Abstract
An isolate, designated strain KIGAM418T was isolated from marine mud below 192 m depth in the Hupo Basin, Republic of Korea. Strain KIGAM418T was Gram-stain positive, spore-forming, rod-shaped, facultatively anaerobic, and grew at 10‒45 °C, in 0‒2% (w/v) NaCl at pH 4.0‒12.0. The strain tested positive for catalase, oxidase, and motility. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain KIGAM418T was related to the genus Fictibacillus. The strain showed the highest similarity to Fictibacillus rigui WPCB074T (98.0–98.1%) and Fictibacillus solisalsi YC1T (97.2–97.8%). The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. The major fatty acids were characterized as anteiso-C15:0 and iso-C15:0. Strain KIGAM418T possessed diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as the major polar lipids and menaquinone-7 as the predominant menaquinone. The genome size and G + C content were 4.56 Mb and 43.2 mol%, respectively. According to predicted functional genes of the genome, the category of amino acid transport and metabolism was mainly distributed. Based on the polyphasic taxonomic data, strain KIGAM418T represents a novel species of the genus Fictibacillus, for which the name Fictibacillus marinisediminis sp. nov. is proposed. The type strain is KIGAM418T (= KCTC 43291 T = JCM 34437 T).
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genome 9:75. https://doi.org/10.1186/1471-2164-9-75
Baik KS, Lim CH, Park SC, Kim EM, Rhee MS, Seong CN (2010) Bacillus rigui sp. nov., isolated from wetland fresh water. Int J Syst Evol Microbiol 60:2204–2209. https://doi.org/10.1099/ijs.0.018184-0
Bauer AW (1966) Antibiotic susceptibility testing by a standardized single disc method. Am J Clin Pathol 45:493–496
Benson HJ (2002) Microbiological applications: a laboratory manual in general microbiology. McGraw-Hill Book Company, New York
Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, Van Wezel GP, Medema MH, Weber T (2021) antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucl Acids Res 49:W29–W35. https://doi.org/10.1093/nar/gkab335
Burford MA, Longmore AR (2001) High ammonium production from sediments in hypereutrophic shrimp ponds. Mar Ecol Prog Ser 224:187–195. https://doi.org/10.3354/meps224187
Chaudhari NM, Gupta VK, Dutta C (2016) BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 6:24373. https://doi.org/10.1038/srep24373
Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33:D325–D328. https://doi.org/10.1093/nar/gki008
Chen J, Liu Y, Diep P, Mahadevan R (2021) Genomic analysis of a newly isolated Acidithiobacillus ferridurans JAGS strain reveals its adaptation to acid mine drainage. Minerals 11:74. https://doi.org/10.3390/min11010074
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genomic data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516
Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316. https://doi.org/10.1128/mr.45.2.316-354.1981
Crab R, Avnimelech Y, Defoirdt T, Bossier P, Verstraete W (2007) Nitrogen removal techniques in aquaculture for a sustainable production. Aquaculture 270:1–14. https://doi.org/10.1016/j.aquaculture.2007.05.006
Dastager SG, Mawlankar R, Srinivasan K, Tang SK, Lee JC, Ramana VV, Shouche YS (2014) Fictibacillus enclensis sp. nov., isolated from marine sediment. Antonie Van Leeuwenhoek 105:461–469. https://doi.org/10.1007/s10482-013-0097-9
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Glaeser SP, Dott W, Busse HJ, Kämpfer P (2013) Fictibacillus phosphorivorans gen. nov., sp. nov. and proposal to reclassify Bacillus arsenicus, Bacillus barbaricus, Bacillus macauensis, Bacillus nanhaiensis, Bacillus rigui, Bacillus solisalsi and Bacillus gelatini in the genus Fictibacillus. Int J Syst Evol Microbiol 63:2934–2944. https://doi.org/10.1099/ijs.0.049171-0
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P (2017) Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol 34:2115–2122. https://doi.org/10.1093/molbev/msx148
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucl Acids Res 28:27–30. https://doi.org/10.1093/nar/28.1.27
Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731. https://doi.org/10.1016/j.jmb.2015.11.006
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066. https://doi.org/10.1093/nar/gkf436
Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351. https://doi.org/10.1099/ijs.0.059774-0
Kimura M (1979) The neutral theory of molecular evolution. Sci Am 241:98–129. https://doi.org/10.1016/j.jmb.2015.11.006
Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of anurans. Syst Biol 18:1–32. https://doi.org/10.1093/sysbio/18.1.1
Komagata K and Suzuki KI (1988) Lipid and cell-wall analysis in bacterial systematics. In: Methods in microbiology (Vol. 19, pp. 161–207). Academic press, London
Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A (2010) A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics 26:1481–1487. https://doi.org/10.1093/bioinformatics/btq229
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Lane DJ (1991) 16S/23S rRNA Sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New Jersey, pp 115–175
Lee I, Kim YO, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760
Lee I, Chalita M, Ha SM, Na SI, Yoon SH, Chun J (2017) ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 67:2053–2057. https://doi.org/10.1099/ijsem.0.001872
Lefort V, Desper R, Gascuel O (2015) FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 32:2798–2800. https://doi.org/10.1093/molbev/msv150
Liu H, Zhou Y, Liu R, Zhang KY, Lai R (2009) Bacillus solisalsi sp. nov., a halotolerant, alkaliphilic bacterium isolated from soil around a salt lake. Int J Syst Evol Microbiol 59:1460–1464. https://doi.org/10.1099/ijs.0.000653-0
Lledó B, Marhuenda-Egea FC, Martínez-Espinosa RM, Bonete MJ (2005) Identification and transcriptional analysis of nitrate assimilation genes in the halophilic archaeon Haloferax mediterranei. Gene 361:80–88. https://doi.org/10.1016/j.gene.2005.07.011
Mahato NK, Gupta V, Singh P, Kumari R, Verma H, Tripathi C, Rani P, Sharma A, Singhvi N, Sood H, Hira P, Kohri P, Nayyar N, Puri A, Bajaj A, Kumar R, Negi V, Talwar C, Khurana H, Nagar S, Sharma M, Mishra H, Singh AK, Dhingra G, Negi RK, Shakarad M, Singh Y, Lal R (2017) Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques. Antonie Van Leeuwenhoek 110:1357–1371. https://doi.org/10.1007/s10482-017-0928-1
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60
Miller LT (1982) Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16:584–586. https://doi.org/10.1128/jcm.16.3.584-586.1982
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6
Moreno-Vivián C, Cabello P, Martínez-Luque M, Blasco R, Castillo F (1999) Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases. J Bacteriol 181:6573–6584. https://doi.org/10.1128/JB.181.21.6573-6584.1999
Morozkina EV, Zvyagilskaya RA (2007) Nitrate reductases: structure, functions, and effect of stress factors. Biochem Mosc 72:1151–1160. https://doi.org/10.1134/S0006297907100124
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. https://doi.org/10.1101/gr.186072.114
Richardson DJ, Berks BC, Russell DA, Spiro S, Taylor CJ (2001) Functional, biochemical and genetic diversity of prokaryotic nitrate reductases. Cell Mol Life Sci 58:165–178. https://doi.org/10.1007/PL00000845
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI technical note 101. MIDI Inc, Newark, DE, USA
Schleifer KH (1985) Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156. https://doi.org/10.1016/S0580-9517(08)70474-4
Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P (ed) Methods for general and molecular bacteriology. American Society for Microbiology, Washington DC, pp 607–654
Sneath PH, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. Freeman, San Francisco
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882. https://doi.org/10.1093/nar/25.24.4876
Tiedje JM (1988) Ecology of denitrification and dissimilatory nitrate reduction to ammonium. In: Zehnder AJB (ed) Environmental microbiology of anaerobes. Wiley, pp 179–244
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613. https://doi.org/10.1099/ijsem.0.001755
Zhang T, Fan X, Hanada S, Kamagata Y, Fang HHP (2006) Bacillus macauensis sp. nov., a long-chain bacterium isolated from a drinking water supply. Int J Syst Evol Microbiol 56:349–353. https://doi.org/10.1099/ijs.0.63868-0
Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61:533–616. https://doi.org/10.1128/mmbr.61.4.533-616.1997
Funding
This work was supported by Research Assistance Program (2021) in the Incheon National University. This work also was supported by grants from the National Institute of Biological Resources funded by the Ministry of Environment (No. NIBR202203112), Republic of Korea.
Author information
Authors and Affiliations
Contributions
ESC and CYH performed all the experiments and drafted the manuscript. DHJ and ITC contributed to analyze the microbial genome. MJS designed all the experiments and supervised the manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that there is no conflict of interest.
Additional information
Communicated by Erko Stackebrandt.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Cho, ES., Hwang, C.Y., Jung, DH. et al. Fictibacillus marinisediminis sp. nov., a nitrate-reducing bacterium isolated from marine sediment in Hupo Basin, Republic of Korea. Arch Microbiol 204, 474 (2022). https://doi.org/10.1007/s00203-022-03067-6
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-022-03067-6