Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans
Michael Visser,Sofiya N. Parshina,Joana I. Alves,Diana Z. Sousa,Diana Z. Sousa,Inês A. C. Pereira,Gerard Muyzer,Jan Kuever,Alexander V. Lebedinsky,Jasper J. Koehorst,Petra Worm,Caroline M. Plugge,Peter J. Schaap,Lynne Goodwin,Lynne Goodwin,Alla Lapidus,Alla Lapidus,Nikos C. Kyrpides,J. C. Detter,Tanja Woyke,Patrick S. G. Chain,Patrick S. G. Chain,Karen W. Davenport,Karen W. Davenport,Stefan Spring,Manfred Rohde,Hans-Peter Klenk,Alfons J. M. Stams,Alfons J. M. Stams +28 more
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TLDR
The genomes of both strains were compared to reveal their differences and led to a reclassification of D. carboxydivorans as a later heterotypic synonym ofD.Abstract:
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.read more
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Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile.
Emily Denise Melton,Dimitry Y. Sorokin,Lex Overmars,Alla Lapidus,Manoj Pillay,Natalia Ivanova,Tijana Glavina del Rio,Nikos C. Kyrpides,Nikos C. Kyrpides,Nikos C. Kyrpides,Tanja Woyke,Gerard Muyzer +11 more
TL;DR: The draft genome sequence of D. alkaliphilus strain AHT1T was sequenced by the Joint Genome Institute as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.
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References
More filters
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
Journal ArticleDOI
Prodigal: prokaryotic gene recognition and translation initiation site identification
Doug Hyatt,Doug Hyatt,Gwo Liang Chen,Philip F. LoCascio,Miriam Land,Frank W. Larimer,Frank W. Larimer,Loren Hauser +7 more
TL;DR: This work developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm), which achieved good results compared to existing methods, and it is believed it will be a valuable asset to automated microbial annotation pipelines.
Journal ArticleDOI
Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics
Lawrence G. Wayne,Don J. Brenner,R. R. Colwell,Patrick A. D. Grimont,O. Kandler,Micah I. Krichevsky,L. H. Moore,W. E. C. Moore,R. G. E. Murray,Erko Stackebrandt,M. P. Starr,H. G. Truper +11 more
Journal ArticleDOI
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
TL;DR: It is proposed that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms.