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The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil

Standards in Genomic Sciences volume 13, Article number: 23 (2018) Cite this article

Abstract

Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin, can use crude oil as its sole source of carbon and energy at 20 °C. The genome of P. maritimus strain Y42 has been sequenced to provide information on its properties. Genomic analysis shows that the genome of strain Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although the strain Y42 did not show a remarkably higher ability in degrading crude oil than other oil-degrading bacteria, the existence of strain Y42 played a significant role to reducing the overall environmental impact as an indigenous oil-degrading bacterium. In addition, genome annotation revealed that strain Y42 has many genes responsible for hydrocarbon degradation. Structural features of the genomes might provide a competitive edge for P. maritimus strain Y42 to survive in oil-polluted environments and be worthy of further study in oil degradation for the recovery of crude oil-polluted environments.

Introduction

Oil spills occur frequently and pose a severe hazard to pristine ecological conditions [1, 2]. On account of the difficulty in degrading crude oil, the pollutant remains in the environment to contaminate ground water and air, affect crop growth and endanger human health [3, 4]. Bioremediation is currently recognized as the preferred strategy to utilize biological activities to rapidly eliminate hydrocarbon pollutants [5]. Many microorganisms, especially bacteria, have been found to participate in the process of biodegradation in contaminated environments [6, 7].

Planococcus , as a psychrotolerant and halotolerant bacterium, was also reported as having the ability to degrade crude oil [8,9,10]. For example, a cultured Planococcus sp. strain S5 was described to be able to grow on salicylate or benzoate [11], and Planococcus alkanoclasticus was capable of degrading linear alkanes [9]. Meanwhile, most of the Planococcus bacteria have showed the ability to withstand heavy metals, produce surfactants and adapt to cold and/or saline environments [12,13,14]. Because of the above properties, Planococcus exhibited a potential capability in the bioremediation of extremely contaminated environments. Although many studies have reported the genomic backgrounds of Planococcus strains, oil biodegradation mechanisms in Planococcus have rarely been discussed. In the present study, we isolated a Planococcus strain from the oil-contaminated soils in the Qinghai-Tibetan Plateau. Our aims were to characterize the genome of this oil-degrading strain and to further seek responsible strategies associated with oil degradation in low-temperature environments.

Organism information

Classification and features

In this experiment, a novel cold-adapted strain Y42 was isolated from oil-contaminated soils in the Lenghu oil field, which is located in the northern margin of the Qaidam Basin (93.34°E, 38.71°N). The molecular identification of the strain was performed using the primers 27F and 1492R to amplify and sequence the 16S rRNA gene [15]. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain Y42 was closely related to members of the genus Planococcus ( Planococcus maritimus (97%)). The strain Y42 was thus recognized as a potential new member of Planococcus (Fig. 1).

Fig. 1
figure 1

Phylogenetic tree of P. maritimus Y42 between known species of Planococcus genus. The phylogenetic tree constructed from the 16S rRNA sequence together with other Planococcus homologs using MEGA 6.0 software suite. The evolutionary history was inferred by using Neighbor-joining method based on model

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The strain Y42 was able to grow at moderately low temperatures, and many members of the genus Planococcus had been predominantly isolated from frozen and/or saline environments [16]. Cell micrographs were obtained by using a scanning electron microscope (SEM) on cells grown in LB medium. Cells of strain Y42 were coccoid, typically 0.7–1 m in diameter, and diplococci were observed, along with cell division septa (Fig. 2a). Colony morphology was determined on LB plates following 3–5 days of growth at 25 °C, which resulted in the formation of orange, round, umbonate colonies (Fig. 2b). Additional characteristics of P. maritimus Y42 are shown in Table 1.

Fig. 2
figure 2

Scanning electron microscope (a) and Colony morphology on the 216 L plate (b) of P. maritimus Y42

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Table 1 Classification and general features of P. maritimus Y42
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Crude oil-degrading characterization of strain Y42 was completed under specified growth conditions with crude oil as the sole carbon source by using a gas chromatography-mass spectrometry (GC-MS) method. The strain Y42 was cultured with MM medium (3.5 g of MgCl2, 1.0 g of NH4NO3, 0.35 g of KCl, 0.05 g of CaCl2, 1.0 g of KH2PO4, 1.0 g of K2HPO4, 0.01 g of FeCl3, 0.08 g of KBr, and 24 mg of SrCl2·6H2O, pH 7.5) with crude oil as a carbon source and incubated at 20 °C for 10 d [17]. A parallel experiment without inoculation was used as the control. The remaining oil from the cultures was extracted with 15 mL of hexane in a separating funnel at room temperature, and anhydrous Na2SO4 was then added to remove residual water. Ultimately, the extracted oil was analysed using a GC-MS method [18]. For GC-MS analysis, one microliter of the filtered solution was injected into a quartz capillary column (DB-WAX, 30 m × 0.25 mm × 0.25 μm). The total area of a detected individual hydrocarbon peak was defined as its hydrocarbon concentration in crude oil. The degradation rate of the components of crude oil was determined according to the following equation: η = (1-n1/n2) × 100%, where η, n1 and n2 are the degradation rate of the components of crude oil, the peak area of the components of crude oil remaining in the samples, and the peak area of the components of crude oil in the controls, respectively [19]. The chromatograms revealed that the concentrations of the components of crude oil, including n-alkanes, branched alkanes, cyclanes, and aromatic hydrocarbons, were lower in the sample treated with the strain P. maritimus Y42 than the abiotic control sample (Fig. 3a). After incubation for 10 days at 20 °C, the preferred degradation occurred in short-chain n-alkanes ranging from C12 to C18, C12 was particular decomposed, by approximately 50%. Meanwhile, the other straight-chain alkanes and aromatic hydrocarbons were decomposed by 20–30% (Fig. 3b). The strain Y42 did not show a remarkably higher ability to degrade different components of crude oil than other strains such as Bacillus [20, 21], Pseudomonas [22, 23], Rhodococcus [24] and etceteras. Even so, as an indigenous oil-degrading bacterium, the existence of the P. maritimus strain Y42 played a significant role in reducing overall environmental impact of the oil [25] and greatly enriched microbial community structures in the oil-contaminated soils in low-temperature environments [26].

Fig. 3
figure 3

The gas chromatograms of crude oil after degradation by P. maritimus Y42. a Total ion currents (TIC) of gas chromatography-mass spectrometer (GC-MS) monitoring the component variations of the residual crude oil (evaporated residue) before (the blue) and after (the red) incubation with strain Y42. b Degradation rates of the hydrocarbon components in evaporated crude oil by strain Y42 after 10 days of incubation at 20 °C

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Genome sequencing information

Genome project history

This organism was selected for sequencing based on its phylogenetic position and its ability to degrade crude oil. The genome project was deposited in the genome online database [27] and the complete genome sequence was available in GenBank (NCBI-Genome). Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information was provided in Table 2.

Table 2 Project information of the whole genome sequence of P. maritimus Y42
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Growth conditions and genomic DNA preparation

P. maritimus strain Y42 was inoculated into LB liquid medium and grown on a gyratory shaker (200 rpm) at 20 °C for 96 h. Genomic DNA of the strain was extracted using the Bacterial Genomic DNA Extraction Kit (AxyPrep) as per its operation instruction.

Genome sequencing and assembly

The complete genome sequence of P. maritimus strain Y42 was generated by combined Illumina MiSeq with PacBio platform [28]. The reads generated with Illumina MiSeq platform were denovo assembled using Newbler (version 2.8). The sub-reads generated from PacBio platform were de novo assembled using Hierarchical Genome Assembly Process (HGAP) [29]. Gaps between contigs were closed by using the SPAdes-3.5.0. This whole genome project (Bioproject ID: PRJNA371518) has been registered and assembled sequence data submitted at NCBI GenBank under the accession no. CP019640.1-CP019643.1. And this finished genome was deposited in IMG database with the Project ID: Gp0209326.

Genome annotation

The completed genomic sequence was predicted using the Glimmer software 3.0 [30]. tRNA genes were predicted using tRNAscan-SE 1.3.1 [31] and rRNA genes were identified using Barrnap 0.4.2 [32]. The rest of the non-coding rRNA genes were predicted by using BLASTp against databases NCBI-NR database (http://www.ncbi.nlm.nih.gov/) and genes function annotations were assigned by the COG database (http://www.ncbi.nlm.nih.gov/COG/).

Genome properties

The assembled genome of P. maritimus Y42 consisted of one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48.8% and three plasmids (329,482; 89,073; and 12,282 bp) (Table 3). Genome project information and genomic features are summarized in Table 4. From a total of 4155 genes, 3947 were annotated as predicted protein-coding sequences (CDS). In addition, the genome included 70 tRNA genes, 27 rRNA genes, 4 ncRNA genes, and 108 pseudogenes. Open reading frames (ORFs) were assigned into 23 functional categories under the Clusters of Orthologous Groups (COGs) and are represented in a circular genome map in Fig. 4. The COG distribution of genes is shown in Table 5. The genome map was visualized by the CG View server.

Table 3 Summary of genome: 1 chromosome and 3 plasmids
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Table 4 Genome statistics of P. maritimus Y42
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Fig. 4
figure 4

The genome map of P. maritimus strain Y42. The circles show the different descriptions of the content in megabases, from the outside to inward: outer two circles represent the predicted protein-coding sequences and CDS regions on the plus and minus strands, respectively. The colors represent COG functional classification. The circle 3 represent the predicted rRNA and tRNA. The 4th circle shows GC content and 5th circle exhibits the percent of GC-skew

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Table 5 Number of genes of P. maritimus Y42 with the general COG functional categories
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Insights from the genome sequence

Genome annotation predicted that many genes support the adaptability of strain Y42 to cold and crude oil-contaminated environments. Based on the COG analysis, the genes related to general function prediction only (R) and amino acid transport and metabolism (E) were relatively enriched over the other functional genes. The results indicate genome-wide selection pressure [33]. Moreover, the abundance of genes related to functions unknown (S) in strain Y42 suggested that the strain may possess many new genes.

Further analysis showed that many key oxygenase genes were located in the P. maritimus Y42 genome, including those of catechol 1,2-dioxygenase (catA), catechol 2,3-dioxygenase (catE), and cytochromes P450. In addition, dehalogenase-coding genes were also found in the chromosome; these genes were involved in numerous metabolic processes such as the degradation of chlorocyclohexane, chlorobenzene, chloroalkane and chloroalkene [34]. A total of 9 genes putatively encoding for crude oil metabolites were identified in this genome (Fig. 5). The existence of these oxygenase genes could regioselectively oxidize substrates, especially natural aromatic compounds, by transferring oxygen to the substrates and transforming non-reactive hydrocarbons into available hydrocarbons [35, 36]. However, genes responsible for n-alkane degradation, such as the alkB gene, which is considered as functional biomarker gene for alkane degradation [37,38,39], were not found in the genome of strain Y42. These results imply that the strain Y42 might have some novel genes that participate in the catabolism of n-alkane pollutants.

Fig. 5
figure 5

Gene clusters in the genome of P. maritimus strain Y42 encoding metabolic functions for oil degradation. The corresponding oil degradation related genes are red colored

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In addition, three cold shock proteins (WP_008296927.1, WP_026692369.1, WP_008298364.1.) were predicted, and these proteins were supposed to play important roles under low-temperature conditions [40]. In total, 238 genes were predicted to be involved in transport systems for aromatic compounds, amino acids, carbohydrates, lipids and inorganic ions. Among these genes, several osmoprotectant transport system (Opu) genes were identified to likely maintain the homeostasis of strain Y42. Furthermore, a large number of divalent cation transport and sulfate/phosphonate/nitrogen uptake systems guarantee the supply of nutrient elements for microbes in crude oil environments [41]. These genes were essential for strain Y42 to gain a competitive edge in oil-polluted soils.

Conclusions

The strain Y42, as a potential new member of Planococcus , was isolated from a cold and crude oil-contaminated environment. A genomic analysis of strain Y42 provided the theoretical basis for the mechanism of oil degradation by bacteria. Genes involved in cold shock and transport systems point to the potential capacity of strain Y42 for soil bioremediation contaminated by aromatic compounds in cold environments. Genomic research on strain Y42 would also provide a blueprint for the application of bioremediation and recovery in cold oil-polluted environments.

Abbreviations

CDSs:

protein-coding sequences

COG:

Clusters of Orthologous Groups categories

GC-MS:

gas chromatography and mass spectrometric Detector

ORFs:

open reading frames

References

  1. Bao M, Wang L, Sun P, Cao L, Zou J, Li Y. Biodegradation of crude oil using an efficient microbial consortium in a simulated marine environment. Mar Pollut Bull. 2012;64:1177–85.

    Article  CAS  PubMed  Google Scholar 

  2. Head IM, Jones DM, Röling WFM. Marine microorganisms make a meal of oil. Nat Rev Microbiol. 2006;4:173–82.

    Article  CAS  PubMed  Google Scholar 

  3. Zhang XX, Cheng SP, Zhu CJ, Sun SL. Microbial PAH-degradation in soil: degradation pathways and contributing factors. Pedosphere. 2006;16:555–65.

    Article  CAS  Google Scholar 

  4. Udo EJ, Fayemi AAA. The effect of oil pollution of soil on germination, growth and nutrient uptake of corn. J Environ Qual. 1975;4(4):537–40.

    Article  CAS  Google Scholar 

  5. Hassanshahian M, Emtiazi G, Cappello S. Isolation and characterization of crude-oil-degrading bacteria from the Persian Gulf and the Caspian Sea. Mar Pollut Bull. 2012;64:7–12.

    Article  CAS  PubMed  Google Scholar 

  6. AL-Saleh E, Drobiova H, Obuekwe C. Predominant culturable crude oil-degrading bacteria in the coast of Kuwait. Int Biodeterior Biodegrad. 2009;63:400–6.

    Article  CAS  Google Scholar 

  7. Kimes NE, Callaghan AV, Suflita JM, Morris PJ. Microbial transformation of the Deepwater horizon oil spill-past, present, and future perspectives. Front Microbiol. 2014;5:603.

    Article  PubMed Central  PubMed  Google Scholar 

  8. Chand R, Liaqat S, Bashir S, Naseer M, Ishrat N. Characterization of crude oil contaminated soil bacteria and laboratory-scale biodegradation experiments. Biologia. 2011;57:47–53.

    Google Scholar 

  9. Engelhardt MA, Daly K, Swannell RP, Head IM. Isolation and characterization of a novel hydrocarbon-degrading, gram positive bacterium, isolated from intertidal beach sediment, and description of Planococcus alkanoclasticus sp. nov. J Appl Microbiol. 2001;90:237–47.

    Article  CAS  PubMed  Google Scholar 

  10. Sun JQ, Xu L, Zhang Z, Li Y, Tang YQ, Wu XL. Diverse bacteria isolated from microtherm oil-production water. Antonie Van Leeuwenhoek. 2014;105:401–11.

    Article  CAS  PubMed  Google Scholar 

  11. Łabużek S, Hupert-Kocurek K, Skurnik M. Isolation and characterisation of new Planococcus sp. strain able for aromatic hydrocarbons degradation. Acta Microbiol Pol. 2003;52:395–404.

    PubMed  Google Scholar 

  12. Li H, Liu YH, Luo N, Zhang XY, Luan TG, Hu JM, et al. Biodegradation of benzene and its derivatives by a psychrotolerant and moderately haloalkaliphilic Planococcus sp. strain ZD22. Res Microbiol. 2006;157:629–36.

    Article  CAS  PubMed  Google Scholar 

  13. Nithya C, Gnanalakshmi B, Pandian SK. Assessment and characterization of heavy metal resistance in Palk Bay sediment bacteria. Mar Environ Res. 2011;71:283–94.

    Article  CAS  PubMed  Google Scholar 

  14. Jacobucci DFC, Oriani MRG, Regina L. Reducing COD level on oily effluent by utilizing biosurfactant-producing bacteria. Braz Arch Biol Technol. 2009;52:1037–42.

    Article  CAS  Google Scholar 

  15. Seemüller E, Schneider B, Mäurer R, Ahrens U, Daire X, Kison H, et al. Phylogenetic classification of phytopathogenic mollicutes by sequence analysis of 16S ribosomal DNA. Int J Syst Bacteriol. 1994;44(3):440–6.

    Article  PubMed  Google Scholar 

  16. Mykytczuk NCS, Wilhelm RC, Whyte LG. Planococcus halocryophilus sp. nov., an extreme sub-zero species from high Arctic permafrost. Int J Syst Evol Microbiol. 2012;62:1937–44.

    Article  CAS  PubMed  Google Scholar 

  17. Wang B, Lai Q, Cui Z, Tan T, Shao Z. A pyrene-degrading consortium from deep-sea sediment of the West Pacific and its key member Cycloclasticus sp. P1. Environ Microbiol. 2008;10:1948–63.

    Article  CAS  PubMed  Google Scholar 

  18. Hassanshahian M, Zeynalipour MS, Musa FH. Isolation and characterization of crude oil degrading bacteria from the Persian Gulf (Khorramshahr provenance). Mar Pollut Bull. 2014;82:39–44.

    Article  CAS  PubMed  Google Scholar 

  19. Deng MC, Li J, Liang FR, Yi M, Xu XM, Yuan JP, et al. Isolation and characterization of a novel hydrocarbon- degrading bacterium Achromobacter sp. HZ01 from the crude oil-contaminated seawater at the Daya bay, southern China. Mar Pollut Bull. 2014;83:79–86.

    Article  CAS  PubMed  Google Scholar 

  20. Parthipan P, Preetham E, Machuca LL, Rahman PK, Murugan K, Rajasekar A. Biosurfactant and degradative enzymes mediated crude oil degradation by bacterium Bacillus subtilis A1. Front Microbiol. 2017;8:193.

    Article  PubMed Central  PubMed  Google Scholar 

  21. Bezza FA, Chirwa EMN. Production and applications of lipopeptide biosurfactant for bioremediation and oil recovery by Bacillus subtilis CN2. Biochem Eng J. 2015;101:168–78.

    Article  CAS  Google Scholar 

  22. Pacwa-Płociniczak M, Płaza GA, Poliwoda A, Piotrowska-Seget Z. Characterization of hydrocarbon-degrading and biosurfactant-producing Pseudomonas sp. P-1 strain as a potential tool for bioremediation of petroleum-contaminated soil. Environ Sci Pollut R. 2014;21(15):9385–95.

    Article  Google Scholar 

  23. Patowary K, Patowary R, Kalita MC, Deka S. Characterization of biosurfactant produced during degradation of hydrocarbons using crude oil as sole source of carbon. Front Microbiol. 2017;8:279.

    Article  PubMed Central  PubMed  Google Scholar 

  24. Li C, Zhou ZX, Jia XQ, Chen Y, Liu J, Wen JP. Biodegradation of crude oil by a newly isolated strain Rhodococcus sp. JZX-01. Appl Biochem Biotech. 2013;171(7):1715–25.

    Article  CAS  Google Scholar 

  25. Atlas RM, Hazen TC. Oil biodegradation and bioremediation: a tale of the two worst spills in US history. Environ Sci Technol. 2011;45(16):6709–15.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Lee J, Han I, Kang BR, Kim SH, Sul WJ, Lee TK. Degradation of crude oil in a contaminated tidal flat area and the resilience of bacterial community. Mar Pollut Bull. 2017;114(1):296–301.

    Article  CAS  PubMed  Google Scholar 

  27. Liolios K, Chen IMA, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, et al. The genomes on line database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2009;38(suppl 1):D346–54.

    PubMed  PubMed Central  Google Scholar 

  28. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, et al. A tale of three next generation sequencing platforms: comparison of ion torrent, Pacific biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13:1–13.

    Article  PubMed Central  PubMed  Google Scholar 

  29. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J Heiner C, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Meth. 2013;10:563–9.

    Article  CAS  Google Scholar 

  30. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics. 2007;23:673–9.

    Article  CAS  PubMed  Google Scholar 

  31. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–64.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  32. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

    Article  CAS  PubMed  Google Scholar 

  33. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28:33–6.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  34. Chain PSG, Denef VJ, Konstantinidis KT, Vergez LM, Agullo L, Reyes VL, et al. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci. 2006;103:15280–7.

    Article  PubMed Central  PubMed  Google Scholar 

  35. Harayama S, Kok M, Neidle EL. Functional and evolutionary relationships among diverse oxygenases. Annu Rev Microbiol. 1992;46:565–601.

    Article  CAS  PubMed  Google Scholar 

  36. Van Beilen JB, Funhoff EG. Expanding the alkane oxygenase toolbox: new enzymes and applications. Curr Opin Biotechnol. 2005;16:308–14.

    Article  CAS  PubMed  Google Scholar 

  37. Emanuele K, Sebben BG, Helena PV. New alk genes detected in Antarctic marine sediments. Appl Environ Microbiol. 2009;11:669–73.

    Google Scholar 

  38. Wallisch S, Gril T, Dong X, Welzl G, Bruns C, Heath E, et al. Effects of different compost amendments on the abundance and composition of alkB harboring bacterial communities in a soil under industrial use contaminated with hydrocarbons. Front Microbiol. 2014;5:96.

    Article  PubMed Central  PubMed  Google Scholar 

  39. Wang W, Wang L, Shao Z. Diversity and abundance of oil-degrading bacteria and alkane hydroxylase (alkB) genes in the subtropical seawater of Xiamen Island. Microb Ecol. 2010;60:429–39.

    Article  PubMed  Google Scholar 

  40. Chattopadhyay MK. Mechanism of bacterial adaptation to low temperature. J Biosci. 2006;31:157–65.

    Article  CAS  PubMed  Google Scholar 

  41. Hamamura N, Olson SH, Ward DM, Inskeep WP. Microbial population dynamics associated with crude-oil biodegradation in diverse soils. Appl Environ Microbiol. 2006;72:6316–24.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  42. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Gibbons NE, Murray RGE. Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol. 1978;28:1–6.

    Article  Google Scholar 

  44. Euzéby J. Validation list no. 132. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol. 2010;60:469–72.

    Article  Google Scholar 

  45. Ludwig W, Schleifer KH, Whitman WB, Class I. Bacilli class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB, editors. Bergey’s man Syst Bacteriol, second edition, vol. 3. New York: Springer-Verlag; 2009. p. 19–20.

    Google Scholar 

  46. Skerman VBD, McGowan V, Sneath PHA. Approved lists of bacterial names. Int J Syst Bacteriol. 1980;30:225–420.

    Article  Google Scholar 

  47. Prévot AR. Dictionnaire des Bactéries Pathogènes. In: Hauderoy P, Ehringer G, Guillot G, Magrou J, Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, 2nd Edition, Masson et Cie, Paris, 1953, p. 1–692.

    Google Scholar 

  48. Krasil’nikov NA. Guide to the Bacteria and Actinomycetes [Opredelitelv Bakterii i Actinomicetov]. Moscow: Akad. Nauk SSSR; 1949. p. 328.

    Google Scholar 

  49. Migula W. Über ein neues System der Bakterien. Arbeiten aus dem bakteriologischen Institut der technischen Hochschule zu Karlsruhe 1894;1:235–238.

  50. Ludwig W, Schleifer KH, Whitman WB. Family VI. Planococcaceae Krasil’nikov 1949, 328AL. Bergey's manual of systematic bacteriology, volume 3, The Firmicutes 2011;3:348–350.

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Funding

This study was financed by the International Scientific and Technological Cooperation Projects of the Ministry of Science and Technology (Grant No. 2014DFA30330) and the National Science Foundation of China (Grant No. 31470544).

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Authors and Affiliations

  1. Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China

    Ruiqi Yang, Guangxiu Liu, Wei Zhang & Gaosen Zhang

  2. Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China

    Ruiqi Yang, Guangxiu Liu, Tuo Chen, Wei Zhang, Gaosen Zhang & Sijing Chang

  3. State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China

    Tuo Chen & Sijing Chang

  4. University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China

    Ruiqi Yang & Sijing Chang

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  1. Ruiqi Yang
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Contributions

RQY, WZ and GSZ initiated the study. GSZ, TC and GXL designed the research and project outline. RQY drafted the manuscript. RQY and SJC isolated the strain. RQY assembled and annotated the genome. All authors read and approved the final manuscript.

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Correspondence to Guangxiu Liu or Tuo Chen.

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Yang, R., Liu, G., Chen, T. et al. The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil. Stand in Genomic Sci 13, 23 (2018). https://doi.org/10.1186/s40793-018-0328-9

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Keywords

Environmental Microbiome

ISSN: 2524-6372