- Short genome report
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High-quality draft genome sequence of Effusibacillus lacus strain skLN1T, facultative anaerobic spore-former isolated from freshwater lake sediment
Standards in Genomic Sciencesvolume 12, Article number: 76 (2017)
Effusibacillus lacus strain skLN1T is the type strain of the type species in the genus Effusibacillus which is the one of the genera in the family Alicyclobacillaceae within the phylum Firmicutes . Effusibacillus lacus strain skLN1T is a Gram-positive, spore-forming thermophilic neutrophile isolated from freshwater lake sediment. Here, we present the draft genome sequence of strain skLN1T, which consists of 3,902,380 bp with a G + C content of 50.38%.
The family Alicyclobacillaceae consists of four genera; Alicyclobacillus , Kyrpidia , Tumebacillus and Effusibacillus. Alicyclobacillus spp. are known as the significant causative microorganisms of fruit juice spoilage [1, 2] Kyrpidia tusciae , a sole characterized species of the genus Kyrpidia is a thermoacidophile which grows best under autotrophic conditions [3, 4]. Members of the genus Tumebacillus are mesoneutrophile which are derived from various environments, such as the Arctic permafrost, wastewater and and soil [5,6,7]. Genus Effusibacillus was established in this family together with the reclassification of Alicyclobacillus pohliae as Effusibacillus pohliae and Alicyclobacillus consociatus as Effusibacillus consociatus . Effusibacillus lacus strain skLN1T is a facultative anaerobic, Gram-positive bacterium isolated from freshwater lake sediment. Here, we descibe draft genome sequence of the type strain of this genus, Effusibacillus lacus strain skLN1T. In this study, we summarize the features of E. lacus strain skLN1T and show an overview of draft genome sequence and annotation of this strain.
Classification and features
E. lacus strain skLN1T was isolated from sediments of a freshwater lake, Lake Yamanashi, Japan . Cell wall structure of this strain is Gram-positive type. Cells of this strain are spore-forming rods varied from 5 to 100 μm in length (Fig. 1, Table 1). The major cellualr fatty acids of this strain are iso-C 14 : 0, iso-C 15 : 0 and iso-C 16 : 0. Respiratory quinones of this strain are MK-7 (99.5%) and MK-8 (0.5%). The cell-wall peptidoglycan of this strain consists of meso-diaminopimelic acid, alanine and glutamic acid, indicating the presence of A1γ-type polymer. This bacterium is facultative anaerobe and is capable of respiration and fermentation. Sugars, organic acids, peptides and amino acids are used for fermentative growth of this strain. Strain skLN1T reduce nitrate to nitrite under anaerobic conditions in the presence of lactate. This strain cannot grow lithoautotrophically with elemental sulfur or thiosulfate under oxic/anoxic conditions in the presence nitrate.
The phylogenetic position of E. lacus strain skLN1T among the members of the family Alicyclobacillaceae is shown in the phylogenetic tree based on the 16S rRNA gene sequence (Fig. 2). Strain skLN1T, E. consociatus and E. pohliae are classified into an independent cluster in the family Alicyclobacillaceae .
Genome sequencing information
Genome project history
E. lacus strain skLN1T was selected for genome sequencing on the basis of its 16S rRNA gene-based phylogenetic position in the family Alicyclobacillaceae (Fig. 2). Table 2 shows a summary of the genome sequencing project information and its association with MIGS version 2.0 compliance . The genome consists of 127 contigs, which has been deposited at DDBJ/EMBL/GenBank under accession number BDUF01000000.
Growth conditions and genomic DNA preparation
E. lacus strain skLN1T (DSM 27172) was grown aerobically on TSB liquid medium (Daigo) at 50 °C without shaking. Genomic DNA was extracted from collected cells using Wizard® genomic DNA purification kit (Promega).
Genome sequencing and assembly
The genome sequence of strain skLN1T was determined using paired-end Illumina sequencing at Hokkaido System Science Co., Ltd. (Japan). The 11,205,386 reads were generated from a library with 100 bp inserts. After trimming of the reads, a total of 11,009,340 high-quality filtered paired end reads with a hash length of 95 bp were obtained. Reads were assembled de novo using Velvet version 1.2.08 into 127 scaffolds.
vhThe genome sequence of strain skLN1T was automatically annotated and analyzed through the MiGAP pipeline . In this pipeline, RNAmmer  and tRNAscan-SE  were used to identify rRNA and tRNA genes, respectively. MetaGene Annotator  was used for prediction of open reading frames likely to encode proteins (coding sequences), and functional annotation was performed based on reference databases, including Reference Sequence, TrEMBL, and Clusters of Orthologous Groups. Manual annotation was performed using IMC-GE software (In Silico Biology; Yokohama, Japan). Putative CDSs possessing BLASTP matches with more than 70% coverage, 35% identity and E-values less than 1 × e−5 were considered potentially functional genes. The CDSs were annotated as hypothetical proteins when these standard values were not satisfied. Transcription start sites of predicted proteins were corrected based on multiple sequence alignments. The protein-coding genes in the genome were also subjected to analysis on WebMGA  for the COGs and Protein family annotations. Transmembrane helices and signal peptides were predicted by using Phobius . CRISPR loci were distinguished using the CRISPR Recognition Tool . General features of Effusibacillus lacus strain skLN1T and the MIxS mandatory information were show in Table 1.
The total genome of E. lacus strain skLN1T was 3,902,380 bp in size with a GC content of 50.38% (Table 3). It was predicted to contain 3733 genes including 3683 protein-coding genes and 50 RNA genes (for tRNA). Approximately 77.5% of the predicted genes were assigned to COG functional categories. The distribution of genes into COGs functional categories is presented in Table 4.
Insights from the genome sequence
E. lacus strain skLN1T possesses genes of key enzymes for dissimilatory nitrate reduction, i.e. napA (locus tag: EFBL_1421), narGHJI (EFBL_3070–3073), nirK (EFBL_0113), norB (EFBL_3053), nrfA (EFBL_2499) and related genes. Both genes for membrane-bound and periplasmic nitrate reductases (narG and napA) were identified in the genome. A protein coded in the 61,298–63,379 bp region of contig095 showed high amino-acid sequence similarity (≤ 74%) to nitrous-oxide reductase (NosZ), although the region was not annotated as nosZ gene because of the internal assembly gaps. Genome of E. lacus strain skLN1T contains the genes for complete denitrification to N2 gas (nirK, norB and nosZ) and dissimilatory ammonification (nrfA), although end product of nitrate reduction identified in the previous study was nitrite . The reduction of nitrate to nitrite was reported in several species in the family Alicylobacillaceae , but denitrifying organisms have not been reported in this family. Genetic components involved in dissimilatory nitrate reduction were not found in the genome of Effucibacillus pohliae strain DSM 22757 T. Kyrpidia tuscia e DSM 2912 T possesses norB gene, but genes for the other denitrification enzymes were not found in the genome of this strain . Additionally, genes for dissimilatory sulfur oxidation were not identified in the genome of E. lacus strain skLN1T, although this organism was isolated from a sulfur-oxidizing enrichment culture .
This study contributed to the knowledge of genome sequences of the genus Effusibacillus within the family Alicyclobacillaceae . The genome of E. lacus strain skLN1T consists of 3683 protein-coding genes and 50 RNA genes. Genes involved in dissimilatory nitrate reduction were identified in the genome of this organism.
Clustered regularly interspaced short palindromic repeat
Microbial genome annotation pipeline
Periplasmic nitrate reductase
Respiratory nitrate reductase
Nitric oxide reductase
Nitrous oxide reductase
Ammonia-forming cytochrome c nitrite reductase subunit c552
Huang X-C, Yuan Y-H, Guo C-F, Gekas V, Yue T-L. Alicyclobacillus in the fruit juice industry: spoilage, detection, and prevention/control. Food Rev Int. 2015 [cited 2017 Jul 26];31:91–124. Available from: http://www.tandfonline.com/doi/full/10.1080/87559129.2014.974266.
Chang S-S, Kang D-H. Alicyclobacillus spp. in the fruit juice industry: history, characteristics, and current isolation/detection procedures. Crit Rev Microbiol.; 2004 [cited 2017 Jul 26];30:55–74. Available from: http://www.tandfonline.com/doi/full/10.1080/10408410490435089.
Klenk H-P, Lapidus A, Chertkov O, Copeland A, Del Rio TG, Nolan M, et al. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and rain. Stand Genomic Sci; 2011 [cited 2017 Jul 25];5:121–134. Michigan State University. Available from: http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.2144922.
Bonjour F, Aragno M. Bacillus tusciae, a new species of thermoacidophilic, facultatively chemolithoautotrophic hydrogen oxidizing sporeformer from a geothermal area. Arch Microbiol. 1984 [cited 2017 Jul 25];139:397–401. Available from: http://link.springer.com/10.1007/BF00408386.
Steven B, Chen MQ, Greer CW, Whyte LG, Niederberger TD. Tumebacillus permanentifrigoris gen. Nov., sp. nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost. Int J Syst Evol Microbiol. 2008 [cited 2017 Jul 26];58:1497–1501. Available from: http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.65101-0.
Wang Q, Xie N, Qin Y, Shen N, Zhu J, Mi H, et al. Tumebacillus flagellatus sp. nov., an -amylase/pullulanase-producing bacterium isolated from cassava wastewater. Int J Syst Evol Microbiol; 2013 [cited 2017 Jul 26];63:3138–3142. Available from: http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.045351-0
Kim J-H, Kim W. Tumebacillus soli sp. nov., isolated from non-rhizosphere soil. Int J Syst Evol Microbiol; 2016 [cited 2017 Jul 26];66:2192–2197. Available from: http://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.001009.
Watanabe M, Kojima H, Fukui M. Proposal of Effusibacillus lacus gen. Nov., sp. nov., and reclassification of Alicyclobacillus pohliae as Effusibacillus pohliae comb. nov. and Alicyclobacillus consociatus as Effusibacillus consociatus comb. nov. Int J Syst Evol Microbiol. 2014;64
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, bacteria, and Eucarya. Proc Natl Acad Sci National Acad Sciences. 1990;87:4576–9.
Sugawara H, Ohyama A, Mori H, Kurokawa K. Microbial genome annotation pipeline (MiGAP) for diverse users. Yokohama, Japan: Softw Demonstr S001–1-2L 20th Int Conf Genome Inform Poster Softw Demonstr; 2009.
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 [cited 2017 Jul 26];35:3100–3108. Available from: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkm160.
Lowe TM, Eddy SR, Meyuhas O. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res; 1997 [cited 2017 Jul 26];25:955–964. Available from: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/25.5.0955.
Noguchi H, Taniguchi T, Itoh T. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res; 2008 [cited 2017 Jul 26];15:387–396. Available from: https://academic.oup.com/dnaresearch/article-lookup/doi/10.1093/dnares/dsn027.
Wu S, Zhu Z, Fu L, Niu B, Li W. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics. 2011;12:444. Available from: https://doi.org/10.1186/1471-2164-12-444
Kall L, Krogh A, Sonnhammer ELL. Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res; 2007 [cited 2017 Jul 26];35:W429–W432. Available from: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkm256.
Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, et al. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 [cited 2017 Jul 26];8:209. Available from: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-209.
Shapleigh JP. Denitrifying Prokaryotes. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. Prokaryotes prokaryotic Physiol Biochem. Berlin, Heidelberg: Springer Berlin Heidelberg; 2013. p. 405–25. Available from: https://doi.org/10.1007/978-3-642-30141-4_71.
Garrity GM, Holt JG. The road map to the manual. Bergey’s Manual® Syst Bacteriol; 2001 [cited 2017 Jul 26]. p. 119–166. Available from: http://link.springer.com/10.1007/978-0-387-21609-6_15.
Gibbons NE, Murray RGE. Proposals concerning the higher Taxa of bacteria. Int J Syst Bacteriol; 1978 [cited 2017 Jul 26];28:1–6. Available from: http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-28-1-1.
Ludwig WSK WW. Class I. Bacilli class. Nov. In: De Vos P, Garrity GM, Jones D, Krieg WNR, Ludwig W, Rainey EA, Schleifer KH WW (eds), editor. Bergey’s man Syst Bacteriol. vol. 3. Springer, Dordrecht, Heidelberg, London, New York; 2009. p. 19–20.
Skerman VBD, McGowan V, Sneath PHA. Approved lists of bacterial names. Int J Syst Evol Microbiol. 1980;30:225–420.
Prevot AR, Hauderoy P, Ehringer G, Guillot G, Magrou J, Prevot AR, et al. Dictionnaire des bactéries pathogens. Hauduroy P, Ehringer G, Guillot G, Magrou J, Prevot AR, Rosset, Urbain A 1953;1–692.
Ludwig W, Schleifer K-H, Whitman WB. Revised road map to the phylum Firmicutes. Syst Bacteriol; 2009 [cited 2017 Jul 26]. p. 1–13. Available from: http://link.springer.com/10.1007/978-0-387-68489-5_1
Kumar S, Stecher G, Tamura K, J G, E P, C Q, et al. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol; 2016 [cited 2017 Jul 28];33:1870–1874. Available from: https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msw054.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics; 2007 [cited 2017 Jul 28];23:2947–2948. Available from: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btm404.
This study was supported by a grant-in-aid for Research Fellow of Japan Society for the Promotion Science to MW and JSPS KAKENHI Grant Number 22370005 to MF.
The authors declare that they have no competing interests.
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