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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 6

sp. nov., a copper-resistant bacterium isolated from soil contaminated with heavy metals in Chapala Basin, Mexico No Access

Abstract

A polyphasic taxonomic study was carried out on the bacterial EZn1, isolated from heavy-metal-contaminated soil in the Chapala Basin, Mexico. This Gram-negative, aerobic, rod-shaped bacterium formed orange-pigmented colonies, producing the pigment flexirubin. Analysis of the 16S rRNA gene sequence revealed that EZn1 represents a member of the genus in the family and is closely related to GSE06 (98.3%), ISE14 (97.7%) and NBCR 14944 (97.5%). The average nucleotide identity between the genomes of strain EZn1 and GSE06 was 90.9%, and digital DNA–DNA hybridization showed values of less than 70% with the type strains for the related species. The polar lipids present in the strain included phosphatidylethanolamine, phosphatidylglycerol, glycolipids and unidentified aminoglycolipids, whereas the major cellular fatty acids included iso-C and iso-C 3-OH. The whole genome of EZn1 was 5,003,090 bp in length, with a DNA G+C content of 36.7 mol %. The strain EZn1 showed physiological characteristics different from those of closely related species. This strain showed resistance to copper (20 mM), and its genome contained genes that may confer resistance to this metal and other heavy metals (As, Cd, Co, Cr, Hg, K, Mg, Mo, Na and Zn). According to the polyphasic analysis, the strain EZn1 (=TSD-322=CAIM 1954) is a novel species that we named sp. nov.

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Keyword(s): Chryseobacterium , contaminated soil , copper resistance , heavy metals and orange-pigmented bacterium
Funding
This study was supported by the:
  • Secretaría de Investigación y Posgrado, Instituto Politécnico Nacional (Award SIP20210819)
    • Principal Award Recipient: MARÍASOLEDAD VÁSQUEZ-MURRIETA
  • Secretaría de Investigación y Posgrado, Instituto Politécnico Nacional (Award 20200229)
    • Principal Award Recipient: MARÍASOLEDAD VÁSQUEZ-MURRIETA
© 2025 The Authors
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References

  1. Vandamme P, Bernardet J-F, Segers P, Kersters K, Holmes B. New perspectives in the classification of the Flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 1994; 44:827–831 [View Article]
     [Google Scholar]
  2. Nover LL, Weber M, Hölzl G, Gisch N, Waldhans C et al. Polar lipid characterization and description of Chryseobacterium capnotolerans sp. nov., isolated from high CO2-containing atmosphere and emended descriptions of the genus Chryseobacterium, and the species C. balustinum, C. daecheongense, C. formosense, C. gleum, C. indologenes, C. joostei, C. scophthalmum and C. ureilyticum. Int J Syst Evol Microbiol 2022; 72:005372
     [Google Scholar]
  3. Wu YF, Wu QL, Liu SJ. Chryseobacterium taihuense sp. nov., isolated from a eutrophic lake, and emended descriptions of the genus Chryseobacterium, Chryseobacterium taiwanense, Chryseobacterium jejuense and Chryseobacterium indoltheticum. Int J Syst Evol Microbiol 2013; 63:913–919 [View Article] [PubMed]
     [Google Scholar]
  4. Kong D, Wang Y, Li Q, Zhou Y, Jiang X et al. Chryseobacterium subflavum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2022; 72:005345 [View Article] [PubMed]
     [Google Scholar]
  5. Kim M, Oh ET, Kim SB. Description of Chryseobacterium fluminis sp. nov., a keratinolytic bacterium isolated from a freshwater river. Int J Syst Evol Microbiol 2024; 74:006261 [View Article] [PubMed]
     [Google Scholar]
  6. Jeong JJ, Lee DW, Park B, Sang MK, Choi IG et al. Chryseobacterium cucumeris sp. nov., an endophyte isolated from cucumber (Cucumis sativus L.) root, and emended description of Chryseobacterium arthrosphaerae. Int J Syst Evol Microbiol 2017; 67:610–616 [View Article] [PubMed]
     [Google Scholar]
  7. Shelomi M, Han C-J, Chen W-M, Chen H-K, Liaw S-J et al. Chryseobacterium oryctis sp. nov., isolated from the gut of the beetle Oryctes rhinoceros, and Chryseobacterium kimseyorum sp. nov., isolated from a stick insect rearing cage. Int J Syst Evol Microbiol 2023; 73:005813 [View Article] [PubMed]
     [Google Scholar]
  8. Kim M, Kim YS, Cha CJ. Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. isolated from the aquatic environment, South Korea. J Microbiol 2023; 61:37–47 [View Article] [PubMed]
     [Google Scholar]
  9. Abou Abdallah R, Okdah L, Bou Khalil J, Anani H, Fournier P-E et al. Draft genome and description of Chryseobacterium phocaeense sp. nov.: a new bacterial species isolated from the sputum of a cystic fibrosis patient. Arch Microbiol 2019; 201:1361–1368 [View Article] [PubMed]
     [Google Scholar]
  10. Mestre R. JE. Integrated approach to river basin management: Lerma-Chapala case study—attributions and experiences in water management in Mexico. Water Int 1997; 22:140–152 [View Article]
     [Google Scholar]
  11. Kou B, He Y, Wang Y, Qu C, Tang J et al. The relationships between heavy metals and bacterial communities in a coal gangue site. Environ Pollut 2023; 322:121136 [View Article] [PubMed]
     [Google Scholar]
  12. Nanda M, Kumar V, Sharma DK. Multimetal tolerance mechanisms in bacteria: the resistance strategies acquired by bacteria that can be exploited to “clean-up” heavy metal contaminants from water. Aquat Toxicol 2019; 212:1–10 [View Article] [PubMed]
     [Google Scholar]
  13. Patra M, Pandey AK, Dubey SK. Genomic insights into multidrug and heavy metal resistance in Chryseobacterium sp. BI5 isolated from sewage sludge. Total Environ Microbiol 2025; 1:100005 [View Article]
     [Google Scholar]
  14. Majewska M, Wdowiak-Wróbel S, Marek-Kozaczuk M, Nowak A, Tyśkiewicz R. Cadmium-resistant Chryseobacterium sp. DEMBc1 strain: characteristics and potential to assist phytoremediation and promote plant growth. Environ Sci Pollut Res Int 2022; 29:83567–83579 [View Article] [PubMed]
     [Google Scholar]
  15. Vásquez-Murrieta MS, Govaerts B, Dendooven L. Microbial biomass C measurements in soil of the central highlands of Mexico. Appl Soil Ecol 2007; 35:432–440 [View Article]
     [Google Scholar]
  16. Adagunodo TA, Sunmonu LA, Emetere ME. Heavy metals’ data in soils for agricultural activities. Data Brief 2018; 18:1847–1855 [View Article] [PubMed]
     [Google Scholar]
  17. Torres Z, Mora MA, Taylor RJ, Alvarez-Bernal D. Tracking metal pollution in lake Chapala: concentrations in water, sediments, and fish. Bull Environ Contam Toxicol 2016; 97:418–424 [View Article] [PubMed]
     [Google Scholar]
  18. Rathnayake IVN, Megharaj M, Krishnamurti GSR, Bolan NS, Naidu R. Heavy metal toxicity to bacteria - are the existing growth media accurate enough to determine heavy metal toxicity?. Chemosphere 2013; 90:1195–1200 [View Article] [PubMed]
     [Google Scholar]
  19. Arroyo-Herrera I, Román-Ponce B, Reséndiz-Martínez AL, Estrada-de Los Santos P, Wang ET et al. Heavy-metal resistance mechanisms developed by bacteria from lerma-chapala basin. Arch Microbiol 2021; 203:1807–1823 [View Article] [PubMed]
     [Google Scholar]
  20. Hoffman CS, Winston F. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 1987; 57:267–272 [View Article] [PubMed]
     [Google Scholar]
  21. Lane D. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematic New York: John Wiley and Sons; 1991 pp 115–175
     [Google Scholar]
  22. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  23. Galtier N, Gouy M, Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Bioinformatics 1996; 12:543–548 [View Article]
     [Google Scholar]
  24. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  25. Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol 2008; 25:1253–1256 [View Article] [PubMed]
     [Google Scholar]
  26. Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2019; 15:e1006650 [View Article] [PubMed]
     [Google Scholar]
  27. Guindon S, Lethiec F, Duroux P, Gascuel O. PHYML online--a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 2005; 33:W557–9 [View Article] [PubMed]
     [Google Scholar]
  28. Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 2008; 9:299–306 [View Article] [PubMed]
     [Google Scholar]
  29. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci 1986; 17:57
     [Google Scholar]
  30. Campanella JJ, Bitincka L, Smalley J. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinf 2003; 4:1–4 [View Article] [PubMed]
     [Google Scholar]
  31. Stackebrand E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  32. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article] [PubMed]
     [Google Scholar]
  33. Wingett SW, Andrews S. FastQ screen: a tool for multi-genome mapping and quality control. F1000Res 2018; 7:1338 [View Article] [PubMed]
     [Google Scholar]
  34. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  35. 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] [PubMed]
     [Google Scholar]
  36. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article]
     [Google Scholar]
  37. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  38. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  39. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf 2013; 14:1–14 [View Article] [PubMed]
     [Google Scholar]
  40. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:1–15 [View Article] [PubMed]
     [Google Scholar]
  41. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  42. Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC. Whole-genome prokaryotic phylogeny. Bioinformatics 2005; 21:2329–2335 [View Article] [PubMed]
     [Google Scholar]
  43. 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]
  44. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432–4450 [View Article] [PubMed]
     [Google Scholar]
  45. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
     [Google Scholar]
  46. Wang J, Wang Y, Zhang Q, Kong D, Xing Z et al. Chryseobacterium pyrolae sp. nov., isolated from the rhizosphere soil of Pyrola calliantha H. Int J Syst Evol Microbiol 2023; 73:006068 [View Article]
     [Google Scholar]
  47. Jung H, Lee D, Lee S, Kong HJ, Park J et al. Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities. Microb Genom 2023; 9:001108 [View Article] [PubMed]
     [Google Scholar]
  48. Duca DR, Glick BR. Indole-3-acetic acid biosynthesis and its regulation in plant-associated bacteria. Appl Microbiol Biotechnol 2020; 104:8607–8619 [View Article] [PubMed]
     [Google Scholar]
  49. Cowan S, Steel KJ. Manual for the identification of medical bacteria. In Manual for the Identification of Medical Bacteria Cambridge: University Press; 1965
     [Google Scholar]
  50. MacFaddin J. Biochemical Tests for Identification of Medical Bacteria Philadelphia: Lippincott Williams & Wilkins; 2000
     [Google Scholar]
  51. Hendricks CW, Doyle JD, Hugley B. A new solid medium for enumerating cellulose-utilizing bacteria in soil. Appl Environ Microbiol 1995; 61:2016–2019 [View Article] [PubMed]
     [Google Scholar]
  52. Castaneda-Agullo M. Studies on the biosynthesis of extracellular proteases by bacteria. I. Serratia marcescens, synthetic and gelatin media. J Gen Physiol 1956; 39:369–375 [View Article] [PubMed]
     [Google Scholar]
  53. Brown MR, Foster JH. A simple diagnostic milk medium for Pseudomonas aeruginosa. J Clin Pathol 1970; 23:172–177 [View Article] [PubMed]
     [Google Scholar]
  54. Lukasz D, Liwia R, Aleksandra M, Aleksandra S. Dissolution of arsenic minerals mediated by dissimilatory arsenate reducing bacteria: estimation of the physiological potential for arsenic mobilization. Biomed Res Int 2014; 2014:841892 [View Article] [PubMed]
     [Google Scholar]
  55. Jain DK, Patriquin DG. Characterization of a substance produced by Azospirillum which causes branching of wheat root hairs. Can J Microbiol 1985; 31:206–210 [View Article]
     [Google Scholar]
  56. Kerovuo J, Lauraeus M, Nurminen P, Kalkkinen N, Apajalahti J. Isolation, characterization, molecular gene cloning, and sequencing of a novel phytase from Bacillus subtilis. Appl Environ Microbiol 1998; 64:2079–2085 [View Article] [PubMed]
     [Google Scholar]
  57. Nautiyal CS. An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol Lett 1999; 170:265–270 [View Article] [PubMed]
     [Google Scholar]
  58. Schwyn B, Neilands JB. Universal chemical assay for the detection and determination of siderophores. Anal Biochem 1987; 160:47–56 [View Article] [PubMed]
     [Google Scholar]
  59. Venil CK, Zakaria ZA, Usha R, Ahmad WA. Isolation and characterization of flexirubin type pigment from Chryseobacterium sp. UTM-3T. Biocatal Agric Biotechnol 2014; 3:103–107 [View Article]
     [Google Scholar]
  60. Khare D, Kumar R, Acharya C. Genomic and functional insights into the adaptation and survival of Chryseobacterium sp. strain PMSZPI in uranium enriched environment. Ecotoxicol Environ Saf 2020; 191:110217 [View Article] [PubMed]
     [Google Scholar]
  61. Spotts E, Guy N, Lengyel G, Franks J, Maltman C. Chryseobacterium metallicongregator, sp. nov., a bacterium possessing metallophore activity towards rare earth elements. Int J Syst Evol Microbiol 2024; 74:74 [View Article] [PubMed]
     [Google Scholar]
  62. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
     [Google Scholar]
  63. Sandoval-Calderón M, Nguyen DD, Kapono CA, Herron P, Dorrestein PC et al. Plasticity of Streptomyces coelicolor membrane composition under different growth conditions and during development. Front Microbiol 2015; 6:1465 [View Article] [PubMed]
     [Google Scholar]
  64. Baddiley J, Buchanan JG, Handschumacher RE, Prescott JF. 551. Chemical studies in the biosynthesis of purine nucleotides. Part I. The preparation of n-glycylglycosylamines. J Chem Soc 19562818 [View Article]
     [Google Scholar]
  65. Sasser M. Technical Note 101: Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI; 1990 pp 1–7
     [Google Scholar]
  66. Indu B, Kumar G, Smita N, Shabbir A, Ch S et al. Chryseobacterium candidae sp. nov., isolated from a yeast (Candida tropicalis). Int J Syst Evol Microbiol 2020; 70:93–99 [View Article]
     [Google Scholar]
  67. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
     [Google Scholar]
  68. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  69. Zhang J, Kapli P, Pavlidis P, Stamatakis A. A general species delimitation method with applications to phylogenetic placements. Bioinformatics 2013; 29:2869–2876 [View Article] [PubMed]
     [Google Scholar]
  70. Fujisawa T, Aswad A, Barraclough TG. A rapid and scalable method for multilocus species delimitation using bayesian model comparison and rooted triplets. Syst Biol 2016; 65:759–771 [View Article] [PubMed]
     [Google Scholar]
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Chryseobacterium cupriresistens sp. nov., a copper-resistant bacterium isolated from soil contaminated with heavy metals in Chapala Basin, Mexico
Int J Syst Evol Microbiol 75, 006806 (2025); https://doi.org/10.1099/ijsem.0.006806
/content/journal/ijsem/10.1099/ijsem.0.006806
/content/journal/ijsem/10.1099/ijsem.0.006806
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