38 results on '"Amann, Rudolf"'
Search Results
2. Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains.
- Author
-
Ludwig W, Viver T, Westram R, Francisco Gago J, Bustos-Caparros E, Knittel K, Amann R, and Rossello-Mora R
- Subjects
- RNA, Ribosomal, 16S genetics, Sequence Alignment, Terminology as Topic, Bacteria classification, Phylogeny
- 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/., (Copyright © 2021 Elsevier GmbH. All rights reserved.)
- Published
- 2021
- Full Text
- View/download PDF
3. Taxonomic study of nine new Winogradskyella species occurring in the shallow waters of Helgoland Roads, North Sea. Proposal of Winogradskyella schleiferi sp. nov., Winogradskyella costae sp. nov., Winogradskyella helgolandensis sp. nov., Winogradskyella vidalii sp. nov., Winogradskyella forsetii sp. nov., Winogradskyella ludwigii sp. nov., Winogradskyella ursingii sp. nov., Winogradskyella wichelsiae sp. nov., and Candidatus "Winogradskyella atlantica" sp. nov.
- Author
-
Alejandre-Colomo C, Viver T, Urdiain M, Francis B, Harder J, Kämpfer P, Amann R, and Rosselló-Móra R
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids, Flavobacteriaceae isolation & purification, Metagenome, North Sea, Phytoplankton, Pigmentation, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Flavobacteriaceae classification, Phylogeny, Seawater microbiology
- Abstract
Evaluation of bacterial succession with cultivation-dependent strategies during a spring phytoplankton bloom in the North Sea led to the isolation of 41 strains that affiliated with the genus Winogradskyella. Fifteen of the strains were selected for a taxonomic study after discarding clonal cultures. A thorough phylogenetic, genomic and phenotypic analysis of the isolates indicated that they represented eight new species that coexisted in North Sea waters. Molecular data revealed the existence of an as yet uncultivated novel species recurrently binned from the North Sea metagenomes. The metagenome-assembled genomes (MAGs) of this new Winogradskyella were used to classify it as a new Candidatus species. This study represented a new example of the use of the tandem approach of whole cell mass spectrometry linked to 16S rRNA gene sequencing in order to facilitate the discovery of new taxa by high-throughput cultivation, which increases the probability of finding more than a single isolate for new species. In addition, we demonstrated the reasons for classifying MAGs representing recurrently retrieved heterotrophic species that evade cultivation even after an important high-throughput effort. The taxonomic study resulted in the classification of eight new species and one new Candidatus species of the genus Winogradskyella for which we propose the names W. schleiferi sp. nov., W. costae sp. nov., W. helgolandensis sp. nov., W. vidalii sp. nov., W. forsetii sp. nov., W. ludwigii sp. nov., W. ursingii sp. nov., W. wichelsiae sp. nov., and Candidatus "W. atlantica" sp. nov., Competing Interests: Declaration of Competing Interest The authors report no declarations of interest., (Copyright © 2020 Elsevier GmbH. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
4. 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.
- Author
-
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, and Rossello-Mora R
- Subjects
- Animals, Cephalopoda classification, DNA, Bacterial genetics, Genome, Bacterial genetics, Marine Biology, Mycoplasma cytology, Phenotype, RNA, Ribosomal, 16S genetics, Salinity, Sequence Analysis, DNA, Species Specificity, Temperature, Cephalopoda microbiology, Mycoplasma classification, Mycoplasma physiology, Phylogeny
- 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 PE
T (DSM 105487T , CIP 111404T ) and 5HT (DSM 105,488T , CIP 111405T ), respectively., (Copyright © 2019 Elsevier GmbH. All rights reserved.)- Published
- 2019
- Full Text
- View/download PDF
5. Candidatus Prosiliicoccus vernus, a spring phytoplankton bloom associated member of the Flavobacteriaceae.
- Author
-
Francis TB, Krüger K, Fuchs BM, Teeling H, and Amann RI
- Subjects
- Flavobacteriaceae genetics, Flavobacteriaceae isolation & purification, Metagenome, North Sea, Phytoplankton, RNA, Ribosomal, 16S genetics, Seasons, Seawater microbiology, Eutrophication, Flavobacteriaceae classification, Phylogeny
- Abstract
Microbial degradation of algal biomass following spring phytoplankton blooms has been characterised as a concerted effort among multiple clades of heterotrophic bacteria. Despite their significance to overall carbon turnover, many of these clades have resisted cultivation. One clade known from 16S rRNA gene sequencing surveys at Helgoland in the North Sea, was formerly identified as belonging to the genus Ulvibacter. This clade rapidly responds to algal blooms, transiently making up as much as 20% of the free-living bacterioplankton. Sequence similarity below 95% between the 16S rRNA genes of described Ulvibacter species and those from Helgoland suggest this is a novel genus. Analysis of 40 metagenome assembled genomes (MAGs) derived from samples collected during spring blooms at Helgoland support this conclusion. These MAGs represent three species, only one of which appears to bloom in response to phytoplankton. MAGs with estimated completeness greater than 90% could only be recovered for this abundant species. Additional, less complete, MAGs belonging to all three species were recovered from a mini-metagenome of cells sorted via flow cytometry using the genus specific ULV995 fluorescent rRNA probe. Metabolic reconstruction indicates this highly abundant species most likely degrades proteins and the polysaccharide laminarin. Fluorescence in situ hybridisation showed coccoid cells, with a mean diameter of 0.78mm, with standard deviation of 0.12μm. Based on the phylogenetic and genomic characteristics of this clade, we propose the novel candidate genus Candidatus Prosiliicoccus, and for the most abundant and well characterised of the three species the name Candidatus Prosiliicoccus vernus., (Copyright © 2018 Elsevier GmbH. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
6. 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.
- Author
-
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, and Rosselló-Móra R
- Subjects
- Altitude, Argentina, Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes isolation & purification, CRISPR-Cas Systems, DNA, Bacterial genetics, RNA, Ribosomal, 16S genetics, Rhodopsin genetics, Sequence Analysis, DNA, Type VI Secretion Systems genetics, Water Microbiology, Bacteroidetes classification, Genome, Bacterial, Lakes microbiology, Phylogeny, Salinity
- Abstract
The application of tandem MALDI-TOF MS screening with 16S rRNA gene sequencing of selected isolates has been demonstrated to be an excellent approach for retrieving novelty from large-scale culturing. The application of such methodologies in different hypersaline samples allowed the isolation of the culture-recalcitrant Salinibacter ruber second phylotype (EHB-2) for the first time, as well as a new species recently isolated from the Argentinian Altiplano hypersaline lakes. In this study, the genome sequences of the different species of the phylum Rhodothermaeota were compared and the genetic repertoire along the evolutionary gradient was analyzed together with each intraspecific variability. Altogether, the results indicated an open pan-genome for the family Salinibacteraceae, as well as the codification of relevant traits such as diverse rhodopsin genes, CRISPR-Cas systems and spacers, and one T6SS secretion system that could give ecological advantages to an EHB-2 isolate. For the new Salinibacter species, we propose the name Salinibacter altiplanensis sp. nov. (the designated type strain is AN15
T =CECT 9105T =IBRC-M 11031T )., (Copyright © 2018 Elsevier GmbH. All rights reserved.)- Published
- 2018
- Full Text
- View/download PDF
7. Description of Gramella forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of Gramella gaetbulicola Cho et al. 2011.
- Author
-
Panschin I, Becher M, Verbarg S, Spröer C, Rohde M, Schüler M, Amann RI, Harder J, Tindall BJ, and Hahnke RL
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacteriaceae genetics, Flavobacteriaceae isolation & purification, Germany, North Sea, Nucleic Acid Hybridization, Phosphatidylethanolamines chemistry, Pigmentation, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Flavobacteriaceae classification, Phylogeny, Seawater microbiology
- Abstract
Strain KT0803
T was isolated from coastal eutrophic surface waters of Helgoland Roads near the island of Helgoland, North Sea, Germany. The taxonomic position of the strain, previously known as 'Gramella forsetii' KT0803, was investigated by using a polyphasic approach. The strain was Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, oxidase- and catalase-positive, rod-shaped, motile by gliding and had orange-yellow carotenoid pigments, but was negative for flexirubin-type pigments. It grew optimally at 22-25 °C, at pH 7.5 and at a salinity between 2-3 %. Strain KT0803T hydrolysed the polysaccharides laminarin, alginate, pachyman and starch. The respiratory quinone was MK-6. Polar lipids comprised phosphatidylethanolamine, six unidentified lipids and two unidentified aminolipids. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and iso-C17 : 1ω7c, with smaller amounts of iso-C15 : 0 2-OH, C15 : 0, anteiso-C15 : 0 and C17 : 1ω6c. The G+C content of the genomic DNA was 36.6 mol%. The 16S rRNA gene sequence identities were 98.6 % with Gramella echinicola DSM 19838T , 98.3 % with Gramella gaetbulicola DSM 23082T , 98.1 % with Gramella aestuariivivens BG-MY13T and Gramella aquimixticola HJM-19T , 98.0 % with Gramella lutea YJ019T , 97.9 % with Gramella portivictoriae DSM 23547T and 96.9 % with Gramella marina KMM 6048T . The DNA-DNA relatedness values were <35 % between strain KT0803T and type strains with >98.2 % 16S rRNA gene sequence identity. Based on the chemotaxonomic, phenotypic and genomic characteristics, strain KT0803T has been assigned to the genus Gramella, as Gramella forsetii sp. nov. The type strain is KT0803T (=DSM 17595T =CGMCC 1.15422T ). An emended description of Gramella gaetbulicolaCho et al. 2011 is also proposed.- Published
- 2017
- Full Text
- View/download PDF
8. Allochromatium humboldtianum sp. nov., isolated from soft coastal sediments.
- Author
-
Serrano W, Schrübbers J, Amann R, and Fischer U
- Subjects
- Bacterial Typing Techniques, Bacteriochlorophyll A metabolism, Base Composition, Carotenoids metabolism, Chromatiaceae genetics, Chromatiaceae isolation & purification, DNA, Bacterial genetics, Fatty Acids chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peru, RNA, Ribosomal, 16S genetics, Seawater microbiology, Sequence Analysis, DNA, Chromatiaceae classification, Geologic Sediments microbiology, Phylogeny
- Abstract
A novel purple sulfur bacterium, strain AX1YPE(T), was isolated from marine sediments sampled at 47 m depth in Callao Bay, Perú. Strain AX1YPE grew anaerobically, synthesizing bacteriochlorophyll a and carotenoid pigments of the spirilloxanthin series. Cells were Gram-stain-negative rods and actively motile by a polar flagellum. Strain AX1YPE was able to grow photolithoautotrophically with sulfide and thiosulfate as electron donors. This new phototrophic organism utilized ammonium salt, N2, urea and glutamate as nitrogen sources. Strain AX1YPE had a DNA base composition of 63.9 mol% G+C. Analysis of the 16S rRNA gene sequence indicated that strain AX1YPE clusters in a separate branch within the genus Allochromatium of the family Chromatiaceae. Strain AX1YPE showed 16S rRNA gene sequence similarities of 98.2% with Allochromatium vinosum DSM 180(T) and Allochromatium minutissimum DSM 1376(T), 98.1% with Allochromatium phaeobacterium JA144(T), 97.3% with Allochromatium renukae DSM 18713(T) and 96.8% with Allochromatium warmingiiDSM 173(T). DNA-DNA hybridization values to the type strains of its closest relatives, A. vinosum and A. minutissimum, were 59 and 64%, respectively. The predominant fatty acid of strain AX1YPE(T) was C18 : 1ω;7c and it notably possessed C20 : 1 as a minor component. PCR-based molecular typing (Box A1R and randomly amplified polymorphic DNA) produced a unique banding pattern for strain AX1YPE(T) in comparison with the type strains of A. vinosum and A. minutissimum. Based on data from this polyphasic taxonomic study, which also includes average nucleotide identity comparison of five concatenated housekeeping genes, strain AX1YPE(T) is considered to represent a novel species of the genus Allochromatium for which the name Allochromatiumhumboldtianum sp. nov. is proposed. The type strain is AX1YPE(T) ( = DSM 21881(T) = KCTC 15448(T)).
- Published
- 2015
- Full Text
- View/download PDF
9. Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names.
- Author
-
Yarza P, Spröer C, Swiderski J, Mrotzek N, Spring S, Tindall BJ, Gronow S, Pukall R, Klenk HP, Lang E, Verbarg S, Crouch A, Lilburn T, Beck B, Unosson C, Cardew S, Moore ER, Gomila M, Nakagawa Y, Janssens D, De Vos P, Peiren J, Suttels T, Clermont D, Bizet C, Sakamoto M, Iida T, Kudo T, Kosako Y, Oshida Y, Ohkuma M, R Arahal D, Spieck E, Pommerening Roeser A, Figge M, Park D, Buchanan P, Cifuentes A, Munoz R, Euzéby JP, Schleifer KH, Ludwig W, Amann R, Glöckner FO, and Rosselló-Móra R
- Subjects
- Classification methods, DNA, Bacterial chemistry, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Bacteria classification, Bacteria genetics, DNA, Bacterial genetics, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA
- 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., (Copyright © 2013 Elsevier GmbH. All rights reserved.)
- Published
- 2013
- Full Text
- View/download PDF
10. Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments.
- Author
-
Kubo K, Lloyd KG, F Biddle J, Amann R, Teske A, and Knittel K
- Subjects
- Archaea genetics, DNA, Archaeal genetics, Estuaries, Methane metabolism, Polymerase Chain Reaction, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Sulfates metabolism, Archaea classification, Biodiversity, Geologic Sediments microbiology, Phylogeny
- Abstract
Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12-100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes.
- Published
- 2012
- Full Text
- View/download PDF
11. Conservation of proteobacterial magnetosome genes and structures in an uncultivated member of the deep-branching Nitrospira phylum.
- Author
-
Jogler C, Wanner G, Kolinko S, Niebler M, Amann R, Petersen N, Kube M, Reinhardt R, and Schüler D
- Subjects
- Bacteria ultrastructure, Base Sequence, Magnetosomes ultrastructure, Metagenomics methods, Micromanipulation, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Sequence Analysis, DNA, Sequence Homology, Species Specificity, Bacteria genetics, Conserved Sequence genetics, Evolution, Molecular, Gene Transfer, Horizontal genetics, Magnetosomes genetics, Multigene Family genetics, Phylogeny
- Abstract
Magnetotactic bacteria (MTB) are a phylogenetically diverse group which uses intracellular membrane-enclosed magnetite crystals called magnetosomes for navigation in their aquatic habitats. Although synthesis of these prokaryotic organelles is of broad interdisciplinary interest, its genetic analysis has been restricted to a few closely related members of the Proteobacteria, in which essential functions required for magnetosome formation are encoded within a large genomic magnetosome island. However, because of the lack of cultivated representatives from other phyla, it is unknown whether the evolutionary origin of magnetotaxis is monophyletic, and it has been questioned whether homologous mechanisms and structures are present in unrelated MTB. Here, we present the analysis of the uncultivated "Candidatus Magnetobacterium bavaricum" from the deep branching Nitrospira phylum by combining micromanipulation and whole genome amplification (WGA) with metagenomics. Target-specific sequences obtained by WGA of cells, which were magnetically collected and individually sorted from sediment samples, were used for PCR screening of metagenomic libraries. This led to the identification of a genomic cluster containing several putative magnetosome genes with homology to those in Proteobacteria. A variety of advanced electron microscopic imaging tools revealed a complex cell envelope and an intricate magnetosome architecture. The presence of magnetosome membranes as well as cytoskeletal magnetosome filaments suggests a similar mechanism of magnetosome formation in "Cand. M. bavaricum" as in Proteobacteria. Altogether, our findings suggest a monophyletic origin of magnetotaxis, and relevant genes were likely transferred horizontally between Proteobacteria and representatives of the Nitrospira phylum.
- Published
- 2011
- Full Text
- View/download PDF
12. Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses.
- Author
-
Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Glöckner FO, and Rosselló-Móra R
- Subjects
- Archaea genetics, Bacteria genetics, Archaea classification, Bacteria classification, Databases, Genetic, Phylogeny, RNA, Ribosomal, 16S genetics, RNA, Ribosomal, 23S genetics
- 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 living-tree@arb-silva.de to provide additional input for the development of this taxonomic tool., (Copyright © 2010 Elsevier GmbH. All rights reserved.)
- Published
- 2010
- Full Text
- View/download PDF
13. Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade.
- Author
-
Schreiber L, Holler T, Knittel K, Meyerdierks A, and Amann R
- Subjects
- Anaerobiosis, DNA, Bacterial genetics, Deltaproteobacteria classification, Deltaproteobacteria genetics, Deltaproteobacteria metabolism, Gene Library, Geologic Sediments microbiology, In Situ Hybridization, Fluorescence, Molecular Sequence Data, Oxidation-Reduction, RNA, Ribosomal, 16S genetics, Sulfur-Reducing Bacteria genetics, Sulfur-Reducing Bacteria metabolism, Symbiosis, Methane metabolism, Microbial Consortia, Phylogeny, Sulfur-Reducing Bacteria classification
- Abstract
The anaerobic oxidation of methane (AOM) with sulfate as terminal electron acceptor is mediated by consortia of methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Whereas three clades of ANME have been repeatedly studied with respect to phylogeny, key genes and genomic capabilities, little is known about their sulfate-reducing partner. In order to identify the partner of anaerobic methanotrophs of the ANME-2 clade, bacterial 16S rRNA gene libraries were constructed from cultures highly enriched for ANME-2a and ANME-2c in consortia with Deltaproteobacteria of the Desulfosarcina/Desulfococcus group (DSS). Phylogenetic analysis of those and publicly available sequences from AOM sites supported the hypothesis by Knittel and colleagues that the DSS partner belongs to the diverse SEEP-SRB1 cluster. Six subclusters of SEEP-SRB1, SEEP-SRB1a to SEEP-SRB1f, were proposed and specific oligonucleotide probes were designed. Using fluorescence in situ hybridization on samples from six different AOM sites, SEEP-SRB1a was identified as sulfate-reducing partner in up to 95% of total ANME-2 consortia. SEEP-SRB1a cells exhibited a rod-shaped, vibrioid, or coccoid morphology and were found to be associated with subgroups ANME-2a and ANME-2c. Moreover, SEEP-SRB1a was also detected in 8% to 23% of ANME-3 consortia in Haakon Mosby Mud Volcano sediments, previously described to be predominantly associated with SRB of the Desulfobulbus group. SEEP-SRB1a contributed to only 0.3% to 0.7% of all single cells in almost all samples indicating that these bacteria are highly adapted to a symbiotic relationship with ANME-2., (© 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.)
- Published
- 2010
- Full Text
- View/download PDF
14. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.
- Author
-
Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, and Rosselló-Móra R
- Subjects
- Archaea genetics, Bacteria genetics, Computational Biology, Internet, RNA, Archaeal genetics, RNA, Bacterial genetics, Ribotyping, Sequence Alignment, Sequence Analysis, RNA, Archaea classification, Bacteria classification, Databases, Nucleic Acid, Phylogeny, RNA, Ribosomal, 16S genetics
- Abstract
The signing authors together with the journal Systematic and Applied Microbiology (SAM) have started an ambitious project that has been conceived to provide a useful tool especially for the scientific microbial taxonomist community. The aim of what we have called "The All-Species Living Tree" is to reconstruct a single 16S rRNA tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria. This tree is to be regularly updated by adding the species with validly published names that appear monthly in the Validation and Notification lists of the International Journal of Systematic and Evolutionary Microbiology. For this purpose, the SAM executive editors, together with the responsible teams of the ARB, SILVA, and LPSN projects (www.arb-home.de, www.arb-silva.de, and www.bacterio.cict.fr, respectively), have prepared a 16S rRNA database containing over 6700 sequences, each of which represents a single type strain of a classified species up to 31 December 2007. The selection of sequences had to be undertaken manually due to a high error rate in the names and information fields provided for the publicly deposited entries. In addition, from among the often occurring multiple entries for a single type strain, the best-quality sequence was selected for the project. The living tree database that SAM now provides contains corrected entries and the best-quality sequences with a manually checked alignment. The tree reconstruction has been performed by using the maximum likelihood algorithm RAxML. The tree provided in the first release is a result of the calculation of a single dataset containing 9975 single entries, 6728 corresponding to type strain gene sequences, as well as 3247 additional high-fquality sequences to give robustness to the reconstruction. Trees are dynamic structures that change on the basis of the quality and availability of the data used for their calculation. Therefore, the addition of new type strain sequences in further subsequent releases may help to resolve certain branching orders that appear ambiguous in this first release. On the web sites: www.elsevier.de/syapm and www.arb-silva.de/living-tree, the All-Species Living Tree team will release a regularly updated database compatible with the ARB software environment containing the whole 16S rRNA dataset used to reconstruct "The All-Species Living Tree". As a result, the latest reconstructed phylogeny will be provided. In addition to the ARB file, a readable multi-FASTA universal sequence editor file with the complete alignment will be provided for those not using ARB. There is also a complete set of supplementary tables and figures illustrating the selection procedure and its outcome. It is expected that the All-Species Living Tree will help to improve future classification efforts by simplifying the selection of the correct type strain sequences. For queries, information updates, remarks on the dataset or tree reconstructions shown, a contact email address has been created (living-tree@arb-silva.de). This provides an entry point for anyone from the scientific community to provide additional input for the construction and improvement of the first tree compiling all sequenced type strains of all prokaryotic species for which names had been validly published.
- Published
- 2008
- Full Text
- View/download PDF
15. Metagenomic approach to the study of halophages: the environmental halophage 1.
- Author
-
Santos F, Meyerdierks A, Peña A, Rosselló-Mora R, Amann R, and Antón J
- Subjects
- Bacteriophages ultrastructure, Base Composition, Base Sequence, Blotting, Southern, Cluster Analysis, Codon genetics, DNA Primers genetics, Genome Components, Microscopy, Electron, Transmission, Molecular Sequence Data, Restriction Mapping, Seawater virology, Sequence Analysis, DNA, Spain, Bacteriophages genetics, Biodiversity, Genome, Viral genetics, Halobacteriaceae virology, Phylogeny, Seawater microbiology, Water Microbiology
- Abstract
Hypersaline environments, such as crystallizer ponds of solar salterns, show one of the highest concentration of viruses reported for aquatic systems. All the halophages characterized so far are isolates obtained by cultivation from described haloarchaeal species that have only low abundance in the environment. We employed a culture-independent metagenomic approach to analyse for the first time complete genomes in the halophage community and explored the in situ diversity by transmission electron microscopy and pulsed-field gel electrophoresis. We report the genomic sequence of a not yet isolated halophage (named as environmental halophage 1 'EHP-1') whose DNA was obtained from crystallizer samples with a salinity of 31%. The sequenced genome has a size of 35 kb and a G + C content around 51%. The G + C content is lower than that of previously characterized halophages. However, G + C content and codon usage in EHP-1 are similar to the recently cultivated and sequenced Haloquadratum walsbyi, the major prokaryotic component in solar salterns around the world. Forty open reading frames have been predicted, including genes that putatively code for proteins involved in DNA replication (ribonucleotide reductases, thymidylate kinase) normally found in lytic viruses.
- Published
- 2007
- Full Text
- View/download PDF
16. Phylogenetic position of Salinibacter ruber based on concatenated protein alignments.
- Author
-
Soria-Carrasco V, Valens-Vadell M, Peña A, Antón J, Amann R, Castresana J, and Rosselló-Mora R
- Subjects
- Algorithms, Bacteroidetes genetics, DNA, Ribosomal genetics, Evolution, Molecular, Likelihood Functions, RNA, Ribosomal, 16S genetics, Sequence Alignment, Sequence Analysis, Protein, Bacterial Proteins genetics, Bacteroidetes classification, Phylogeny
- Abstract
A total of 22 genes from the genome of Salinibacter ruber strain M31 were selected in order to study the phylogenetic position of this species based on protein alignments. The selection of the genes was based on their essential function for the organism, dispersion within the genome, and sufficient informative length of the final alignment. For each gene, an individual phylogenetic analysis was performed and compared with the resulting tree based on the concatenation of the 22 genes, which rendered a single alignment of 10,757 homologous positions. In addition to the manually chosen genes, an automatically selected data set of 74 orthologous genes was used to reconstruct a tree based on 17,149 homologous positions. Although single genes supported different topologies, the tree topology of both concatenated data sets was shown to be identical to that previously observed based on small subunit (SSU) rRNA gene analysis, in which S. ruber was placed together with Bacteroidetes. In both concatenated data sets the bootstrap was very high, but an analysis with a gradually lower number of genes indicated that the bootstrap was greatly reduced with less than 12 genes. The results indicate that tree reconstructions based on concatenating large numbers of protein coding genes seem to produce tree topologies with similar resolution to that of the single 16S rRNA gene trees. For classification purposes, 16S rRNA gene analysis may remain as the most pragmatic approach to infer genealogic relationships.
- Published
- 2007
- Full Text
- View/download PDF
17. Phylogeny of 16S rRNA, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5'-phosphosulfate reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (oligochaeta) from Bermuda and the Bahamas.
- Author
-
Blazejak A, Kuever J, Erséus C, Amann R, and Dubilier N
- Subjects
- Adenosine Phosphosulfate metabolism, Alphaproteobacteria enzymology, Alphaproteobacteria genetics, Animals, Gammaproteobacteria enzymology, Gammaproteobacteria genetics, Molecular Sequence Data, Oxidoreductases genetics, Ribulose-Bisphosphate Carboxylase genetics, Sequence Analysis, DNA, Alphaproteobacteria classification, Gammaproteobacteria classification, Oligochaeta microbiology, Phylogeny, RNA, Ribosomal, 16S genetics, Symbiosis
- Abstract
Gutless oligochaetes are small marine worms that live in obligate associations with bacterial endosymbionts. While symbionts from several host species belonging to the genus Olavius have been described, little is known of the symbionts from the host genus Inanidrilus. In this study, the diversity of bacterial endosymbionts in Inanidrilus leukodermatus from Bermuda and Inanidrilus makropetalos from the Bahamas was investigated using comparative sequence analysis of the 16S rRNA gene and fluorescence in situ hybridization. As in all other gutless oligochaetes examined to date, I. leukodermatus and I. makropetalos harbor large, oval bacteria identified as Gamma 1 symbionts. The presence of genes coding for ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) and adenosine 5'-phosphosulfate reductase (aprA) supports earlier studies indicating that these symbionts are chemoautotrophic sulfur oxidizers. Alphaproteobacteria, previously identified only in the gutless oligochaete Olavius loisae from the southwest Pacific Ocean, coexist with the Gamma 1 symbionts in both I. leukodermatus and I. makropetalos, with the former harboring four and the latter two alphaproteobacterial phylotypes. The presence of these symbionts in hosts from such geographically distant oceans as the Atlantic and Pacific suggests that symbioses with alphaproteobacterial symbionts may be widespread in gutless oligochaetes. The high phylogenetic diversity of bacterial endosymbionts in two species of the genus Inanidrilus, previously known only from members of the genus Olavius, shows that the stable coexistence of multiple symbionts is a common feature in gutless oligochaetes.
- Published
- 2006
- Full Text
- View/download PDF
18. Archaea-like genes for C1-transfer enzymes in Planctomycetes: phylogenetic implications of their unexpected presence in this phylum.
- Author
-
Bauer M, Lombardot T, Teeling H, Ward NL, Amann RI, and Glöckner FO
- Subjects
- Amidohydrolases chemistry, Amidohydrolases genetics, Amino Acid Sequence, Catalysis, Conserved Sequence, Genome, Bacterial, Methylobacterium extorquens chemistry, Methylobacterium extorquens genetics, Molecular Sequence Data, Sequence Alignment, Archaea enzymology, Archaea genetics, Bacteria enzymology, Bacteria genetics, Genes, Archaeal genetics, Genes, Bacterial genetics, Phylogeny
- Abstract
The unexpected presence of archaea-like genes for tetrahydromethanopterin (H4MPT)-dependent enzymes in the completely sequence geiome of the aerobic marine planctomycete Pirellula sp. strain 1 ("Rhodopirellula baltica") and in the currently sequenced genome of the aerobic freshwater planctomycete Gemmata obscuriglobus strain UQM2246 revives the discussion on the origin of these genes in the bacterial domain. We compared the genomic arrangement of these genes in Planctomyetes and methylotrophic proteobacteria and perormed a phylogenetic analysis of the encoded protein sequences to address the question whether the genes have been present in the common ancestor of Bacteria and Archaea or were transferred laterally from the archaeal to the bacterial domain and herein. Although this question could not be solved using the data presented here, some constraints on the evolution of the genes involved in archaeal and )acterial H4MPT-dependent C1-transfer may be proposed: (i) lateral gene transfer (LGT) from Archea to a common ancestor of Proteobacteria and Planctomycetes seems more likely than the presence of the genes in the common ancestor of Bacteria and Archaea; (ii) a single event of interdomain LGT can e favored over two independent events; and (iii) the irchacal donor of the genes might have been a repesentative of the Methanosarcinales. In the bacterial domain, the acquired genes evolved according to distinct environmental and metabolic constraints, reflected by specific rearrangements of gene order, gene recruitment, and gene duplication, with subsequent functional specialization. During the course of evolution, genes were lost from some planctomycete genomes or replaced by orthologous genes from proteobacterial lineages.
- Published
- 2004
- Full Text
- View/download PDF
19. Roadmap for naming uncultivated Archaea and Bacteria
- Author
-
Murray, Alison E, Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T, Lane, Christopher E, Papke, R Thane, Parks, Donovan H, Rossello-Mora, Ramon, Stott, Matthew B, Sutcliffe, Iain C, Thrash, J Cameron, Venter, Stephanus N, Whitman, William B, Acinas, Silvia G, Amann, Rudolf I, Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J, Barco, Roman A, Bode, Helge B, Boyd, Eric S, Brady, Carrie L, Carini, Paul, Chain, Patrick SG, Colman, Daniel R, DeAngelis, Kristen M, de los Rios, Maria Asuncion, Estrada-de los Santos, Paulina, Dunlap, Christopher A, Eisen, Jonathan A, Emerson, David, Ettema, Thijs JG, Eveillard, Damien, Girguis, Peter R, Hentschel, Ute, Hollibaugh, James T, Hug, Laura A, Inskeep, William P, Ivanova, Elena P, Klenk, Hans-Peter, Li, Wen-Jun, Lloyd, Karen G, Löffler, Frank E, Makhalanyane, Thulani P, Moser, Duane P, Nunoura, Takuro, Palmer, Marike, Parro, Victor, Pedrós-Alió, Carlos, Probst, Alexander J, Smits, Theo HM, Steen, Andrew D, Steenkamp, Emma T, Spang, Anja, Stewart, Frank J, Tiedje, James M, Vandamme, Peter, Wagner, Michael, Wang, Feng-Ping, Yarza, Pablo, Hedlund, Brian P, and Reysenbach, Anna-Louise
- Subjects
Microbiology ,Biological Sciences ,Ecology ,Archaea ,Bacteria ,DNA ,Bacterial ,Metagenome ,Phylogeny ,Prokaryotic Cells ,Sequence Analysis ,DNA ,Terminology as Topic ,Medical Microbiology - 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.
- Published
- 2020
20. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.
- Author
-
Kyrpides, Nikos C, Hugenholtz, Philip, Eisen, Jonathan A, Woyke, Tanja, Göker, Markus, Parker, Charles T, Amann, Rudolf, Beck, Brian J, Chain, Patrick SG, Chun, Jongsik, Colwell, Rita R, Danchin, Antoine, Dawyndt, Peter, Dedeurwaerdere, Tom, DeLong, Edward F, Detter, John C, De Vos, Paul, Donohue, Timothy J, Dong, Xiu-Zhu, Ehrlich, Dusko S, Fraser, Claire, Gibbs, Richard, Gilbert, Jack, Gilna, Paul, Glöckner, Frank Oliver, Jansson, Janet K, Keasling, Jay D, Knight, Rob, Labeda, David, Lapidus, Alla, Lee, Jung-Sook, Li, Wen-Jun, Ma, Juncai, Markowitz, Victor, Moore, Edward RB, Morrison, Mark, Meyer, Folker, Nelson, Karen E, Ohkuma, Moriya, Ouzounis, Christos A, Pace, Norman, Parkhill, Julian, Qin, Nan, Rossello-Mora, Ramon, Sikorski, Johannes, Smith, David, Sogin, Mitch, Stevens, Rick, Stingl, Uli, Suzuki, Ken-Ichiro, Taylor, Dorothea, Tiedje, Jim M, Tindall, Brian, Wagner, Michael, Weinstock, George, Weissenbach, Jean, White, Owen, Wang, Jun, Zhang, Lixin, Zhou, Yu-Guang, Field, Dawn, Whitman, William B, Garrity, George M, and Klenk, Hans-Peter
- Subjects
Bacteria ,Archaea ,Sequence Analysis ,DNA ,Genomics ,Phylogeny ,Genome ,Bacterial ,Genome ,Archaeal ,Databases ,Genetic ,Biotechnology ,Genetics ,Human Genome ,Developmental Biology ,Biological Sciences ,Agricultural and Veterinary Sciences ,Medical and Health Sciences - Abstract
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.
- Published
- 2014
21. rRNA based identification and detection systems for rhizobia and other bacteria
- Author
-
Ludwig, Wolfgang, Amann, Rudolf, Martinez-Romero, Esperanza, Schönhuber, Wilhelm, Bauer, Stephan, Neef, Alexander, Schleifer, Karl-Heinz, Hardarson, G., editor, and Broughton, W. J., editor
- Published
- 1998
- Full Text
- View/download PDF
22. Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria.
- Author
-
Salmana, Verena, Amann, Rudolf, Shub, David A., and Schulz-Vogt, Heide N.
- Subjects
- *
PHYLOGENY , *ORGANISMS , *HETEROGENEITY , *RNA , *IN situ hybridization , *RIBOSOMES , *SULFUR bacteria - Abstract
The gene encoding the small subunit rRNA serves as a prominent tool for the phylogenetic analysis and classification of Bacteria and Archaea owing to its high degree of conservation and its fundamental function in living organisms. Here we show that the 16S rRNA genes of not-yet-cultivated large sulfur bacteria, among them the largest known bacterium Thiomargarita namibiensis, regularly contain numerous self-splicing introns of variable length. The 16S rRNA genes can thus be enlarged to up to 3.5 kb. Remarkably, introns have never been identified in bacterial 16S rRNA genes before, although they are the most frequently sequenced genes today. This may be caused in part by a bias during the PCR amplification step that discriminates against longer homologs, as we show experimentally. Such length heterogeneity of 16S rRNA genes has so far never been considered when constructing 16S rRNA-based clone libraries, even though an elongation of rRNA genes due to intervening sequences has been reported previously. The detection of elongated 16S rRNA genes has profound implications for common methods in molecular ecology and may cause systematic biases in several techniques. In this study, catalyzed reporter deposition-fluorescence in situ hybridization on both ribosomes and rRNA precursor molecules as well as in vitro splicing experiments were performed and confirmed self-splicing of the introns. Accordingly, the introns do not inhibit the formation of functional ribosomes. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
23. Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean.
- Author
-
Gómez-Pereira, Paola R., Schüler, Margarete, Fuchs, Bernhard M., Bennke, Christin, Teeling, Hanno, Waldmann, Jost, Richter, Michael, Barbe, Valérie, Bataille, Elodie, Glöckner, Frank Oliver, and Amann, Rudolf
- Subjects
BACTEROIDES ,MARINE microbiology ,BIODEGRADATION ,BACTERIAL genetics ,PHYLOGENY ,BIOMARKERS ,PHYTOPLANKTON - Abstract
Summary Bacteroidetes are widespread in marine systems where they play a crucial role in organic matter degradation. Whole genome analysis of several strains has revealed a broad glycolytic and proteolytic potential. In this study, we used a targeted metagenomic approach to investigate the degradation capabilities of distinct Bacteroidetes clades from two contrasting regions of the North Atlantic Ocean, the Polar Biome (BPLR) and the North Atlantic Subtropical (NAST). We present here the analysis of 76 Bacteroidetes fosmids, of which 28 encode the 16S rRNA gene as phylogenetic marker, and their comparison to complete Bacteroidetes genomes. Almost all of the 16S rRNA harbouring fosmids belonged to clades that we previously identified in BPLR and NAST. The majority of sequenced fosmids could be assigned to Bacteroidetes affiliated with the class Flavobacteria. We also present novel genomic information on the classes Cytophagia and Sphingobacteria, suggesting a capability of the latter for attachment to algal surfaces. In our fosmid set we identified a larger potential for polysaccharide degradation and cell surface attachment in the phytoplankton-rich BPLR. Particularly, two flavobacterial fosmids, one affiliated with the genus Polaribacter, showed a whole armoury of enzymes that likely function in degradation of sulfated polysaccharides known to be major constituents of phytoplankton cell walls. Genes involved in protein and peptidoglycan degradation, although present in both fosmid sets, seemed to have a slight preponderance in NAST. This study provides support for the hypothesis of a distinct specialization among marine Bacteroidetes for the degradation of certain types of polymers. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
24. A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria.
- Author
-
Salman, Verena, Amann, Rudolf, Girnth, Anne-Christin, Polerecky, Lubos, Bailey, Jake V., Høgslund, Signe, Jessen, Gerdhard, Pantoja, Silvio, and Schulz-Vogt, Heide N.
- Subjects
SULFUR bacteria ,BACTERIA morphology ,MICROBIOLOGY ,PHYLOGENY ,NUCLEOTIDE sequence ,RNA - Abstract
Abstract: The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properties, leading to polyphyletic taxa. We performed sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, together with detailed morphological analysis of hand-picked individuals of novel non-filamentous as well as known filamentous large sulfur bacteria, including the hitherto only partially sequenced species Thiomargarita namibiensis, Thioploca araucae and Thioploca chileae. Based on 128 nearly full-length 16S rRNA-ITS sequences, we propose the retention of the family Beggiatoaceae for the genera closely related to Beggiatoa, as opposed to the recently suggested fusion of all colorless sulfur bacteria into one family, the Thiotrichaceae. Furthermore, we propose the addition of nine Candidatus species along with seven new Candidatus genera to the family Beggiatoaceae. The extended family Beggiatoaceae thus remains monophyletic and is phylogenetically clearly separated from other related families. [Copyright &y& Elsevier]
- Published
- 2011
- Full Text
- View/download PDF
25. GeneFISH - an in situ technique for linking gene presence and cell identity in environmental microorganisms C. Moraru et al. GeneFISH in environmental microorganisms.
- Author
-
Moraru, Cristina, Lam, Phyllis, Fuchs, Bernhard M., Kuypers, Marcel M. M., and Amann, Rudolf
- Subjects
MICROORGANISMS ,SEQUENCE alignment ,PHYLOGENY ,RNA ,GENES - Abstract
Our knowledge concerning the metabolic potentials of as yet to be cultured microorganisms has increased tremendously with the advance of sequencing technologies and the consequent discoveries of novel genes. On the other hand, it is often difficult to reliably assign a particular gene to a phylogenetic clade, because these sequences are usually found on genomic fragments that carry no direct marker of cell identity, such as rRNA genes. Therefore, the aim of the present study was to develop geneFISH - a protocol for linking gene presence with cell identity in environmental samples, the signals of which can be visualized at a single cell level. This protocol combines rRNA-targeted catalysed reporter deposition - fluorescence in situ hybridization and in situ gene detection. To test the protocol, it was applied to seawater samples from the Benguela upwelling system. For gene detection, a polynucleotide probe mix was used, which was designed based on crenarchaeotal amoA clone libraries prepared from each seawater sample. Each probe in the mix was selected to bind to targets with up to 5% mismatches. To determine the hybridization parameters, the T of probes, targets and hybrids was estimated based on theoretical calculations and in vitro measurements. It was shown that at least 30%, but potentially the majority of the Crenarchaeota present in these samples harboured the amoA gene and were therefore likely to be catalysing the oxidation of ammonia. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
26. Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria.
- Author
-
Yan, Shi, Fuchs, Bernhard M., Lenk, Sabine, Harder, Jens, Wulf, Jörg, Jiao, Nian-Zhi, and Amann, Rudolf
- Subjects
BIOGEOGRAPHY ,PHYLOGENY ,BACTERIAL ecology ,PHOTOSYNTHETIC bacteria ,NUCLEOTIDE sequence ,FLUORESCENCE in situ hybridization - Abstract
Abstract: The phylogeny, abundance, and biogeography of the NOR5/OM60 clade was investigated. This clade includes “Congregibacter litoralis” strain KT71, the first cultured representative of marine aerobic anoxygenic phototrophic Gammaproteobacteria. More than 500 16S rRNA sequences affiliated with this clade were retrieved from public databases. By comparative sequence analysis, 13 subclades could be identified, some of which are currently restricted to discrete habitat types. Almost all sequences in the largest subclade NOR5-1 and related subclade NOR5-4 originated from marine surface water samples. Overall, most of the NOR5/OM60 sequences were retrieved from marine coastal settings, whereas there were fewer from open-ocean surface waters, deep-sea sediment, freshwater, saline lakes and soil. The abundance of members of the NOR5/OM60 clade in various marine sites was determined by fluorescence in situ hybridization using a newly designed and optimized probe set. Relative abundances in coastal marine waters off Namibia and the Yangtze estuary were up to 3% of the total 4′,6-diamidino-2-phenylindole (DAPI) counts, and in the German Bight off Helgoland the abundance was even up to 7%. In an open-ocean North Atlantic transect, between Iceland and the Azores, the NOR5/OM60 group was much less abundant (0.1–0.5%). Interestingly, the surface layer of North Sea intertidal sediments was very rich in NOR5/OM60, with absolute numbers >10
8 cellscm−3 (or 4% of the total DAPI). An analysis of the frequencies of NOR5/OM60 16S rRNA genes in the Global Ocean Survey datasets provided further support for a marine cosmopolitan occurrence of NOR5/OM60, and a clear preference for coastal marine waters. [Copyright &y& Elsevier]- Published
- 2009
- Full Text
- View/download PDF
27. A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones.
- Author
-
Woebken, Dagmar, Lam, Phyllis, Kuypers, Marcel M. M., Naqvi, S. Wajih A., Kartal, Boran, Strous, Marc, Jetten, Mike S. M., Fuchs, Bernhard M., and Amann, Rudolf
- Subjects
OXIDATION ,MARINE bacteria ,GENETIC markers ,PHYLOGENY ,MICROORGANISM populations ,NITRIFICATION ,NITROGEN ,MICROBIOLOGY - Abstract
The anaerobic oxidation of ammonium (anammox) contributes significantly to the global loss of fixed nitrogen and is carried out by a deep branching monophyletic group of bacteria within the phylum Planctomycetes. Various studies have implicated anammox to be the most important process responsible for the nitrogen loss in the marine oxygen minimum zones (OMZs) with a low diversity of marine anammox bacteria. This comprehensive study investigated the anammox bacteria in the suboxic zone of the Black Sea and in three major OMZs (off Namibia, Peru and in the Arabian Sea). The diversity and population composition of anammox bacteria were investigated by both, the 16S rRNA gene sequences and the 16S-23S rRNA internal transcribed spacer (ITS). Our results showed that the anammox bacterial sequences of the investigated samples were all closely related to the Candidatus Scalindua genus. However, a greater microdiversity of marine anammox bacteria than previously assumed was observed. Both phylogenetic markers supported the classification of all sequences in two distinct anammox bacterial phylotypes: Candidatus Scalindua clades 1 and 2. Scalindua 1 could be further divided into four distinct clusters, all comprised of sequences from either the Namibian or the Peruvian OMZ. Scalindua 2 consisted of sequences from the Arabian Sea and the Peruvian OMZ and included one previously published 16S rRNA gene sequence from Lake Tanganyika and one from South China Sea sediment (97.9–99.4% sequence identity). This cluster showed only ≤ 97% sequence identity to other known Candidatus Scalindua species. Based on 16S rRNA gene and ITS sequences we propose that the anammox bacteria of Scalindua clade 2 represent a novel anammox bacterial species, for which the name Candidatus Scalindua arabica is proposed. As sequences of this new cluster were found in the Arabian Sea, the Peruvian OMZ, in Lake Tanganyika and in South China sediment, we assume a global distribution of Candidatus Scalindua arabica as it is observed for Candidatus Scalindua sorokinii/brodae (or Scalindua clade 1). [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
28. Archaea-Like Genes for C1-Transfer EnzymesinPlanctomycetes: Phylogenetic Implications of Their Unexpected Presence in This Phylum.
- Author
-
Bauer, Margarete, Lombardot, Thierry, Teeling, Hanno, Ward, Naomi L., Amann, Rudolf I., and Glöckner, Frank O.
- Subjects
ARCHAEBACTERIA ,PHYLOGENY ,BIOLOGY ,MOLECULAR evolution ,ORIGIN of life ,EVOLUTIONARY theories ,MOLECULAR biology - Abstract
The unexpected presence of archaea-like genes for tetrahydromethanopterin (H
4 MPT)-dependent enzymes in the completely sequenced genome of the aerobic marine planctomycetePirellulasp. strain 1 (“Rhodopirellula baltica”) and in the currently sequenced genome of the aerobic freshwater planctomyceteGemmata obscuriglobusstrain UQM2246 revives the discussion on the origin of these genes in the bacterial domain. We compared the genomic arrangement of these genes inPlanctomycetesand methylotrophic proteobacteria and performed a phylogenetic analysis of the encoded protein sequences to address the question whether the genes have been present in the common ancestor ofBacteriaandArchaeaor were transferred laterally from the archaeal to the bacterial domain and therein. Although this question could not be solved using the data presented here, some constraints on the evolution of the genes involved in archaeal and bacterial H4 MPT-dependent C1 -transfer may be proposed: (i) lateral gene transfer (LGT) fromArchaeato a common ancestor ofProteobacteriaandPlanctomycetesseems more likely than the presence of the genes in the common ancestor ofBacteriaandArchaea; (ii) a single event of interdomain LGT can be favored over two independent events; and (iii) the archaeal donor of the genes might have been a representative of theMethanosarcinales. In the bacterial domain, the acquired genes evolved according to distinct environmental and metabolic constraints, reflected by specific rearrangements of gene order, gene recruitment, and gene duplication, with subsequent functional specialization. During the course of evolution, genes were lost from some planctomycete genomes or replaced by orthologous genes from proteobacterial lineages. [ABSTRACT FROM AUTHOR]- Published
- 2004
- Full Text
- View/download PDF
29. Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages.
- Author
-
Warnecke, Falk, Amann, Rudolf, and Pernthaler, Jakob
- Subjects
- *
BACTERIAL genetics , *GENES , *FRESHWATER ecology , *MARINE ecology , *PHYLOGENY , *PLANKTON - Abstract
We analysed the phylogenetic relatedness of 16S rRNA genes from freshwater bacteria affiliated with the class Actinobacteria. A polymerase chain reaction assay was developed to identify reliably rare Actinobacteria-related inserts within 16S rRNA gene clone libraries. In 18 libraries constructed from seven freshwater systems, altogether 63 actinobacterial sequence types were collected from a total of > 1800 clones. Sixty of the newly obtained sequences grouped within four distinct phylogenetic lineages. They constitute approximately 75% of the nearly complete sequences within these clusters that are presently available. A comparison with > 300 sequences from various soil habitats revealed that two of these monophyletic actinobacterial clades (acI and acII) almost exclusively harbour 16S rRNA sequence types from freshwaters and estuaries. This may indicate that such bacteria are not inoculated to freshwaters from terrestrial sources, but are autochthonous components of freshwater microbial assemblages. In contrast, sequence types from freshwaters, marine sediments and soils were clearly mixed in another of the actinobacterial lineages (acIV). Sequence divergence within acIV was the highest of all four lineages (88% minimum similarity), which potentially reflects its radiation across several habitat types. Within the freshwater lineages, groups of essentially identical sequence types were retrieved from geographically distant aquatic systems with strikingly different hydrological and limnological characteristics. This points to the necessity to investigate genotypic variability, in situ abundances and activities of these Actinobacteria in freshwater plankton in greater detail by cultivation-independent techniques. [ABSTRACT FROM AUTHOR]
- Published
- 2004
- Full Text
- View/download PDF
30. Phylogeny and distribution of nitrate-storing Beggiatoa spp. in coastal marine sediments.
- Author
-
Mußmann, Marc, Schulz, Heide N., Strotmann, Bettina, Kjær, Thomas, Nielsen, Lars P., Rosselló-Mora, Ramon A., Amann, Rudolf I., and Jørgensen, Bo Barker
- Subjects
MARINE bacteria ,PHYLOGENY - Abstract
Summary Filamentous sulphide-oxidizing Beggiatoa spp. often occur in large numbers in the coastal seabed without forming visible mats on the sediment surface. We studied the diversity, population structure and the nitrate-storing capability of such bacteria in the Danish Limfjorden and the German Wadden Sea. Their distribution was compared to the vertical gradients of O
2 , NO3 – and H2 S as measured by microsensors. The main Beggiatoa spp. populations occurred in a 0.5–3 cm thick intermediate zone, below the depth of oxygen and nitrate penetration but above the zone of free sulphide. The Beggiatoa spp. filaments were found to store nitrate, presumably in liquid vacuoles up to a concentration of 370 mM NO3 – , similar to the related large marine sulphur bacteria, Thioploca and Thiomargarita . The observations indicate that marine Beggiatoa spp. can live anaerobically and conserve energy by coupling sulphide oxidation with the reduction of nitrate to dinitrogen and/or ammonia. Calculations of the diffusive nitrate flux and the potential sulphide oxidation by Beggiatoa spp. show that the bacteria may play a critical role for the sulphur cycling and the nitrogen balance in these coastal environments. 16S rDNA sequence analysis shows a large diversity of these uncultured, nitrate-storing Beggiatoa spp. Smaller (9–17 µm wide) and larger (33–40 µm wide) Beggiatoa spp. represent novel phylogenetic clusters distinct from previously sequenced, large marine Beggiatoa spp. and Thioploca spp. Fluorescence in situ hybridization (FISH) of the natural Beggiatoa spp. populations showed that filament width is a conservative character of each phylogenetic species but a given filament width may represent multiple phylogenetic species in a mixed population. [ABSTRACT FROM AUTHOR]- Published
- 2003
- Full Text
- View/download PDF
31. Corrigendum to “Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov” [Syst. Appl. Microbiol. 39 (7) (2016) 491–492].
- Author
-
Munoz, Raul, Rosselló-Móra, Ramon, and Amann, Rudolf
- Subjects
BACTEROIDETES ,PHYLOGENY ,RHODOBACTER - Published
- 2017
- Full Text
- View/download PDF
32. Coexistence of Bacterial Sulfide Oxidizers, Sulfate Reducers, and Spirochetes in a Gutless Worm (Oligochaeta) from the Peru Margin.
- Author
-
Blazejak, Anna, Erséus, Christer, Amann, Rudolf, and Dubilier, Nicole
- Subjects
- *
OXIDIZING agents , *SPIROCHETES , *BACTERIA , *WORMS , *PHYLOGENY - Abstract
Olavius crassitunicatus is a small symbiont-bearing worm that occurs at high abundance in oxygen-deficient sediments in the East Pacific Ocean. Using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization, we examined the diversity and phylogeny of bacterial symbionts in two geographically distant O. crassitunicatus populations (separated by 385 km) on the Peru margin (water depth, ∼300 m). Five distinct bacterial phylotypes co-occurred in all specimens from both sites: two members of the γ-Proteobacteria (Gamma 1 and 2 symbionts), two members of the δ-Proteobacteria (Delta 1 and 2 symbionts), and one spirochete. A sixth phylotype belonging to the δ-Proteobacteria (Delta 3 symbiont) was found in only one of the two host populations. Three of the O. crassitunicatus bacterial phylotypes are closely related to symbionts of other gutless oligochaete species; the Gamma 1 phylotype is closely related to sulfide-oxidizing symbionts of Olavius algarvensis, Olavius loisae, and Inanidrilus leukodermatus, the Delta 1 phylotype is closely related to sulfate-reducing symbionts of O. algarvensis, and the spirochete is closely related to spirochetal symbionts of O. loisae. In contrast, the Gamma 2 phylotype and the Delta 2 and 3 phylotypes belong to novel lineages that are not related to other bacterial symbionts. Such a phylogenetically diverse yet highly specific and stable association in which multiple bacterial phylotypes coexist within a single host has not been described previously for marine invertebrates. [ABSTRACT FROM AUTHOR]
- Published
- 2005
- Full Text
- View/download PDF
33. Quantitative Molecular Analysis of the Microbial Community in Marine Arctic Sediments (Svalbard).
- Author
-
Ravenschlag, Katrin, Sahm, Kerstin, and Amann, Rudolf
- Subjects
- *
SEDIMENTS , *PHYLOGENY , *FLUORESCENCE in situ hybridization - Abstract
Investigates the phylogenetic composition of a marine Arctic sediment using fluorescence in situ hybridization and rRNA slot blot hybridization. Detection of a large fraction of microbes living in the top 5 cm of the sediment; Cell counts hybridized to the bacterial probe.
- Published
- 2001
- Full Text
- View/download PDF
34. Dual Symbiosis in a Bathymodiolus sp. Mussel from a Methane Seep on the Gabon Continental Margin (Southeast Atlantic): 16S rRNA Phylogeny and Distribution of the Symbionts in Gills.
- Author
-
Duperron, Sébastien, Nadalig, Thierry, Caprais, Jean-Claude, Sibuet, Myriam, Fiala-Médioni, Aline, Amann, Rudolf, and Dubilier, Nicole
- Subjects
- *
MUSSELS , *MARINE bacteria , *TRANSMISSION electron microscopy , *SYMBIOSIS , *PHYLOGENY , *NUCLEOTIDE sequence - Abstract
Deep-sea mussels of the genus Bathymodiolus (Bivalvia: Mytilidae) harbor symbiotic bacteria in their gills and are among the dominant invertebrate species at cold seeps and hydrothermal vents. An undescribed Bathymodiolus species was collected at a depth of 3,150 m in a newly discovered cold seep area on the southeast Atlantic margin, close to the Zaire channel. Transmission electron microscopy, comparative 16S rRNA analysis, and fluorescence in situ hybridization indicated that this Bathymodiolus sp. lives in a dual symbiosis with sulfide- and methane-oxidizing bacteria. A distinct distribution pattern of the symbiotic bacteria in the gill epithelium was observed, with the thiotrophic symbiont dominating the apical region and the methanotrophic symblant more abundant in the basal region of the bacteriocytes. No variations in this distribution pattern or in the relative abundances of the two symbionts were observed in mussels collected from three different mussel beds with methane concentrations ranging from 0.7 to 33.7 μM. The 16S rRNA sequence of the methanotrophic symbiont is most closely related to those of known methanotrophic symbionts from other bathymodiolid mussels. Surprisingly, the thiotrophic Bathymodiolus sp. 16S rRNA sequence does not fall into the monophyletic group of sequences from thiotrophic symbionts of all other Bathymodiolus hosts. While these mussel species all come from vents, this study describes the first thiotrophic sequence from a seep mussel and shows that it is most closely related (99% sequence identity) to an environmental clone sequence obtained from a hydrothermal plume near Japan. [ABSTRACT FROM AUTHOR]
- Published
- 2005
- Full Text
- View/download PDF
35. Diversity studies and molecular analyses with single cells and filaments of large, colorless sulfur bacteria
- Author
-
Salman, Verena, Schulz-Vogt, Heide, and Amann, Rudolf
- Subjects
Thiopilula ,Thiomargarita ,ddc:570 ,introns ,570 Life sciences ,biology ,large sulfur bacteria ,Thioploca ,Thiophysa ,Beggiatoa ,phylogeny - Abstract
Large sulfur bacteria feature conspicuous morphologies that are usually visible with the naked eye. Most representatives were already described in the 19th and early 20th century and it needed nearly another 100 years until a new morphotype of large sulfur bacteria was discovered. This discovery encouraged a search for other yet unknown types in this group of bacteria and indeed led to the finding of a new type in two marine seep settings. This novel morphotype is presented in Chapter 2 and is the first non-filamentous member in the family Beggiatoaceae that shows a dimorphic life cycle, exhibiting alternation between sessile and free-living forms. In Chapter 3, another three novel morphotypes are presented, which were discovered in Namibian sediments. The detection of these novel morphotypes of large sulfur bacteria led to the necessity for an improved phylogenetic classification of the entire group. Earlier attempts to sequence the 16S rRNA genes of the large sulfur bacteria resulted in only few nearly full-length sequences, whereas some genera were even represented by only partial sequences. Accordingly, differentiation of genera in this group is still based on morphological features. Now, Chapter 3 presents the sequencing of 16S rRNA genes and ITS regions of more than 100 individual cells and filaments of large sulfur bacteria, revealing a major insight into the phylogeny of these extraordinary bacteria. It is demonstrated that the traditional, morphology-based classification does not correlate with the phylogeny derived from 16S rRNA gene sequences. Consequently, a reclassification of the entire family is proposed, being completely independent from former morphological categories. Sequencing single cells and filaments of large sulfur bacteria furthermore revealed that they represent the first group of bacteria, which commonly contain large and numerous introns in their 16S rRNA genes. In Chapter 4, it is demonstrated that the introns are removed efficiently from the rRNA precursor, thereby ligating the two exons, and are not present in the native ribosome. Furthermore, it was experimentally verified that a commonly applied PCR approach introduces a length heterogeneity bias and systematically discriminates against enlarged genes and favors the amplification of shorter homologues. Consequently, this fact questions the universality of 16S rRNA-based clone libraries for diversity studies. At least the group of large sulfur bacteria is systematically discriminated against in such universal PCR approaches and it can be assumed that this PCR bias also affects a yet unknown amount of other microorganisms.
- Published
- 2011
36. Molekulare Ökologie der NOR5/OM60-Gruppe der Gammaproteobacteria
- Author
-
Yan, Shi, Amann, Rudolf, and Fischer, Ulrich
- Subjects
ddc:570 ,570 Life sciences ,biology ,molecular ecology ,phylogeny ,bacteria ,biogeography - Abstract
In this thesis, a newly discovered gammaproteobacterial group - the NOR5/OM60 clade, which includes the novel aerobic anoxygenic phototrophs (AAnPs), was studied in the aspects of phylogeny, biogeography and physiology using both molecular and culturing methods.By means of 16S rRNA phylogenetic analysis, NOR5/OM60 group was defined as a monophyletic clade inside the class Gammaproteobacteria. More than 500 16S rRNA sequences of this clade were retrieved from public databases. Further studies classified the sequences into 13 subclades. My studies on the biogeography of NOR5/OM60 clade showed a cosmopolitan distribution. They were found in all oceans and at the coasts of all the continents. NOR5/OM60 seems to be most abundant in marine coastal water and sediment. However, they have also been encountered in surface water of open ocean, deep-sea sediment, freshwater, saline lakes and soil.The abundance of members of the NOR5/OM60 clade in various marine sites was determined by fluorescence in situ hybridization (FISH) with a newly designed and optimized probe set. In the ocean, the common relative abundance ranges from
- Published
- 2009
37. Diversität und Ökologie von limnischen Actinobakterien
- Author
-
Warnecke, Falk, Jürgens, Klaus, Amann, Rudolf, and Filser, Juliane
- Subjects
ddc:570 ,microbiology ,570 Life sciences ,biology ,actinobacteria ,16S rRNA ,microbial ecology ,phylogeny ,freshwater ,fluorescence in situ hybridization (FISH) ,diversity - Abstract
Actinobacteria are highly abundant in freshwater bacterioplankton. However, little is known about their diversity, distribution, physiology and ecological role in the aquatic environment. In this thesis the rRNA approach was applied to elucidate the diversity and distribution of freshwater Actinobacteria (limnic Actinobacteria = LAB). The selected cloning strategy and a specifically designed screening method yielded many nearly complete 16S rRNA sequences originating from diverse freshwater habitats. Thereby, the available sequence dataset and the awareness of diversity of LAB was comprehensively expanded.Comparative Sequence analysis revealed that most sequence motifs along with published sequences from mainly freshwater habitats formed four monophyletic clades. The newly defined clusters acI to acIV were distinct from those from marine habitats and soils. Based on phylogenetic reconstructions specific probes for fluorescence-in situ-hybridization (FISH) were designed to analyze the population structure of LAB. For five probes stringent hybridization conditions were determined by custom-developed testing strategies. The application of these probes demonstrated the abundance and importance of the actinobacterial acI-cluster in freshwater bacterioplankton. A subset of three probes targeting subgroups of the acI-cluster revealed differences in the community composition between different lakes. Clones of the acII-cluster appeared equally abundant in 16S rRNA gene libraries, but the respective organisms were of minor numerical importance in the investigated habitats.In a field study ten high mountain lakes in the Tyrolean Alps (Austria) were sampled. These lakes differed in e.g. their altitude and the water visibility leading to distinct exposures of aquatic organisms to UV-B radiation. The UV-B radiation damages DNA mainly by dimerisation of adjacent thymin bases. The genomic DNA of Actinobacteria contains a high molar G C content and thus a higher number of CC-dimers than TT-dimers. CC-dimers are thermodynamically more stable. Thus, bacteria with genomes rich in G C likely are more resistant to UV-B radiation. Therefore the hypothesis was tested, if there is a link between the relative abundance of LAB and the exposure to UV-B in surface layers of high mountain lakes. A positive correlation (r2=0,73) between the abundances of Actinobacteria and UV-B was shown for high mountain lakes above the timberline, whereas no correlation was found for two lakes at lower altitudes. Previous studies have speculated that LAB are relatively inactive organisms surviving mainly due to their resistance to grazing by protists. To test this hypothesis DNA-synthesizing populations in high mountain lakes were identified. The results indicate that the proportion of active cells of all Actinobacteria was similar to the average proportion of active bacterial cells of total bacteria. A clear preference of LAB for glucose-uptake was found in lake Fuchskuhle as demonstrated by combined micro-autoradiography and FISH (MAR-FISH). In cultivation attempts in the laboratory, growth of representatives of the environmentally important acI cluster was successfully stimulated. Future studies will focus on isolation of these bacteria into pure culture. This thesis gives clear evidence that Actinobacteria of the acI cluster are an abundant and metabolically active group of freshwater bacterioplankton. Hence, they constitute an important autochthonous part of such microbial communities.
- Published
- 2004
38. Aspects of the bioinformatic analysis and annotation of the genome of Rhodopirellula baltica
- Author
-
Teeling, Hanno, Amann, Rudolf, and Ludwig, Wolfgang
- Subjects
Tetranucleotides ,Genome ,Bioinformatics ,Annotation ,Planctomycete ,Metagenomics ,Phylogeny ,ddc:80 ,Rhodopirellula - Abstract
This thesis focuses on the bioinformatic analysis and annotation of the genome of the marine planctomycete Rhodopirellula baltica. A comprehensive bioinformatic pipeline was set up and established that comprises gene prediction, annotation and visualization tools. Considerable effort was put into the manual annotation process.The annotation of the genome of Rhodopirellula baltica revealed that this organism is specialized on the aerobic degradation of complex carbohydrates. Its genome harbors 110 sulfatases, which are likely excreted to get access to the carbon skeletons of sulfated heteropolysaccharides like chondroitin sulfate or carrageen.Phylogenetic analysis of numerous marker genes from the genome support a relationship with the Chlamydia or at least an affiliation with the Chlamydia-Spirochaetes superclade. This is in agreement with earlier 16S rRNA-based analysis and contradicts the recently proposed deepest branching position of the Planctomycetes within the bacterial domain. The presence of many genes for peptidoglycan biosynthesis indicates that the proteinaceous cell envelopes of planctomycetes are secondary adaptions rather than a relict from a time preceding peptidoglycan cell walls. This is also consistent with findings that suggest that the Planctomycetes originated from organisms with Gram negative-type cell envelopes (e.g. genes for lipid A biosynthesis) and that the outer ribosome-free compartments of Planctomycetes descended from a former periplasmic space.Two spin-off projects from the annotation of the Rhodopirellula baltica genome have lead to independent software developments. The first is MORFind, a flexible and extensible meta-tool for the in silico prediction of protein-coding genes. The second is a method for the probability-based assignment of genomic fragments originating from metagenome projects that is based on skewed tetranucleotide distributions. A dedicated program named TETRA has been developed for this purpose.
- Published
- 2004
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.