The tree was inferred from 1,470 aligned characters [10,11] of th

The tree was inferred from 1,470 aligned characters [10,11] of the 16S rRNA gene sequence under the maximum … Cells of the strain Yu37-1T are vibrio-shaped, 0.4-0.5 x 1.4-2.0 ��m in size, occur singly or in pairs and stain Gram-negative [1] (Table 1 and Figure 2). No spore formation was detected for Yu37-1T [1]. No data is available on the generation time of strain Yu37-1T. Nitrate is the only electron acceptor utilized, with ammonium as the end product [1]. Elemental sulfur, sulfate, sulfite, nitrite, iron (III) oxide, manganese (IV) oxide, selenate, selenite, arsenate, arsenite, fumarate and oxygen are not used as alternative electron acceptors [1]. Acetate, pyruvate, lactate, fumarate, succinate, malate, yeast extract, peptone and Casamino acids are utilized as electron donors with nitrate as the electron acceptor; fermentative growth has not been observed [1].

Strain Yu37-1T is strictly anaerobic and catalase negative [1]. Table 1 Classification and general features of C. nitroreducens Yu37-1T according to the MIGS recommendations [16] Figure 2 Scanning electron micrograph of C. nitroreducens Yu37-1T Chemotaxonomy The predominant compounds in whole cell lipids of C. nitroreducens strain Yu37-1T are saturated branched-chain fatty acids: iso-C14:0 (26.3%), anteiso-C15:0 (24.1%), iso-C13:0 (7.7%), C18:0 (7.2%), C16:0 (6.2%), iso-C16:0 (5.7%) and anteiso-C13:0 (5.3%) [1]. Menaquinone MK-8 was identified as the major quinone [1]. Genome sequencing and annotation Genome project history This organism was selected for sequencing on the basis of its phylogenetic position [26], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [27].

The genome project is deposited in the Genomes On Line Database [14] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2. Table 2 Genome sequencing project information Growth conditions and DNA isolation C. nitroreducens Yu37-1T, DSM 19672, was grown anaerobically in DSMZ medium 1112 (Calditerrivibrio medium) [28] at 55��C. DNA was isolated from 0.5-1 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) following the standard protocol as recommended by the manufacturer, with modification st/DL for cell lysis as described in [27].

DNA is available through the DNA Bank Network [29]. Genome sequencing and assembly The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [30]. Pyrosequencing reads were assembled using the Newbler assembler (Table 2). The initial Newbler assembly, consisting of seven contigs in four scaffolds, Dacomitinib was converted into a phrap assembly [31] by making fake reads from the consensus to collect the read pairs in the 454 paired end library.

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