Amann R

References (8)

Title : Complete genome, catabolic sub-proteomes and key-metabolites of Desulfobacula toluolica Tol2, a marine, aromatic compound-degrading, sulfate-reducing bacterium - Wohlbrand_2013_Environ.Microbiol_15_1334
Author(s) : Wohlbrand L , Jacob JH , Kube M , Mussmann M , Jarling R , Beck A , Amann R , Wilkes H , Reinhardt R , Rabus R
Ref : Environ Microbiol , 15 :1334 , 2013
Abstract : Among the dominant deltaproteobacterial sulfate-reducing bacteria (SRB), members of the genus Desulfobacula are not only present in (hydrocarbon-rich) marine sediments, but occur also frequently in the anoxic water bodies encountered in marine upwelling areas. Here, we present the 5.2 Mbp genome of Desulfobacula toluolica Tol2, which is the first of an aromatic compound-degrading, marine SRB. The genome has apparently been shaped by viral attacks (e.g. CRISPRs) and its high plasticity is reflected by 163 detected genes related to transposases and integrases, a total of 494 paralogous genes and 24 group II introns. Prediction of the catabolic network of strain Tol2 was refined by differential proteome and metabolite analysis of substrate-adapted cells. Toluene and p-cresol are degraded by separate suites of specific enzymes for initial arylsuccinate formation via addition to fumarate (p-cresol-specific enzyme HbsA represents a new phylogenetic branch) as well as for subsequent modified beta-oxidation of arylsuccinates to the central intermediate benzoyl-CoA. Proteogenomic evidence suggests specific electron transfer (EtfAB) and membrane proteins to channel electrons from dehydrogenation of both arylsuccinates directly to the membrane redox pool. In contrast to the known anaerobic degradation pathways in other bacteria, strain Tol2 deaminates phenylalanine non-oxidatively to cinnamate by phenylalanine ammonia-lyase and subsequently forms phenylacetate (both metabolites identified in (13) C-labelling experiments). Benzoate degradation involves CoA activation, reductive dearomatization by a class II benzoyl-CoA reductase and hydrolytic ring cleavage as found in the obligate anaerobe Geobacter metallireducens GS-15. The catabolic sub-proteomes displayed high substrate specificity, reflecting the genomically predicted complex and fine-tuned regulatory network of strain Tol2. Despite the genetic equipment for a TCA cycle, proteomic evidence supports complete oxidation of acetyl-CoA to CO2 via the Wood-Ljungdahl pathway. Strain Tol2 possesses transmembrane redox complexes similar to that of other Desulfobacteraceae members. The multiple heterodisulfide reductase-like proteins (more than described for Desulfobacterium autotrophicum HRM2) may constitute a multifaceted cytoplasmic electron transfer network.
ESTHER : Wohlbrand_2013_Environ.Microbiol_15_1334
PubMedSearch : Wohlbrand_2013_Environ.Microbiol_15_1334
PubMedID: 23088741
Gene_locus related to this paper: destt-k0nmq2

Title : Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains - Pena_2010_ISME.J_4_882
Author(s) : Pena A , Teeling H , Huerta-Cepas J , Santos F , Yarza P , Brito-Echeverria J , Lucio M , Schmitt-Kopplin P , Meseguer I , Schenowitz C , Dossat C , Barbe V , Dopazo J , Rossello-Mora R , Schuler M , Glockner FO , Amann R , Gabaldon T , Anton J
Ref : Isme J , 4 :882 , 2010
Abstract : Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.
ESTHER : Pena_2010_ISME.J_4_882
PubMedSearch : Pena_2010_ISME.J_4_882
PubMedID: 20164864
Gene_locus related to this paper: salrd-q2rzy1 , salrd-q2s0e4 , salrd-q2s1i8

Title : Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group - Meyerdierks_2010_Environ.Microbiol_12_422
Author(s) : Meyerdierks A , Kube M , Kostadinov I , Teeling H , Glockner FO , Reinhardt R , Amann R
Ref : Environ Microbiol , 12 :422 , 2010
Abstract : Microbial consortia mediating the anaerobic oxidation of methane with sulfate are composed of methanotrophic Archaea (ANME) and Bacteria related to sulfate-reducing Deltaproteobacteria. Cultured representatives are not available for any of the three ANME clades. Therefore, a metagenomic approach was applied to assess the genetic potential of ANME-1 archaea. In total, 3.4 Mbp sequence information was generated based on metagenomic fosmid libraries constructed directly from a methanotrophic microbial mat in the Black Sea. These sequence data represent, in 30 contigs, about 82-90% of a composite ANME-1 genome. The dataset supports the hypothesis of a reversal of the methanogenesis pathway. Indications for an assimilatory, but not for a dissimilatory sulfate reduction pathway in ANME-1, were found. Draft genome and expression analyses are consistent with acetate and formate as putative electron shuttles. Moreover, the dataset points towards downstream electron-accepting redox components different from the ones known from methanogenic archaea. Whereas catalytic subunits of [NiFe]-hydrogenases are lacking in the dataset, genes for an [FeFe]-hydrogenase homologue were identified, not yet described to be present in methanogenic archaea. Clustered genes annotated as secreted multiheme c-type cytochromes were identified, which have not yet been correlated with methanogenesis-related steps. The genes were shown to be expressed, suggesting direct electron transfer as an additional possible mode to shuttle electrons from ANME-1 to the bacterial sulfate-reducing partner.
ESTHER : Meyerdierks_2010_Environ.Microbiol_12_422
PubMedSearch : Meyerdierks_2010_Environ.Microbiol_12_422
PubMedID: 19878267
Gene_locus related to this paper: 9arch-d1j9b3 , 9arch-d1ja37 , 9arch-d1jaz1 , 9arch-q64ad0

Title : Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide - Strittmatter_2009_Environ.Microbiol_11_1038
Author(s) : Strittmatter AW , Liesegang H , Rabus R , Decker I , Amann J , Andres S , Henne A , Fricke WF , Martinez-Arias R , Bartels D , Goesmann A , Krause L , Puhler A , Klenk HP , Richter M , Schuler M , Glockner FO , Meyerdierks A , Gottschalk G , Amann R
Ref : Environ Microbiol , 11 :1038 , 2009
Abstract : Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp(-1)) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood-Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO(2) but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII-c(3), Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2.
ESTHER : Strittmatter_2009_Environ.Microbiol_11_1038
PubMedSearch : Strittmatter_2009_Environ.Microbiol_11_1038
PubMedID: 19187283
Gene_locus related to this paper: desah-c0q9m7 , desah-c0qb70 , desah-c0qf45 , desah-c0qhm8

Title : Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis - Fuchs_2007_Proc.Natl.Acad.Sci.U.S.A_104_2891
Author(s) : Fuchs BM , Spring S , Teeling H , Quast C , Wulf J , Schattenhofer M , Yan S , Ferriera S , Johnson J , Glockner FO , Amann R
Ref : Proc Natl Acad Sci U S A , 104 :2891 , 2007
Abstract : Members of the gammaproteobacterial clade NOR5/OM60 regularly form an abundant part, up to 11%, of the bacterioplankton community in coastal systems during the summer months. Here, we report the nearly complete genome sequence of one cultured representative, Congregibacter litoralis strain KT71, isolated from North Sea surface water. Unexpectedly, a complete photosynthesis superoperon, including genes for accessory pigments, was discovered. It has a high sequence similarity to BAC clones from Monterey Bay [Beja O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, et al. (2002) Nature 415:630-633], which also share a nearly identical gene arrangement. Although cultures of KT71 show no obvious pigmentation, bacteriochlorophyll a and spirilloxanthin-like carotenoids could be detected by HPLC analysis in cell extracts. The presence of two potential BLUF (blue light using flavin adenine dinucleotide sensors), one of which was found adjacent to the photosynthesis operon in the genome, indicates a light- and redox-dependent regulation of gene expression. Like other aerobic anoxygenic phototrophs (AAnPs), KT71 is able to grow neither anaerobically nor photoautotrophically. Cultivation experiments and genomic evidence show that KT71 needs organic substrates like carboxylic acids, oligopeptides, or fatty acids for growth. The strain grows optimally under microaerobic conditions and actively places itself in a zone of approximately 10% oxygen saturation. The genome analysis of C. litoralis strain KT71 identifies the gammaproteobacterial marine AAnPs, postulated based on BAC sequences, as members of the NOR5/OM60 clade. KT71 enables future experiments investigating the importance of this group of gammaproteobacterial AAnPs in coastal environments.
ESTHER : Fuchs_2007_Proc.Natl.Acad.Sci.U.S.A_104_2891
PubMedSearch : Fuchs_2007_Proc.Natl.Acad.Sci.U.S.A_104_2891
PubMedID: 17299055
Gene_locus related to this paper: 9gamm-a4a7a9 , 9gamm-a4a9u6 , 9gamm-a4a440 , 9gamm-a4a484 , 9gamm-a4a590 , 9gamm-a4a746 , 9gamm-a4a758 , 9gamm-a4aa23 , 9gamm-a4acc1 , 9gamm-a4ada0 , 9gamm-a4ae00 , 9gamm-a4acf4 , 9gamm-a4acr9

Title : Insights into the genomes of archaea mediating the anaerobic oxidation of methane - Meyerdierks_2005_Environ.Microbiol_7_1937
Author(s) : Meyerdierks A , Kube M , Lombardot T , Knittel K , Bauer M , Glockner FO , Reinhardt R , Amann R
Ref : Environ Microbiol , 7 :1937 , 2005
Abstract : The anaerobic oxidation of methane is a globally significant process which is mediated by consortia of yet uncultivated methanotrophic archaea (ANME) and sulfate-reducing bacteria. In order to gain deeper insights into genome characteristics of the different ANME groups, large-insert genomic libraries were constructed using DNA extracted from a methanotrophic microbial mat growing in the anoxic part of the Black Sea, and from sediments above gas hydrates at the Hydrate Ridge off the coast of Oregon. Analysis of these fosmid libraries with respect to archaeal 16S rRNA gene diversity revealed a single ANME-1b ribotype for the Black Sea libraries, whereas the sequences derived from the Hydrate Ridge library phylogenetically affiliated with the ANME-2a, ANME-2c and ANME-3 group. Genome walking for ANME-1b resulted in a contiguous 155 kb composite genome fragment. The comparison of a set of four genomic fragments belonging to the different ANME groups revealed differences in the rRNA operon structure and the average G+C content, with the ANME-2c contig showing the highest divergence within the set. A detailed analysis of the ANME contigs with respect to genes putatively involved in the anaerobic oxidation of methane led to the identification of: (i) a putative N5,N10-methenyltetrahydromethanopterin cyclohydrolase gene, (ii) a gene cluster supposedly encoding a novel type of heterodisulfide reductase/dehydrogenase complex and (iii) a gene cluster putatively encoding a new type of CO dehydrogenase/acetyl-CoA synthase enzyme complex.
ESTHER : Meyerdierks_2005_Environ.Microbiol_7_1937
PubMedSearch : Meyerdierks_2005_Environ.Microbiol_7_1937
PubMedID: 16309392

Title : The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments - Rabus_2004_Environ.Microbiol_6_887
Author(s) : Rabus R , Ruepp A , Frickey T , Rattei T , Fartmann B , Stark M , Bauer M , Zibat A , Lombardot T , Becker I , Amann J , Gellner K , Teeling H , Leuschner WD , Glockner FO , Lupas AN , Amann R , Klenk HP
Ref : Environ Microbiol , 6 :887 , 2004
Abstract : Desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is able to grow at in situ temperatures below 0 degrees C. As abundant members of the microbial community in permanently cold marine sediments, D. psychrophila-like bacteria contribute to the global cycles of carbon and sulfur. Here, we describe the genome sequence of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 663 bp. Analysis of the genome gave insight into the metabolic properties of the organism, e.g. the presence of TRAP-T systems as a major route for the uptake of C(4)-dicarboxylates, the unexpected presence of genes from the TCA cycle, a TAT secretion system, the lack of a beta-oxidation complex and typical Desulfovibrio cytochromes, such as c(553), c(3) and ncc. D. psychrophila encodes more than 30 two-component regulatory systems, including a new Ntr subcluster of hybrid kinases, nine putative cold shock proteins and nine potentially cold shock-inducible proteins. A comparison of D. psychrophila's genome features with those of the only other published genome from a sulfate reducer, the hyperthermophilic archaeon Archaeoglobus fulgidus, revealed many striking differences, but only a few shared features.
ESTHER : Rabus_2004_Environ.Microbiol_6_887
PubMedSearch : Rabus_2004_Environ.Microbiol_6_887
PubMedID: 15305914
Gene_locus related to this paper: desps-q6ajw5 , desps-q6ak51 , desps-q6ak75 , desps-q6akv7 , desps-q6and7 , desps-q6anv2 , desps-q6ar42 , desps-q6ara4

Title : Complete genome sequence of the marine planctomycete Pirellula sp. strain 1 - Glockner_2003_Proc.Natl.Acad.Sci.U.S.A_100_8298
Author(s) : Glockner FO , Kube M , Bauer M , Teeling H , Lombardot T , Ludwig W , Gade D , Beck A , Borzym K , Heitmann K , Rabus R , Schlesner H , Amann R , Reinhardt R
Ref : Proc Natl Acad Sci U S A , 100 :8298 , 2003
Abstract : Pirellula sp. strain 1 ("Rhodopirellula baltica") is a marine representative of the globally distributed and environmentally important bacterial order Planctomycetales. Here we report the complete genome sequence of a member of this independent phylum. With 7.145 megabases, Pirellula sp. strain 1 has the largest circular bacterial genome sequenced so far. The presence of all genes required for heterolactic acid fermentation, key genes for the interconversion of C1 compounds, and 110 sulfatases were unexpected for this aerobic heterotrophic isolate. Although Pirellula sp. strain 1 has a proteinaceous cell wall, remnants of genes for peptidoglycan synthesis were found. Genes for lipid A biosynthesis and homologues to the flagellar L- and P-ring protein indicate a former Gram-negative type of cell wall. Phylogenetic analysis of all relevant markers clearly affiliates the Planctomycetales to the domain Bacteria as a distinct phylum, but a deepest branching is not supported by our analyses.
ESTHER : Glockner_2003_Proc.Natl.Acad.Sci.U.S.A_100_8298
PubMedSearch : Glockner_2003_Proc.Natl.Acad.Sci.U.S.A_100_8298
PubMedID: 12835416
Gene_locus related to this paper: rhoba-DHLA , rhoba-EPHA , rhoba-pepx , rhoba-PLDB , rhoba-q7tty3 , rhoba-q7ufy7 , rhoba-q7ug04 , rhoba-q7uh76 , rhoba-q7uhj7 , rhoba-q7uik0 , rhoba-q7uit3 , rhoba-q7ujb6 , rhoba-q7ujc7.1 , rhoba-q7ujc7.2 , rhoba-q7ujd0 , rhoba-q7ujp7 , rhoba-q7ujv7 , rhoba-q7uk55 , rhoba-q7uk83 , rhoba-q7ul52 , rhoba-q7ule9 , rhoba-q7umh7 , rhoba-q7upt9 , rhoba-q7uq60 , rhoba-q7uqf1 , rhoba-q7uqr5 , rhoba-q7uqz0 , rhoba-q7ur17 , rhoba-q7ur85 , rhoba-q7urv6 , rhoba-q7us57 , rhoba-q7usu9 , rhoba-q7ut87 , rhoba-q7ut89 , rhoba-q7utj6 , rhoba-q7uua2 , rhoba-q7uvu6 , rhoba-q7uw49 , rhoba-q7uw53 , rhoba-q7uwf0 , rhoba-q7uwf1 , rhoba-q7uxn0 , rhoba-q7uyb7 , rhoba-q7uyh2 , rhoba-q7uz96 , rhoba-RB3694 , rhoba-RB4467 , rhoba-RB7907 , rhoba-RB9080 , rhoba-RB9565 , rhoba-RB13257