomenclatural type is listed first followed by the remaining taxa in alphabetical order. Taxa appearing on the Approved Lists are denoted by the superscript AL. Taxa that were otherwise validly published are denoted by the superscript VP. Taxa that have not been validly published are presented in quotations.
[Show abstract][Hide abstract] ABSTRACT: Comparative rRNA gene sequence analysis currently represents the standard approach in microbial phylogeny, taxonomy and identification. Special database projects provide quality checked rRNA alignments as well as online facilities for data processing. With respect to taxonomy and identification, expert maintained type strain rRNA web resources have been established. Various software packages and tools are available for user controlled data handling, information retrieval, phylogeny reconstruction, and identification. Despite all these facilities, careful data analysis is needed to avoid misinterpretation resulting from improper data selection, limited information content, noise in the data, as well as shortcomings of procedures and software tools. Recommendations and references for appropriate data handling and interpretation are given in this chapter. The rRNA approach presumably will retain its standing as a phylogenetic and taxonomic backbone in the era of high throughput technologies and full genome sequencing. The rRNA based picture is globally supported by the (small) conserved core of microbial genomes.
No preview · Article · Dec 2011 · Methods in Microbiology
[Show abstract][Hide abstract] ABSTRACT: Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
Full-text · Article · May 2011 · Nature Biotechnology
[Show abstract][Hide abstract] ABSTRACT: This revised road map updates previous outlines of Garrity and Holt (2001) and Garrity et al. (2005) with the description
of additional taxa and new phylogenetic analyses. While the outline/road map seeks to be complete for all taxa validated prior
to July 1, 2006, some taxa described after that date are included.
[Show abstract][Hide abstract] ABSTRACT: We present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
Full-text · Article · Nov 2010 · Nature Precedings
[Show abstract][Hide abstract] ABSTRACT: The " All-Species Living Tree Project" (LTP) provides the scientific community with a useful taxonomic tool consisting of a curated database of type strain sequences, a universal and optimized alignment and a single phylogenetic tree harboring all the type strains of the hitherto classified species . On the website http://www.arb-silva.de/projects/living-tree an update has been regularly maintained by including the 1301 new descriptions that have appeared in the validation and notification lists of the IJSEM journal. The topology of the 16S rRNA-based tree was validated with a detailed comparison against a collection of taxa-specific and broad-range trees made using different approaches, subsets of sequences and alignments. Seven percent of the classified species is still missing, as their type strains do not have a good quality SSU sequence. In addition, a new database of type strains for which adequate 23S rRNA entries existed in public repositories was built. Among the 8602 species with validly published names until February 2010, we were able to find good quality LSU representatives for 792 type strains, whereas around 91% of the complete catalogue still remains unsequenced. Despite the scarce representation of some groups in LSU databases, we have devised a highly optimized alignment and a reliable LSU tree in order to set up a stable phylogenetic starting point for taxonomic purposes. The current release corresponds to the fourth update of the project (LTPs102), and contains additional features which increase usability and compatibility. Use the contact address [email protected]
/* */ to provide additional input for the development of this taxonomic tool.
No preview · Article · Oct 2010 · Systematic and Applied Microbiology
[Show abstract][Hide abstract] ABSTRACT: The order Rickettsiales (Alphaproteobacteria) is a well-known group containing obligate endocellular prokaryotes. The order encompasses three families (Rickettsiaceae, Anaplasmataceae, and Holosporaceae) and a fourth, family-level cluster, which includes only one candidate species, “Candidatus Midichloria mitochondrii,” as well as several unnamed bacterial symbionts. The broad host range exhibited by the members
of the “Candidatus Midichloria” clade suggests their eventual relevance for a better understanding of the evolution of symbiosis and host specificity
of Rickettsiales. In this paper, two new bacteria belonging to the “Candidatus Midichloria” clade, hosted by two different strains of the ciliate protist Euplotes harpa, are described on the basis of ultrastructural observations, comparative 16S rRNA gene sequence analysis, and an estimation
of the percentage of infection. Ultrastructure of these bacteria shows some unusual features: one has an electron-dense cytoplasm,
and the other one lacks a symbiosomal membrane. The latter was up to now considered an exclusive feature of bacteria belonging
to the family Rickettsiaceae. 16S rRNA gene phylogenetic analysis unambiguously places the new bacteria in the “Candidatus Midichloria” clade, although their phylogenetic relationships with other members of the clade are not clearly resolved. This
is the first report of a ciliate-borne bacterium belonging to the “Candidatus Midichloria” clade. On the basis of the data obtained, the two bacteria are proposed as two new candidate genera and species,
“Candidatus Anadelfobacter veles” and “Candidatus Cyrtobacter comes.”
Full-text · Article · Jun 2010 · Applied and Environmental Microbiology
[Show abstract][Hide abstract] ABSTRACT: A Gram-negative, oxidase- and catalase-positive, flagellated, rod-shaped bacterium, designated strain EM 1(T), was isolated from purified water. 16S rRNA gene sequence analysis indicated that the novel strain belonged to the family Oxalobacteraceae within the class Betaproteobacteria; the closest phylogenetic relative was Undibacterium pigrum DSM 19792(T) (96.7 % gene sequence similarity). The new isolate could be distinguished from the type strain of U. pigrum DSM 19792(T) (=CCUG 49009(T)=CIP 109318(T)) and from strain CCUG 49012(T), which has been described as a second genomovar of this species, on the basis of genotypic data and several phenotypic properties. An S-layer was present in the cell envelope in U. pigrum DSM 19792(T), but was absent in strains EM 1(T) and CCUG 49012(T). Test conditions were established that enabled strain CCUG 49012(T) to be distinguished from U. pigrum DSM 19792(T). As found for U. pigrum, the main fatty acids of strains EM 1(T) and CCUG 49012(T) were summed feature 3 (including unsaturated C(16 : 1)ω7c), straight-chain C(16 : 0) and unsaturated C(18 : 1)ω7c (low percentage in strain CCUG 49012(T)), and C(10 : 0) 3-OH was the sole hydroxylated fatty acid. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The polyamine profile was mainly composed of the major compound putrescine and moderate amounts of 2-hydroxyputrescine. In contrast to U. pigrum and strain CCUG 49012(T), where ubiquinone Q8 was reported as the sole quinone component, the quinone system of strain EM 1(T) consisted of ubiquinone Q-8 (64 %) and Q-7 (36 %). The 16S rRNA gene sequence similarity, the polar lipid profile and the absence of C(12)-hydroxylated fatty acids all indicated that strain EM 1(T) was affiliated with the genus Undibacterium. 16S rRNA gene sequence similarity values lower than 97.0 % and several differentiating phenotypic traits demonstrated that strain EM 1(T) represents a novel species for which the name Undibacterium oligocarboniphilum sp. nov. is proposed (type strain EM 1(T)=DSM 21777(T)=CCUG 57265(T)). In addition, based on previously published results and this study, a separate species, Undibacterium parvum sp. nov., is proposed with strain CCUG 49012(T) (=DSM 23061(T)=CIP 109317(T)) as the type strain.
Preview · Article · Mar 2010 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract] ABSTRACT: All taxa recognized within this volume of the rank of genus and above are listed below. Within each classification, the nomenclatural type is listed first followed by the remaining taxa in alphabetical order. Taxa appearing on the Approved Lists are denoted by the superscript AL. Taxa that were otherwise validly published are denoted by the superscript VP. Taxa that have not been validly published are presented in quotations. Taxa which were described after the deadline of July 1, 2006, and are therefore not included in this volume are indicated by an asterisk (*).
[Show abstract][Hide abstract] ABSTRACT: Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.
Full-text · Article · Sep 2009 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract] ABSTRACT: Despite their widespread occurrence in soils, the ecology of Acidobacteria and their response to environmental perturbations due to human activities remain very poorly documented. This study was aimed at assessing changes in the diversity and abundance of Acidobacteria in soils contaminated with 2,4,6-trinitrotoluene (TNT) compared with nonpolluted soils. The analysis of Acidobacteria communities at two sites with long-term and short-term contamination revealed that TNT has a drastic impact on the relative abundance of Acidobacteria in soil bacterial 16S rRNA gene libraries. The disappearance of most Acidobacteria from these soils was concomitant with a shift in Acidobacteria community composition and a loss of diversity, although the extent of diversity erosion depended on the sampling site.
Full-text · Article · Jun 2009 · FEMS Microbiology Letters