- Short genome report
- Open Access
Complete genome sequence of Arcticibacterium luteifluviistationis SM1504T, a cytophagaceae bacterium isolated from Arctic surface seawater
Standards in Genomic Sciencesvolume 13, Article number: 33 (2018)
Arcticibacterium luteifluviistationis SM1504T was isolated from Arctic surface seawater and classified as a novel genus of the phylum Bacteroides. To date, no Arcticibacterium genomes have been reported, their genomic compositions and metabolic features are still unknown. Here, we reported the complete genome sequence of A. luteifluviistationis SM1504T, which comprises 5,379,839 bp with an average GC content of 37.20%. Genes related to various stress (such as radiation, osmosis and antibiotics) resistance and gene clusters coding for carotenoid and flexirubin biosynthesis were detected in the genome. Moreover, the genome contained a 245-kb genomic island and a 15-kb incomplete prophage region. A great percentage of proteins belonging to carbohydrate metabolism especially in regard to polysaccharides utilization were found. These related genes and metabolic characteristics revealed genetic basis for adapting to the diverse extreme Arctic environments. The genome sequence of A. luteifluviistationis SM1504T also implied that the genus Arcticibacterium may act as a vital organic carbon matter decomposer in the Arctic seawater ecosystem.
As the third most abundant bacterial group in the seawater system, phylum Bacteroidetes plays a vital role in diverse oceanic biogeochemical processes . It has been reported that phylum Bacteroidetes could mediate the degradation of HMW compounds especially in the respect of algal organic matter [2, 3]. Many heterotrophic microorganisms such as the SAR11 clade and marine Gammaproteobacteria grow partly due to phylum Bacteroidetes -derived organic products [4, 5]. Thus, phylum Bacteroidetes groups may play crucial roles in the nutrient utilization and cycling in the seawater ecosystem.
The family Cytophagaceae , currently comprising 31 genera, is one of the largest groups in the phylum Bacteroidetes . The species in the family Cytophagaceae have been isolated from various habitats including freshwater river , seawater , permafrost soil  and even polar glacial till . The genus Arcticibacterium , belonging to the family Cytophagaceae , accommodates only one recognized species: A. luteifluviistationis SM1504T (=KCTC 42716T=CCTCC AB 2015348T) . Strain SM1504T was isolated from surface seawater of King’s Fjord, Arctic. However, to date, no genomes of the genus Arcticibacterium have been reported, their genomic compositions and metabolic pathways are still lacking. In the study, we reported the first genome sequence of the genus Arcticibacterium to better understand its survival strategy and ecological niche in the Arctic seawater.
Classification and features
As the type strain of A. luteifluviistationis in the family Cytophagaceae , strain SM1504T is a Gram-negative, aerobic, non-motile and rod bacterium (Fig. 1). The yellow-pigmented colony was found after incubation at 20 °C for 2 days on a TYS agar plate. The strain could utilize glycerol, D-xylose, D-glucose, D-fructose, dulcitol, inositol D-mannitol, D-sorbitol, N-acetylglucosamine, arbutin, aesculin, cellobiose, maltose, sucrose, trehalose, starch, turanose and potassium gluconate for energy and growth, which were summarized in Table 1. Then it hydrolyzed aesculin, gelatin, tyrosine, Tween 20, 40 and 60 but did not hydrolyze DNA, agar, casein, elastin, lecithin, starch, Tween 80. In addition, various enzymes such as alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, valine arylamidase, cystine arylamidase, trypsin and glucosidase were produced for degrading organic matter . The phylogenetic placement of strain SM1504T (based on complete 16S rRNA gene sequence) through neighbor-joining phylogenetic tree was identified (Fig. 2). It formed a distinct phylogenetic branch within the family Cytophagaceae and closely relatives were species of the genera Lacihabitans , Emticicia , Fluviimonas and Leadbetterella with low sequence similarities between 88.9 and 91.6%.
Genome sequencing information
Genome project history
Isolated from an extreme Arctic environment, A. luteifluviistationis SM1504T was selected for genome sequencing to elucidate the special abilities of adapting to diverse extreme stresses. We have accomplished the genome sequencing of strain SM1504T as reported in this paper. The complete genome data has been deposited in the GenBank database under the accession number CP029480.1. The project information and its association with MIGS are provided in Table 2 .
Growth conditions and genomic DNA preparation
A. luteifluviistationis SM1504T was cultivated in TYS broth at 20 °C. After cultivation for two days, genomic DNA for sequencing was extracted by using a commercial bacterial DNA isolation kit (OMEGA).
Genome sequencing and assembly
Genome sequencing was performed on both the Illumina Hiseq and the PacBio RS sequencing platforms. 400-bp Illumina paired-end libraries and 20-kb PacBio libraries were constructed and sequenced yielding 315 × and 45 × average coverages, respectively (Table 2). About 1.69 Gb and 243 Mb data from the Illumina and PacBio sequencing were assembled using SOAPdenovo [13, 14] and HGAP . The final assembly resulted in one scaffold.
Coding gene sequences were predicted and annotated through Prodigal v2.6.3  and RAST v2.0 . Functional categorization and carbohydrate-active enzymes CAZy of the predicted genes were annotated against EggNOG and CAZy databases, respectively. Then rRNAs and tRNAs were predicted by RNAmmer v1.2  and tRNAscan-SE v1.3.1 . In addition, the CARD analyses were performed to find resistance genes. Genomic islands and secondary metabolite biosynthesis were predicted through IslandViewer 4  and antiSMASH .
The total size of the genome of A. luteifluviistationis SM1504T is 5,379,839 bp with an average GC content of 37.20% (Fig. 3). Total 4595 protein-coding genes (CDSs) were identified, which occupied 89.73% of the genome. Therein, 3045 CDSs were annotated with putative functions and 1550 CDSs matched hypothetical proteins (Table 3). Then 4 rRNAs and 36 tRNAs were found in the genome. CRISPR repeat, transmembrane helice, signal peptide and Pfam protein family predictions were done. In addition, distribution of genes into COG functional categories was shown in Table 4.
Insights from the genome sequence
Adaption to diverse stresses
Strain SM1504T genome owned two putative gene clusters for secondary metabolite biosynthesis. The cluster 1 belonged to terpene type - the largest group of natural products , matching the carotenoid biosynthesis. The cluster 2, affiliated to arylpolyene type, was predicted to produce flexirubin. Furthermore, we found that the yellow-pigmented strain SM1504T harbors a complete set of genes required for zeaxanthin biosynthesis (e.g., isopentenyl-diphosphate delta-isomerase, phytoene synthase, phytoene dehydrogenase, lycopene cyclase and beta-carotene hydroxylase), which was commonly detected in other species of the phylum Bacteroidetes [23, 24]. The pigment maybe help the strain to obtain energy and for cold adaption and ultraviolet light protection in the Arctic environments .
A total of 150 resistance genes were found to encode 24 kinds of antibiotics (such as gentamicin, kanamycin, tetracycline and streptomycin), which was consistent with the experimental antibiotic susceptibility results . The genes encoding heat shock proteins dnaK and cold shock protein cspA were detected in the genome. In line with this, SM1504T had a wider growth temperature ranges (4–30 °C) . Besides, the genome harbored several genes coding for catalase and superoxide dismutase to assist the strain at cellular and molecular levels in dealing harsh radiation in the Arctic. Dozens of genes related to osmotic stress (such as choline and betaine uptake and betaine biosynthesis) and carbon starvation responses were discovered in the A. luteifluviistationis genome, which would endow cells with tolerance to hyperhaline and oligotrophic environments.
As another feature, a 245-kb genomic island coding for 208 genes was predicted. Therein, 9 genes encoded proteins related to glucide biosynthesis, such aslipopolysaccharide core biosynthesis glycosyltransferase (lpsD), UDP-glucose dehydrogenase and capsular polysaccharide synthesis enzyme (Cap8C). In addition, the presence of transposases, integrases and mobile element proteins indicated that gene transfer has occurred in the A. luteifluviistationis SM1504T genome . Also, phage tail fiber proteins were predicted, which was in line with the analysis by PHAST  that a 15-kb incomplete prophage region could encode phage tail fiber proteins in the genome.
Degradation and utilization of carbohydrates
Totally, 3319 (71.61%) genes could be assigned a COG function, of which the wall/membrane/envelope biogenesis (5.89%), carbohydrate transport and metabolism (4.94%) and inorganic ion transport and metabolism (4.83%) were enriched (Table 4). The high percentage of proteins related to carbohydrate transport and metabolism suggested that the strain SM1504T could use various carbohydrates. On the other hand, the analyses from dbCAN showed that the strain SM1504T possessed 341 genes which encoded carbohydrate metabolism enzymes, including 69 carbohydrate esterases (11 families), 125 glycoside hydrolases (46 families), 62 glycosyltransferases (22 families), 17 polysaccharide lyases (6 families), 12 auxiliary activities (3 families) and 56 carbohydrate-binding modules (15 families). Therein, a variety of enzymes are related to the degradation of macromolecular polysaccharides (e.g., xylanase, chitinase, mannanase, alpha amylase, endoglucanase, glucoamylase and alginate lyase) derived from marine macroalgae and phytoplankton. Those polysaccharases could hydrolyze a variety of macromolecular polysaccharides into small molecules that can be absorbed and metabolized by strain SM1504T and other microorganisms in the seawater [4, 5].
The genomic analyses showed that the strain SM1504T could adapt to extreme Arctic seawater environments, such as high solar radiation, cold temperature and high salinity. Besides, it may act as a vital macromolecular polysaccharide decomposer and would play an important role in organic carbon cycling in the Arctic seawater ecosystem.
Comprehensive antibiotic resistance database
Clustered regularly interspaced short palindromic repeats
High molecular weight
Minimum information on the genome sequence
Rapid annotation using subsystem technology
Tryptone-yeast extract-sea salt
Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG, González JM, et al. Ecology of marine Bacteroidetes: a comparative genomics approach. The ISME Journal. 2013;7:1026.
GPP R, Margarete S, FB M, Christin B, Hanno T, Jost W, et al. Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environ Microbiol. 2012;14:52–66.
Sun C, Fu G-Y, Zhang C-Y, Hu J, Xu L, Wang R-J, et al. Isolation and complete genome sequence of Algibacter alginolytica sp. nov., a novel seaweed-degrading Bacteroidetes bacterium with diverse putative polysaccharide utilization loci. Appl Environ Microbiol. 2016;82:2975–87.
WT J, David W, Emilie L, Flavia E, DM Z, RM J, et al. The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics. Environ Microbiol. 2013;15:1302–17.
Bunse C, Pinhassi J. Marine Bacterioplankton seasonal succession dynamics. Trends Microbiol. 2017;25:494–505.
Imhoff JF. The Family Chlorobiaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. (eds) The Prokaryotes. Berlin, Heidelberg: Springer; 2014. p. 501.
Sheu S-Y, Chen Y-S, Shiau Y-W, Chen W-M. Fluviimonas pallidilutea gen. Nov., sp. nov., a new member of the family Cytophagaceae isolated from a freshwater river. Int J Syst Evol Microbiol. 2013;63:3861–7.
Kang JY, Chun J, Choi A, Cho J-C, Jahng KY. Nibrella saemangeumensis gen. Nov., sp. nov. and Nibrella viscosa sp. nov., novel members of the family Cytophagaceae, isolated from seawater. Int J Syst Evol Microbiol. 2013;63:4508–14.
Finster KW, Herbert RA, Lomstein BA. Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma. Int J Syst Evol Microbiol. 2009;59:839–44.
Chang X, Jiang F, Wang T, Kan W, Qu Z, Ren L, et al. Spirosoma arcticum sp. nov., isolated from high Arctic glacial till. Int J Syst Evol Microbiol. 2014;64:2233–7.
Li D-D, Peng M, Wang N, Wang X-J, Zhang X-Y, Chen X-L, et al. Arcticibacterium luteifluviistationis gen. Nov., sp. nov., isolated from Arctic seawater. Int J Syst Evol Microbiol. 2017;67:664–9.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24:713–4.
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010;20:265–72.
Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013;10:563.
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.
Aziz RK, Bartels D, Best AA, De Jongh M, Disz T, Edwards RA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100–8.
Avni D, Biberman Y, Meyuhas O. The 5′ terminal Oligopyrimidine tract confers translational control on top Mrnas in a cell type-and sequence context-dependent manner. Nucleic Acids Res. 1997;25:995–1001.
Bertelli C, Laird MR, Williams KP, Simon Fraser University research computing group, Lau BY, Hoad G, et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 2017;45:30–5.
Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015;43:237–43.
Zhao B, Liao L, Yu Y, Chen B. Complete genome of Brachybacterium sp. P6-10-X1 isolated from deep-sea sediments of the Southern Ocean. Mar Genomics. 2017;35:27–9.
Hameed A, Shahina M, Huang H-C, Lai W-A, Lin S-Y, Stothard P, et al. Complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1T, a flavobacterium isolated from coastal surface seawater. Mar Genomics. 2018;37:21–5.
Klassen JL. Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics. PLoS One. 2010;5:e11257.
Mueller DR, Vincent WF, Bonilla S, Laurion I. Extremotrophs, extremophiles and broadband pigmentation strategies in a high arctic ice shelf ecosystem. FEMS Microbiol Ecol. 2005;53:73–87.
Oh J, Choe H, Kim BK, Kim KM. Complete genome of a coastal marine bacterium Muricauda lutaonensis KCTC 22339T. Marine Genomis. 2015;23:51–3.
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: A Fast Phage Search Tool. Nucleic Acids Res. 2011;39:347–52.
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains archaea, Bacteria, and Eucarya. Proc Natl Acad Sci. 1990;87:4576–9.
Krieg N, Ludwig W, Euzéby J, Whitman W, Phylum XIV. Bacteroidetes phyl. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB, editors. Bergey’s manual of systematic bacteriology, second edition vol. 4 (the Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes). New York: Springer; 2010: p. 25.
Ohren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol. 2012;62:1–4.
Nakagawa Y, Class IV. Cytophagia class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB, editors. Bergey’s manual of systematic bacteriology, second edition, vol. 4 (The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes). New York: Springer; 2010: 370.
Skerman VBD, McGOWAN V, Sneath PHA. Approved lists of bacterial names. Int J Syst Bacteriol. 1980;30:225–420.
Leadbetter E, Order II. Cytophagales nomen novum. In: Buchanan RE, Gibbons NE, editors. Bergey’s manual of determinative bacteriology. 8th ed. Baltimore: The Williams and Wilkins Co; 1974. p. 99.
Stanier RY. Studies on the Cytophagas. J Bacteriol. 1940;40:619–35.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.
This work was supported by the National Science Foundation of China (31670063, 31670038, 31630012 and 31770412), AoShan Talents Cultivation Program Supported by Qingdao National Laboratory for Marine Science and Technology (2017ASTCP-OS14), the Program of Shandong for Taishan Scholars (TS20090803), the Science and Technology Basic Resources Investigation Program of China (2017FY100804), the National Postdoctoral Program for Innovative Talents (BX201700145), the funding from key laboratory of global change and marine-atmospheric chemistry of the state oceanic administration (2018GCMAC16), Young Scholars Program of Shandong University (2016WLJH36).
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.