Draft Genome Sequence of Pseudoruegeria sp. SK021, a Representative of the Marine Roseobacter Group, Isolated from North Sea Sediment

The Roseobacter group is globally distributed in the marine environment and represents a significant part of pelagic and benthic microbial communities (1–3). Their broad metabolic versatility make roseobacters successful in a variety of habitats (4, 5). In coastal sediments, roseobacters can constitute up to 10% of all cells (6). Although 28% of all described species in this group are of benthic origin (7), the metabolic properties of roseobacters in sediments are poorly understood. Pseudoruegeria sp. SK021, analyzed in this study, was isolated from surface sediment of the North Sea (7.1667 E, 57.8145 N) at a water depth of 181 m below sea level (8). It is closely related to P. aestuarii and represents a new benthic member of this genus.

Pseudoruegeria sp. SK021 was grown on marine broth agar (Difco) amended with dimethyl sulfide (100 µM) and lactate (5 mM) at 20°C. DNA was extracted using the innuPREP DNA mini kit (Analytik Jena) and a sequencing library was prepared using the Nextera XT kit (Illumina). Genome sequencing was performed using the Illumina MiSeq platform with the MiSeq reagent kit version 3 and generated approximately 3.8 million reads, representing ~0.98 Gb of data (fastq-stats version 1.01, http://expressionanalysis.github.io/ea-utils ). Reads were trimmed and adapters removed using Trimmomatic version 0.36 (9) with the following parameters: CROP:288, HEADCROP:19, SLIDINGWINDOW:4:20, MINLEN:100, ILLUMINACLIP:bbmap/adapters.fa:2:40:15. Paired reads were assembled with SPAdes version 3.9.1 (10) using “--careful” and multiple k-mer sizes (-k 21, 33, 55, 77, 99, 127). Only contigs with a G+C content of 40 to 68%, an average read coverage > 7.5×, and a minimum size of 200 bp were retained to eliminate potential contamination. After decontamination, the assembled draft genome of Pseudoruegeria sp. SK021 had a total length of 3,948,746 bp, 128 contigs (>500 bp), and approximately 245-fold coverage. The average G+C content was 60.17% and the N₅₀ length was 94,596 bp, as determined by QUAST version 4.3 (11). Genome completeness was 99.27%, estimated by CheckM version 1.0.7 (12) using marker genes for the family Rhodobacteraceae. Annotation by Prokka version 1.12-beta (13), on the basis of three published and annotated genomes of Pseudoruegeria spp., identified 3,747 protein-coding sequences, 3 rRNA-encoding sequences (5S, 16S, 23S rRNA), and 48 tRNAs. Even though Pseudorugeria sp. SK021 is nonmotile, genes for the formation of the complete flagellar apparatus were found in the annotated genome, including genes for the motor switch (e.g., FliG, FliM, MotA), the basal body (e.g., FlgB, FlgC), the different rings (FliF, FlgH, FlgI), the flagellar hook (e.g., FlgE, FlgK, FlgL), and the flagella itself (flagellin). Although motility is not essential in sediments, the presence of flagellar genes shows that the strain might be motile under specific conditions.

We acknowledge Saranya Kanukollu and Jana Schmidt (both University of Oldenburg), for isolating the strain and for providing support during the cultivation, and Britta Poulsen (Aarhus University) for performing the Illumina MiSeq sequencing. This study was funded by the Deutsche Forschungsgemeinschaft (DFG) within the Transregional Collaborative Research Center TRR51 and the Graduate School of Science and Technology, University of Oldenburg. Furthermore, the Aarhus University Graduate School of Science and Technology, the Danish National Research Foundation (grant no. DNRF104), an ERC Advanced Grant MICROENERGY (grant no. 294200), and a Marie Curie IIF fellowship “ATP_adapt_low_energy” (both European Union Seventh Framework Programs) supported this work financially.