Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium
Kuever, J. ; Visser, M. ; Loeffler, C. ; Boll, M. ; Worm, P. ; Sousa, D.Z. ; Plugge, C.M. ; Schaap, P.J. ; Muyzer, G. ; Pereira, I.A. ; Parshina, S.N. ; Goodwin, L.A. ; Kyrpides, N.C. ; Detter, J. ; Woyke, T. ; Chain, P. ; Davenport, K.W. ; Rohde, M. ; Spring, S. ; Klenk, H.P. ; Stams, A.J.M. - \ 2014
Standards in Genomic Sciences 9 (2014)3. - ISSN 1944-3277 - p. 821 - 839.
Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. For growth it does not require any vitamins. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp., so far. A total of 4666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway possibly involved in heterotrophic growth, and in CO2 fixation during autotrophic growth are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes.
Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans
Visser, M. ; Parshina, S.N. ; Alves, J.I. ; Sousa, D.Z. ; Pereira, I.A.C. ; Muyzer, G. ; Kuever, J. ; Lebedinsky, A.V. ; Koehorst, J.J. ; Worm, P. ; Plugge, C.M. ; Schaap, P.J. ; Goodwin, L.A. ; Lapidus, A. ; Kyrpides, N.C. ; Detter, J.C. ; Woyke, T. ; Chain, P. ; Davenport, K.W. ; Spring, S. ; Rohde, M. ; Klenk, H.P. ; Stams, A.J.M. - \ 2014
Standards in Genomic Sciences 9 (2014)3. - ISSN 1944-3277 - p. 655 - 675.
reducing bacterium - sp nov. - sequence - growth - classification - hydrogenase - evolution - standard - archaea - system
Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to ‘subgroup a’ of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans
Complete genome sequence of Dehalobacter restrictus PER-K23T
Kruse, T.K. ; Maillard, J. ; Goodwin, L.A. ; Woyke, T. ; Teshima, H. ; Bruce, D.C. ; Detter, J.C. ; Tapia, R. ; Han, C. ; Huntemann, M. ; Wei, C.L. ; Han, J. ; Chen, A. ; Kyrpides, N. ; Szeto, E. ; Markowitz, V. ; Ivanova, N. ; Pagani, I. ; Pati, A. ; Pitluck, S. ; Nolan, M. ; Holliger, C. ; Smidt, H. - \ 2013
Standards in Genomic Sciences 8 (2013)3. - ISSN 1944-3277 - p. 375 - 388.
tetrachloroethene reductive dehalogenase - hafniense strain tce1 - desulfitobacterium-hafniense - dehalococcoides-ethenogenes - rna genes - bacteria - respiration - geobacter - protein - halorespiration
Dehalobacter restrictus strain PER-K23 (DSM 9455) is the type strain of the species Dehalobacter restrictus. D. restrictus strain PER-K23 grows by organohalide respiration, coupling the oxidation of H2 to the reductive dechlorination of tetra- or trichloroethene. Growth has not been observed with any other electron donor or acceptor, nor has fermentative growth been shown. Here we introduce the first full genome of a pure culture within the genus Dehalobacter. The 2,943,336 bp long genome contains 2,826 protein coding and 82 RNA genes, including 5 16S rRNA genes. Interestingly, the genome contains 25 predicted reductive dehalogenase genes, the majority of which appear to be full length. The reductive dehalogenase genes are mainly located in two clusters, suggesting a much larger potential for organohalide respiration than previously anticipated
Genome analysis of Desulfotomaculum kuznetsovii strain 17T reveals a physiological similarity with Pelotomaculum thermopropionicum SIT
Visser, M. ; Worm, P. ; Muyzer, G. ; Pereira, I.A.C. ; Schaap, P.J. ; Plugge, C.M. ; Kuever, J. ; Parshina, S.N. ; Nazina, T.N. ; Ivanova, A.E. ; Bernier-Latmani, R. ; Goodwin, L.A. ; Kyrpides, N. ; Woyke, T. ; Chain, P. ; Davenport, K.W. ; Spring, S. ; Klenk, H.P. ; Stams, A.J.M. - \ 2013
Standards in Genomic Sciences 8 (2013)1. - ISSN 1944-3277 - p. 69 - 87.
sulfate-reducing bacteria - clostridium-thermoaceticum - carbon-monoxide - gen. nov. - sequence - prediction - biosynthesis - oxidation - methanol - enzymes
Desulfotomaculum kuznetsovii is a moderately thermophilic member of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. This species is of interest because it originates from deep subsurface thermal mineral water at a depth of about 3000 m. D. kuznetsovii is a rather versatile bacterium as it can grow with a large variety of organic substrates, including short-chain and long-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow methylotrophically with methanol and sulfate and autotrophically with H2 + CO2 and sulfate. For growth it does not require any vitamins. Here, we describe the features of D. kuznetsovii together with the genome sequence and annotation. The chromosome has 3,601,386 bp organized in one contig. A total of 3567 candidate protein-encoding genes and 58 RNA genes were identified. Genes of the acetyl-CoA pathway possibly involved in heterotrophic growth with acetate and methanol, and in CO2 fixation during autotrophic growth are presented. Genomic comparison revealed that D. kuznetsovii shows a large similarity with Pelotomaculum thermopropionicum. Genes involved in propionate metabolism of these two strains show a strong similarity. However, main differences are found in genes involved in the electron acceptor metabolism
Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis
Sessitsch, A. ; Hardoim, P.R. ; Doring, J. ; Weilharter, A. ; Krause, A. ; Woyke, T. ; Mitter, B. ; Hauberg-Lotte, L. ; Friedrich, F. ; Rahalkar, M. ; Hurek, T. ; Sarkar, A. ; Bodrossy, L. ; Overbeek, L.S. van; Brar, D. ; Elsas, J.D. ; Reinhold-Hurek, B. - \ 2012
Molecular Plant-Microbe Interactions 25 (2012)1. - ISSN 0894-0282 - p. 28 - 36.
oryza-sativa l. - sp strain bh72 - microbial communities - bacterial endophytes - complete genome - rhizosphere - plant - sequence - nitrogen - growth
Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N2-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.
Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)
Spring, S. ; Visser, M. ; Lu, M. ; Copeland, A. ; Lapidus, A. ; Lucas, S. ; Cheng, J.F. ; Han, C. ; Tapia, R. ; Goodwin, L.A. ; Pitluck, S. ; Ivanova, N. ; Land, M. ; Hauser, L. ; Larimer, F. ; Rohde, M. ; Göker, M. ; Detter, J.C. ; Kyrpides, N. ; Woyke, T. ; Schaap, P.J. ; Plugge, C.M. ; Muyzer, G. ; Kuever, J. ; Pereira, I.A.C. ; Parshina, S.N. ; Bernier-Latmani, R. ; Stams, A.J.M. ; Klenk, H.P. - \ 2012
Standards in Genomic Sciences 7 (2012). - ISSN 1944-3277 - p. 304 - 319.
bacterial names - classification - hydrogenases - database - archaea - system - site - tool
Strain DLT (= DSM 2154 = ATCC 23193 = NCIMB 8452) is the type strain of the species Desulfotomaculum ruminis , one out of current-ly 30 species with validly published names in the paraphyletic genus Desulfotomaculum [2,3]. Strain DLT was initially isolated by G. S. Coleman in the 1950s from the rumen of hay-fed sheep . Dissimilatory reduction of sulfate to sulfide in the rumen was first demonstrated by Lewis , who dosed fistulated sheep with sulfate and deter-mined the amount of sulfide produced. As high amounts of sulfide may be toxic to animals, bacte-rial sulfate-reduction in ruminants was a concern due to the presence of sulfate in grass and hay. D. ruminis represented the first pure culture of a sul-fate-reducing bacterium isolated from the rumen. The genus name was derived from the Latin words 'de', from, ‘sulfur’, sulfur, and 'tomaculum', a kind of sausage, meaning 'a sausage-shaped sul-fate reducer' [2,6]. The species epithet is derived from the Latin word 'rumen', throat, first stomach (rumen) of a ruminant, meaning of a rumen [1,2]. Here, we present a summary classification and a set of features for D. ruminis strain DLT, together with the description of the complete genomic se-quencing and annotation. The complete genome sequence of strain DLT will provide valuable in-formation for defining a more adequate descrip-tion of the currently paraphyletic genus Desulfotomaculum
|The rice endophyte metagenome
Sessitsch, A. ; Hardoim, P.R. ; Döring, J. ; Krause, A. ; Weilharter, A. ; Woyke, T. ; Mitter, B. ; Hauberg, L. ; Friedrich, F. ; Rahalkar, M. ; Hurek, T. ; Overbeek, L.S. van; Elsas, J.D. van - \ 2010
In: Program & Abstract. BAGECO 10: Bacterial Genetics and Ecology - Coexisting on a Changing Planet, Uppsala, Sweden, 15-19 June 2010. - Uppsala, Sweden : Swedish University of Agricultural Sciences (SLU), Uppsala Universitet, Uppsala Microbiomis Center (UMC) - p. 41 (OR25) - 41 (OR25).