Complete Genome Sequences of Desulfosporosinus orientis DSM765^T, Desulfosporosinus youngiae DSM17734^T, Desulfosporosinus meridiei DSM13257^T, and Desulfosporosinus acidiphilus DSM22704^T

Abstract

g Desulfosporosinus species are sulfate-reducing bacteria belonging to the Firmicutes. Their genomes will give insights into the genetic repertoire and evolution of sulfate reducers typically thriving in terrestrial environments and able to degrade toluene (Desulfosporosinus youngiae), to reduce Fe(III) (Desulfosporosinus meridiei, Desulfosporosinus orientis), and to grow under acidic conditions (Desulfosporosinus acidiphilus).T he sequenced Desulfosporosinus type strains (2,3,14,20) represent four out of eight described species belonging to the genus Desulfosporosinus and cover its phylogenetic and physiological breadth. Besides their ability to reduce sulfate for energy conservation, some Desulfosporosinus species can also grow by using nitrate, Fe(III), or As(V) as terminal electron acceptors or by fermentative processes. They can utilize a wide spectrum of energy sources, ranging from aromatic compounds to short-chained fatty acids. A characteristic feature of many Desulfosporosinus species, distinguishing them from their closest sulfate-reducing relatives of the genus Desulfotomaculum, is their ability to grow chemolithoautotrophically on hydrogen (3,14,15,19,(21)(22)(23). Members of the genus Desulfosporosinus are found in low-sulfate freshwater and soil environments but also in sulfate-rich heavymetal-contaminated environments, such as acid mine/rock drainage sites. In addition, Desulfosporosinus species are often observed in low-pH habitats (1, 3, 5-7, 12, 13, 17, 18), with the sequenced Desulfosporosinus acidiphilus strain being the first validly described sulfate-reducing acidophile (3).Genomic DNA was isolated using the Jetflex genomic DNA purification kit (GENOMED, Löhne, Germany) and subjected to sequencing using a combination of 454 Titanium (16) and Illumina (4) technologies. Sequences were assembled with Newbler (version 2.3-PreRelease-6/30/2009) and Velvet (version 1.0.13) (24) for 454 and Illumina data, respectively. Consensus sequences were obtained using computationally shredded Illumina and 454 reads together with 454 paired-end data using parallel Phrap (version SPS-4.24; High Performance Software, LLC). Identification of sequencing errors and improvement of consensus quality were done with Polisher (A. Lapidus, unpublished data) using Illumina data. GapResolution (C. Han, unpublished data), Dupfinisher (11), or sequencing cloned bridging PCR fragments with subcloning were used to correct misassemblies. Gaps between contigs were closed by editing in Consed (8-10), by PCR, and by Bubble PCR (J.-F. Cheng, unpublished data) primer walks. Automated genome annotation was performed at the Oak Ridge National Laboratory and is available at http://genome.ornl.gov/.The circular chromosomes of Desulfosporosinus orientis, Desulfosporosinus youngiae, Desulfosporosinus meridiei, and D. acidiphilus have sizes of 5,863,081 bp, 5,660,978 bp, 4,873,567 bp, and 4,926,837 bp, respectively. The genome of D. acidiphilus additionally harbors two plasmids of 60,447 bp and 3,897 bp. The genomes, in the order listed...

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

“…In many Gram-positive SRP (and also C. maquilingensis and T. tenax), only the cytoplasmic-facing dsrMK genes are present, suggesting that this is the minimally functional module ( Junier et al, 2010;Pereira et al, 2011). The main exception to this is the genus Desulfosporosinus (Pester, Brambilla, et al, 2012), members of which have a complete set of dsrMKJOP genes, and curiously have several copies of the dsrJ gene, in contrast to other SRP. The Dsr complex was first isolated from the archaeon A. fulgidus (where it was named Hme for Hdr-like menaquinol-oxidizing enzyme) (Mander et al, 2002), and later from D. desulfuricans ATCC 27774 (Pires et al, 2006).…”

Microbial Electroreduction: Screening for New Cathodic Biocatalysts

“…[32] This species was also shown to grow in a sulfate-free medium with formate, methanol, ethanol, lactate, or pyruvate with production of acetate and CO 2 . [31,33] Recently, its genome has been fully sequenced, [34] however a careful in silico or combined experimental physiological analysis for this organism has not been reported, yet. With its fairly strong cathodic activity in our screening and the physiological capacity to produce and secrete acetate from CO 2 , we consider this species as an especially promising biocatalyst for microbial electrosynthesis applications, but also for elucidating the physiology of microbial electron utilization from a cathode.…”

A Genomic Signature and the Identification of New Sporulation Genes

“…However, endospore formers are found in other classes within the Firmicutes and encompass aerobic or anaerobic organisms with a wide range of morphologies, lifestyles, and metabolic traits, including rods, cocci, branching species, plant or animal pathogens or symbionts, syntrophs, sulfate reducers, phototrophs (11)(12)(13)(14)(15)(16)(17), and remarkably, didermic species (18). Despite the extreme diversity of endospore-forming bacteria, the basic architecture of an endospore is conserved across species (19).…”