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[…] f this project is shown in Table .Table 2 , Strain S3-2T was grown at 25 °C in TSB (10 g L−1) supplemented with 5 mM nitrate. The cells were harvested by centrifugation and DNA was extracted from the pellet using the PowerLyser® PowerSoil® DNA extraction kit (MoBio, Carlsbad, CA, USA) according to the manufacturer’s protocol., The genome of strain S3-2T was sequenced with the Illumina MiSeq Reagent Kit V3 (Illumina Inc. San Diego, CA, USA). Sequencing libraries were prepared using the Nextera XT Library Preparation Kit (Illumina). The sequencing library produced 3,761,645 paired end reads totalling ~2.11 Gbp. In total, 2,868,634 reads remained after quality trimming and adapter removal with Trimmomatic-0.33 [] and the following trimming parameters: CROP:235 HEADCROP:25 SLIDINGWINDOW:4:20. Read quality before and after trimming was assessed by FastQC version 0.11.4 []. The trimmed reads (~1.04 Gbp) represented an average genome coverage of ~178-fold based on the size of the assembled draft genome of strain S3-2T. Reads were assembled using SPAdes 3.6.1 []. Contigs shorter than 1,000 bp were removed after the assembly., The draft genome was annotated using the standard operation procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) supported by the JGI (Walnut Creek, CA; USA) []. Briefly, CRISPR elements were determined by the programs CRT [] and PILER-CR v1.06 []. Non-coding RNAs, and tRNAs, were predicted by tRNAscan-SE 1.3.1 []. rRNA genes were identified by HMMER 3.1b2 []. Protein-coding genes were determined by Prodigal v2.6.2 []. Functional annotation was based on assigning the genes to different databases: the COG & KOG database (November, 2014) [], the KEGG database (release 71.0, July 2014) [], the MetaCyc database (release 18.1, June 2014) [], the Pfam database (version 28.0, May, 2015) [], the TIGRfam database (release 14.0, January, 2014) [], and the InterPro Scan database (release 48) []. In silico DNA-DNA hybridization (GGDC 2.0) was carried out with the online genome-to-genome calculator provided by the DSMZ []., The properties of the draft genome of strain S3-2T are summarized in Table , and the assignment of genes into COG functional categories is shown in Table . The assembled draf […]

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