Abstract
A Gram-stain negative, strictly aerobic, and rod-shaped bacterium, designated as strain L182T, was isolated from coastal sediment in Beihai, Guangxi Province, PR China. Colonies of strain L182T were yellow, 2 mm in diameter, round, opaque, smooth and convex after incubation on marine ager at 30 °C for 3 days. Cells were catalase-positive but oxidase-negative. Growth of strain L182T was observed at 4–40 °C (optimum, 25 °C), pH 5.5–10.0 (optimum, pH 5.5–8.0) and with 0–6% (w/v) NaCl (optimum, 0.5–4.0%). The G + C content based on the genome sequence was 36.0%. The only respiratory quinone was MK-6. The main polar lipids included phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, one unidentified glycolipids, four unidentified aminolipids and six unidentified lipids. The major fatty acids (> 10%) were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The 16S rRNA gene sequence similarity between strain L182T and Aestuariibaculum suncheonense SC17T was 98.2%, and the similarities with other type strains of the genus Aestuariibaculum were 96.1–97.2%. The average nucleotide identity and in silicon DNA–DNA hybridization values between the strain L182T and its closely related Aestuariibaculum species were 80.8–85.2% and 22.0–29.5%. According to the above results, Aestuariibaculum lutulentum sp. nov. was proposed as a novel species. The type strain is L182T (= MCCC 1K08065T = KCTC 92530T).
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- MA:
-
Marine agar
- ANI:
-
Average nucleotide identity
- DDH:
-
DNA–DNA hybridization
- MB:
-
Marine broth
- ML:
-
Maximum-likelihood
- NJ:
-
Neighbour-joining
- MK-6:
-
Menaquinone-6
- PE:
-
Phosphatidylethanolamine
- PG:
-
Phosphatidylglycerol
- PL:
-
Phospholipid
- GL:
-
Glycolipids
- L:
-
Lipid
References
Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75. https://doi.org/10.1186/1471-2164-9-75
Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973. https://doi.org/10.1093/bioinformatics/btp348
Choi J, Lee D, Jang JH et al (2018) Aestuariibaculum marinum sp. nov., a marine bacterium isolated from seawater in South Korea. J Microbiol 56:614–618. https://doi.org/10.1007/s12275-018-8134-z
Chun J, Oren A, Ventosa A et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516
Do K-A (1992) A simulation study of balanced and antithetic bootstrap resampling methods. J Stat Comput Simul 40:153–166
Emms DM, Kelly S (2019) OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20:238. https://doi.org/10.1186/s13059-019-1832-y
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Gavriilidou A, Gutleben J, Versluis D et al (2020) Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis. BMC Genom 21:569
Huang M-M, Guo L-L, Wu Y-H et al (2018) Pseudooceanicola lipolyticus sp. nov., a marine alphaproteobacterium, reclassification of Oceanicola flagellatus as Pseudooceanicola flagellatus comb. nov. and emended description of the genus Pseudooceanicola. Int J Syst Evol Microbiol 68:409–415
Jeong SH, Park MS, Jin HM et al (2013) Aestuariibaculum suncheonense gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a tidal flat and emended descriptions of the genera Gaetbulibacter and Tamlana. Int J Syst Evol Microbiol 63:332–338. https://doi.org/10.1099/ijs.0.037846-0
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. https://doi.org/10.1093/molbev/mst010
Kim M, Oh H-S, Park S-C, 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
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/BF01731581
Komagata K, Suzuki K-I (1988) 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol. https://doi.org/10.1016/S0580-9517(08)70410-0
Lagesen K, Hallin P, Rødland EA et al (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108
Lee J-B, Kim B-C, Kim H et al (2013) Aestuariibaculum scopimerae sp. nov., isolated from the globular ghost crab. Scopimera Globosa J Microbiol 51:736–740. https://doi.org/10.1007/s12275-013-3499-5
Li O, Li A, Zhang C-J et al (2018) Identification and characterization of six glycosyltransferases involved in the biosynthesis of a new bacterial exopolysaccharide in Paenibacillus elgii. Appl Microbiol Biotechnol 102:1357–1366. https://doi.org/10.1007/s00253-017-8673-y
Meier-Kolthoff JP, Auch AF, Klenk H-P, 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
Minnikin DE, O’Donnell AG, Goodfellow M et al (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
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274
Parks DH, Imelfort M, Skennerton CT et al (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
Romero S, Schell RF, Pennell DR (1988) Rapid method for the differentiation of gram-positive and gram-negative bacteria on membrane filters. J Clin Microbiol 26:1378–1382. https://doi.org/10.1128/jcm.26.7.1378-1382.1988
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sun C, Fu G, Zhang C et al (2016) 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 82:2975–2987. https://doi.org/10.1128/AEM.00204-16
Sun C, Xu L, Yu X-Y et al (2018) Minwuia thermotolerans gen. nov., sp. nov., a marine bacterium forming a deep branch in the Alphaproteobacteria, and proposal of Minwuiaceae fam. nov. and Minwuiales ord. nov. Int J Syst Evol Microbiol 68:3856–3862. https://doi.org/10.1099/ijsem.0.003073
Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Wu Z-C, Zhang X-Y, Sun C et al (2021) Aestuariibaculum sediminum sp. nov., a marine bacterium isolated from a tidal flat in Zhoushan. Arch Microbiol 203:2953–2960. https://doi.org/10.1007/s00203-021-02262-1
Xu L, Wu Y-H, Jian S-L et al (2016) Pseudohongiella nitratireducens sp. nov., isolated from seawater, and emended description of the genus Pseudohongiella. Int J Syst Evol Microbiol 66:5155–5160. https://doi.org/10.1099/ijsem.0.001489
Yoon SH, Ha SM, Kwon S et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617
Funding
This study was supported by National Science and Technology Fundamental Resources Investigation Program of China (2019FY100700), National Natural Science Foundation of China (No. 31900003), the Fundamental Research Funds of Zhejiang Sci-Tech University (22042315-Y) and the Open Foundation from Marine Sciences in the First-Class Subjects of Zhejiang (No. OFMS013).
Author information
Authors and Affiliations
Contributions
Tests were designed by SC, data collection and analysis were mainly performed by GJW and HDY, supplementary figures and tables were prepared by GJW, ZWW, WYR, QW and SY, sample was collected WZC and SC. The manuscript was written by GJW and YJJ, reviewed by XL and SC. All authors reviewed the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Communicated by Yusuf Akhter.
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
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Gao, JW., He, DY., Zhang, WW. et al. Aestuariibaculum lutulentum sp. nov., a marine bacterium isolated from coastal sediment in Beihai. Arch Microbiol 205, 187 (2023). https://doi.org/10.1007/s00203-023-03535-7
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-023-03535-7