Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation

Data in Brief Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation Aide Lasa, Jesús L. Romalde ⁎ Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología. Universidade de Santiago de Compostela, Campus Vida s/n. 15782, Santiago de Compostela, Spain abstractarticle info Article history: Received 29 December 2016 Received in revised form 3 January 2017 Accepted 25 January 2017 Available online 14 February 2017 To date, the genus Psychrobacter consists of 37 recognized species isolated from different sources, however they are more frequently found in cold and other non-polar environments of low water activity. Some strains belonging to the genus have shown different enzymatic activities with potential applications in bioremediation or food industry. In the present study, the whole genome sequences of three Psychrobacter-like strains (C 20.9, Cmf 22.2 and Rd 27.2) isolated from reared clams in Galicia (Spain) are described. The sequenced genomes resulted in an assembly size of 3,143,782 bp for C 20.9 isolate, 3,168,467 bp for Cmf 22.2 isolate and 3,028,386 bp for Rd 27.2 isolate. Among the identified coding sequences of the genomes, mercury detoxification and biogeochemistry genes were found, as well as genes related to heavy metals and antibiotic resistance. Also virulence-related features were identified such as the siderophore vibrioferrin or an aerobactin-like siderophore. The phylogenetic analysis of the 16S rRNA gene suggested that these strains may represent novel species of the Psychrobacter genus. The genome sequences of the Psychrobacter sp. strains have been deposited at DDBJ/EMBL/GenBank under the accession numbers MRYA00000000 (Cmf 22.2), MRYB00000000 (Rd 27.2) and MRYC00000000 (C 20.9), and the sequences could be found at the site https://www.ncbi.nlm.nih.gov/bioproject/PRJNA353858. © 2017 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Keywords: Psychrobacter Genome sequencing Mercury detoxification Virulence factors Phylogenetic analysis Specifications Organism/cell line/tissue Psychrobacter spp. Strain C 20.9, Cmf 22.2, Rd 27.2 Sex N/A Sequencer or array type Illumina paired-end Data format Analyzed Experimental factors Genomic DNA extracted from pure bacterial isolated from clams Experimental features Draft genome sequences of Psychrobacter sp. C 20.9, Cmf 22.2 and Rd 27.2, assembly and annotation Consent N/A Sample source locations Galicia, Spain. C 20.9 (8° 47′0″N, 42° 37′0″W), Cmf 22.2 (43° 07′48, N, 9° 11′06″W), Rd 27.2 (42° 17′00″N, 8° 36′00″W) 1. Direct link to deposited data https://www.ncbi.nlm.nih.gov/bioproject/PRJNA353858 2. Introduction The genus Psychrobacter was first proposed by Juni and Heym [9], with the description of Psychrobacter inmobilis asthetypespecies, to accommodate a non-motile and psychrotolerant bacterium with aerobic metabolism. To date, the genus Psychrobacter consists of 37 recognized species isolated from a great variety of sources including fish, poultry, meat products and human pathological specimens. Members of the genus have been detected in air samples collected from different geographical locations including north-western Colorado [3] and the Baltic Sea coast [6]. Although Psychrobacter species have a global distribution, they are most frequently found in cold and other non-polar environments of low water activity [18].Thus,atleast18 species of the genus were isolated from low-temperature environments, including Antarctic glacier mud and sediment [5],Antarctic ornithogenic soils [4],seaice[19], alpine soil [20], Siberian permafrost [1] and Arctic seawater [23]. Different strains of this genus are of industrial interest since they have shown different enzymatic activities with potential applications in bioremediation or food industry [17]. Microbially induced carbonate precipitation (MICP) is a recent well-recognized process that has the potential to precipitate heavy metals [10].Some Genomics Data 12 (2017) 7–10 ⁎Corresponding author. E-mail address: [email protected] (J.L. Romalde). http://dx.doi.org/10.1016/j.gdata.2017.01.005 2213-5960/© 2017 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Contents lists available at ScienceDirect Genomics Data journal homepage: www.elsevier.com/locate/gdata Psychrobacter strains have shown valuable activities involved in bioremediation by producing carbonic anhydrase enzyme [13].Onthe other hand, the genome sequence of P. alimentarius displayed two interesting pathways involved in the biosynthesis of terpenoids and benzoate degradation [12]. In this study, we report the complete genome sequences of three strains (C 20.9, Cmf 22.2 and Rd 27.2) isolated from reared clams in Galicia (Spain) and designated as Psychrobacter spp., that will provide fundamental information for further research. 3. Methods 3.1. Sample collection and identification Psychrobacter isolates C 20.9, Cmf 22.2 and Rd 27.2 were obtained between 2007 and 2008 during a sampling program of reared clams in Galicia (NW Spain). The isolates were cultured in Marine Agar (MA, Pronadisa) at 25 °C for 24 h and stored at −80C° in Marine Broth containing 15% glycerol. Phenotypic characterization and 16S rRNA gene sequence analysis allowed the identification of these strains as members of the Psychrobacter genus. C 20.9 strain is phylogenetically most closely related to P. piscatorii (98.1%), Cmf 22.2 to P. maritimus (98.1%) and Rd 27.2 to P. celer (98.2%). 3.2. Genome sequencing, assembly and annotation High Pure PCR Template Preparation kit (Roche) was employed for isolation of genomic DNA for whole genome sequencing at Sistemas Genómicos (Valencia, Spain) using Illumina paired-end sequencing technology. The Illumina reads were analyzed for quality control using FASTQC (Brabaham Bioinformatics). Reads were trimmed and filtered to remove adapters and low quality bases, using Trimmomatic 0.32 [2] program. The remaining reads were used for the genome assembly, performed with the SPAdes 3.6.2 the novo assembler tool [15], and QUAST [8] software was used to evaluate the assembly. The draft genomes of the three strains were annotated using the Rapid Annotations using Subsystems Technology (RAST) server [16] and tRNAs were identified by tRNAscan-SE v1.21 [14]. CRISPRfinder tool [7] was used to assess the presence of CRISPR repeats in the genomes of the clam isolates. The G + C content of the chromosomal DNA was calculated on the basis of its whole genome sequence. 3.3. Phylogenetic analysis To evaluate the relatedness among the three Psychrobacter sp. strains and the closest relatives, 16S rRNA sequences were aligned using CLUSTALW tool [11], and phylogenetic trees were reconstructed using the neighbour-joining (NJ) algorithms in MEGA software package version 6.06 [22]. 4. Results The genome assembly of the Psychrobacter sp. strains resulted in a genome size of 3,143,782 bp for C 20.9 isolate, 3,168,467 bp for Cmf 22.2 isolate and 3,028,386 for Rd 27.2 isolate. The G + C content of C 20.9, Cmf 22.2 and Rd 27.2 strains was 43.9%, 42.6% and 47.1% respectively. The genomic features of the C 20.9 included 2777 coding sequences and 52 RNAs, of which 44 were transfer RNA sequences. Meanwhile, Cmf 22.2 genome contained 2652 coding sequences and 47 RNAs sequences, including 44 tRNA sequences. The Rd 27.2 genome displayed a total of 2596 coding sequences and 46 RNAs, of which 43 were tRNAs. CRISPR arrays were only found in the Rd 27.2 genome that included Cas1, Cas2, Cas3, Cas5e and Cse1–4 family proteins (Table 1). Accordingto the annotation results, the genomes of the clam isolates revealed the presence of genes responsible for resistance to antibiotics and toxic compounds, copper homeostasis, copper tolerance, cobalt-zinc-cadmium resistance, resistance to fluoroquinolones, arsenic resistance, and multidrug resistance efflux pump subsystems. In addition, the analysis identified mercuric reductase in the three strains involved in mercury detoxification and biogeochemistry. Also, C 20.9 displayed a mercury resistance operon (Fig. 1), which included a regulatory protein (MerR), transport proteins (MerT and MerC), a periplasmic mercury binding protein (MerP) and a mercury ion reductase. Virulence-related proteins were found in the genomes that could play roles in bacterial pathogenicity and virulence. For instance, a cluster of five genes for biosynthesis of the siderophore vibrioferrin was found in Cmf 22.2 and Rd 27.2 strains. On the other hand, in C 20.9 strain an aerobactin-like siderophore was annotated. Sequence similarity of the 16S rRNA gene of the Psychrobacter sp. strains isolated from clams is below the threshold (98.7%) proposed by Stackebrandt and Ebers [21] for delimitation of new bacterial Table 1 Genome statistics for the three clams isolates. Attribute C 20.9 Cmf 22.2 Rd 27.2 Genome size (bp) 3,143,782 3,168,467 3,028,386 Contigs 60 100 197 N50 151,201 640,377 182,392 G + C content 43.9 42.6 47.1 Coding sequences 2.777 2652 2596 Total RNA genes 52 47 46 tRNA genes 44 44 43 CRISPR repeats ––7 Fig. 1. Representation of the genomic region containing the mercuric resistance operon in the C 20.9 strain. 8A. Lasa, J.L. Romalde / Genomics Data 12 (2017) 7–10 species. The phylogenetic reconstruction based on the 16S rRNA gene sequences showed that the clam isolates can be distinguished among them and to the closest relatives (Fig. 2). These results suggest that each isolate may constitute a novel species within the Psychrobacter genus. 5. Nucleotide sequence accession number This Whole Genome Shotgun projects has been deposited at DDBJ/ ENA/GenBank under the accession numbers MRYA00000000 (Cmf 22.2), MRYB00000000 (Rd 27.2) and MRYC00000000 (C 20.9). The versions described in this paper are version MRYA01000000, MRYB01000000 and MRYC01000000 respectively. Conflict of interest statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Fig. 2. Phylogenetic tree based on 16S rRNA gene sequences using the Neighbour-Joining algorithm, showing the relationships of Psychrobacter sp. strains within the genus. Bootstrap values (N50%) based on 1000 replications are shown at the nodes of the trees. Bar, substitutions per nucleotide position. Accession numbers for all Psychrobacter strains included in the study are given in parentheses. 9A. Lasa, J.L. Romalde / Genomics Data 12 (2017) 7–10 Acknowledgements This research was supported in part by grants AGL2013-42628-R and AGL2016-77539-R from Ministerio de Economia y Competitividad (Spain). References [1] C. Bakermans, H.L. Ayala-del-Río, M.A. Ponder, T. 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