Zeimonas sediminis sp. nov., isolated from mangrove sediment

References

1. Lin S-Y, Hameed A, Tsai C-F, Young C-C. Zeimonas arvi gen. nov., sp. nov., of the family Burkholderiaceae, harboring biphenyl- and phenolic acid-metabolizing genes, isolated from a long-term ecological research field. Antonie Van Leeuwenhoek 2021; 114:2101–2111 [View Article]
   [Google Scholar]
2. Zhang CJ, Pan J, Duan CH, Wang YM, Liu Y et al. Prokaryotic diversity in mangrove sediments across Southeastern China fundamentally differs from that in other biomes. mSystems 2019; 4:e00442-19 [View Article]
   [Google Scholar]
3. Hiraishi A. Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett Appl Microbiol 1992; 15:210–213 [View Article] [PubMed]
   [Google Scholar]
4. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article]
   [Google Scholar]
5. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
   [Google Scholar]
6. Zhang W, Sun Z. Random local neighbor joining: a new method for reconstructing phylogenetic trees. Mol Phylogenet Evol 2008; 47:117–128 [View Article]
   [Google Scholar]
7. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
   [Google Scholar]
8. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
   [Google Scholar]
9. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
   [Google Scholar]
10. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article]
    [Google Scholar]
11. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article]
    [Google Scholar]
12. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
    [Google Scholar]
13. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
14. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
    [Google Scholar]
15. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
16. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article]
    [Google Scholar]
17. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
    [Google Scholar]
18. Ghosh W, Mallick S, DasGupta SK. Origin of the Sox multienzyme complex system in ancient thermophilic bacteria and coevolution of its constituent proteins. Res Microbiol 2009; 160:409–420 [View Article] [PubMed]
    [Google Scholar]
19. Blasco F, Iobbi C, Ratouchniak J, Bonnefoy V, Chippaux M. Nitrate reductases of Escherichia coli: sequence of the second nitrate reductase and comparison with that encoded by the narGHJI operon. Mol Gen Genet 1990; 222:104–111 [View Article]
    [Google Scholar]
20. Li Y, Wu J, Wang W, Ding P, Feng L. Proteomics analysis of aromatic catabolic pathways in thermophilic Geobacillus thermodenitrificans NG80-2. J Proteomics 2012; 75:1201–1210 [View Article]
    [Google Scholar]
21. Hein S, Tran H, Steinbüchel A. Synechocystis sp. PCC6803 possesses a two-component polyhydroxyalkanoic acid synthase similar to that of anoxygenic purple sulfur bacteria. Arch Microbiol 1998; 170:162–170 [View Article] [PubMed]
    [Google Scholar]
22. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 1990
    [Google Scholar]
23. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article]
    [Google Scholar]
24. Milton S. Da Costa L, Wait R. The identification of polar lipids in prokaryotes. In Methods in Microbiology vol 38 2011 pp 165–181
    [Google Scholar]
25. Hanif M, Atsuta Y, Fujie K, Daimon H. Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples. Molecules 2012; 17:2628–2642 [View Article] [PubMed]
    [Google Scholar]