Skip to content
1887

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

Volume 74, Issue 6

sp. nov., a novel actinomycete isolated from tidal flat sediment No Access

Abstract

Two Gram-stain-positive, aerobic, oxidase- and catalase-negative, non-motile, and short rod-shaped actinomycetes, named SYSU T00b441 and SYSU T00b490, were isolated from tidal flat sediment located in Guangdong province, PR China. The 16S rRNA gene sequence similarity, average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between SYSU T00b441 and SYSU T00b490 were 99.3, 99.5 and 97.1 %, respectively. Strains SYSU T00b441 and SYSU T00b490 exhibited the highest 16S rRNA gene sequence similarities to CF 5-4 (97.1 %/98.2 %), with ANI values of 74.01/73.88 % and dDDH values of 20.5/20.4 %. In the phylogenomic tree, the two isolates were affiliated with the genus . The genomes of strains SYSU T00b441 and SYSU T00b490 were 3.31 and 3.34 Mb, and both had DNA G+C contents of 72.8 mol%, coding 3077 and 3085 CDSs, three and three rRNA genes, and 53 and 51 tRNAs, respectively. Growth occurred at 15–40 °C (optimum, 28–30 °C), pH 4.0–10.0 (optimum, 7.0) and in the presence of 0–7 % (w/v) NaCl (optimum, 3 %). The major fatty acids (>10  %) of strains SYSU T00b441 and SYSU T00b490 were anteiso-C and C. The major respiratory quinone was identified as MK-10(H). The polar lipids of strains SYSU T00b441 and SYSU T00b490 were diphosphatidyl glycerol, phosphatidylglycerol, phosphoglycolipid, phosphatidyl ethanolamine, two phosphatidylinositol mannosides, two glycolipids and two phospholipids. Based on these data, the two strains (SYSU T00b441 and SYSU T00b490) represent a novel species of the genus , for which the name sp. nov is proposed. The type strain is SYSU T00b441 (=GDMCC 1.3827=KCTC 49943).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Actinotalea lenta sp. nov. , polyphasic taxonomy and tidal flat sediment
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 32000005)
    • Principle Award Recipient: LeiDong
  • National Natural Science Foundation of China (Award 32270076)
    • Principle Award Recipient: LeiDong
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2019FY100700)
    • Principle Award Recipient: Bao-ZhuFang
  • Key-Area Research and Development Program of Guangdong Province (Award 2022B0202110001)
    • Principle Award Recipient: Wen-JunLi
© 2024 Sun Yat-Sen University
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006436
2024-06-19
2025-05-18
Loading full text...

Full text loading...

References

  1. Murray NJ, Phinn SR, DeWitt M, Ferrari R, Johnston R et al. The global distribution and trajectory of tidal flats. Nature 2019; 565:222–225 [View Article] [PubMed]
     [Google Scholar]
  2. Gao S. Geomorphology and sedimentology of tidal flats. Coastal Wetlands 2019359–381
     [Google Scholar]
  3. Wilms R, Sass H, Köpke B, Köster J, Cypionka H et al. Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters. Appl Environ Microbiol 2006; 72:2756–2764 [View Article] [PubMed]
     [Google Scholar]
  4. Underwood G, Kromkamp J. Primary production by phytoplankton and microphytobenthos in estuaries. Adv Ecol Res 1999; 29:93–153
     [Google Scholar]
  5. Beam JP, George S, Record NR, Countway PD, Johnston DT et al. Mud, microbes, and macrofauna: seasonal dynamics of the iron biogeochemical cycle in an intertidal mudflat. Front Mar Sci 2020; 7:562617 [View Article]
     [Google Scholar]
  6. Yi H, Schumann P. Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bagnara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov. Int J Syst Evol Microbiol 2007; 57:151–156 [View Article]
     [Google Scholar]
  7. Li Y, Chen F, Dong K, Wang G. Actinotalea ferrariae sp. nov., isolated from an iron mine, and emended description of the genus Actinotalea. Int J Syst Evol Microbiol 2013; 63:3398–3403 [View Article] [PubMed]
     [Google Scholar]
  8. Du J, Ping W, Chen Y, Pang H, Bai P et al. Actinotalea soli sp. nov., isolated from Kubuqi Desert soil. Int J Syst Evol Microbiol 2022; 72:005660 [View Article] [PubMed]
     [Google Scholar]
  9. Yan ZF, Lin P, Li CT, Kook M, Yi TH. Actinotalea solisilvae sp. nov., isolated from forest soil and emended description of the genus Actinotalea. Int J Syst Evol Microbiol 2018; 68:788–794 [View Article] [PubMed]
     [Google Scholar]
  10. Jin L, Ko S-R, Lee CS, Ahn C-Y, Lee J-S et al. Actinotalea caeni sp. nov., isolated from a sludge sample of a biofilm reactor. Int J Syst Evol Microbiol 2017; 67:1595–1599 [View Article] [PubMed]
     [Google Scholar]
  11. Lu CY, Dong L, Li S, Lian WH, Lin ZL et al. Salinibacterium sedimenticola sp. nov., isolated from tidal flat sediment. Curr Microbiol 2023; 80:142
     [Google Scholar]
  12. 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] [PubMed]
     [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  14. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 4:406–416 [View Article]
     [Google Scholar]
  17. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
     [Google Scholar]
  18. Harrison PG, Strulo B. SPADES – a process algebra for discrete event simulation. J Log Comput 2000; 10:3–42 [View Article]
     [Google Scholar]
  19. 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]
  20. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
     [Google Scholar]
  21. Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalizedand complete genome-based taxonomy. Nucleic Acids Res 2022; 50:D785–D794 [View Article] [PubMed]
     [Google Scholar]
  22. 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] [PubMed]
     [Google Scholar]
  23. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  24. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361 [View Article] [PubMed]
     [Google Scholar]
  25. Yoon SH, Ha SM, 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]
  26. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  27. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
     [Google Scholar]
  28. Yin YB, Mao XZ, Yang JC, Chen X, Mao FL et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2012; 40:W445–W451 [View Article] [PubMed]
     [Google Scholar]
  29. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
     [Google Scholar]
  30. Li S, Shi L, Lian WH, Lin ZL, Lu CY et al. Arenibaculum pallidiluteum gen. nov., sp. nov., a novel bacterium in the family Azospirillaceae, isolated from desert soil, and reclassification of Skermanella xinjiangensis to a new genus Deserticella as Deserticella xinjiangensis comb. nov., and transfer of the genera Indioceanicola and Oleisolibacter from the family Rhodospirillaceae to the family Azospirillaceae.. Int J Syst Evol Microbiol 2021; 71:004874
     [Google Scholar]
  31. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article] [PubMed]
     [Google Scholar]
  32. Narsing Rao MP, Dong ZY, Kan Y, Zhang K, Fang BZ et al. Description of Paenibacillus antri sp. nov. and Paenibacillus mesophilus sp. nov., isolated from cave soil. Int J Syst Evol Microbiol 2020; 70:1048–1054 [View Article]
     [Google Scholar]
  33. Li S, Lian WH, Han JR, Ali M, Lin ZL et al. Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis. NPJ Biofilms Microbiomes 2023; 9:67 [View Article] [PubMed]
     [Google Scholar]
  34. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
     [Google Scholar]
  35. Dong L, Ming H, Liu L, Zhou EM, Yin YR et al. Zhizhongheella caldifontis gen. nov., sp. nov., a novel member of the family Comamonadaceae. Antonie van Leeuwenhoek 2014; 105:755–761 [View Article]
     [Google Scholar]
  36. Zheng ML, Jiao JY, Dong L, Han MX, Li LH et al. Pseudofrancisella aestuarii gen. nov., sp. nov., a novel member of the family Francisellaceae isolated from estuarine seawater. Antonie van Leeuwenhoek 2019; 112:877–886 [View Article] [PubMed]
     [Google Scholar]
  37. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  38. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth 1984; 2:233–241 [View Article]
     [Google Scholar]
  39. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  40. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986; 123:251–256 [View Article] [PubMed]
     [Google Scholar]
  41. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006436
Loading
Actinotalea lenta sp. nov., a novel actinomycete isolated from tidal flat sediment
Int J Syst Evol Microbiol 74, 006436 (2024); https://doi.org/10.1099/ijsem.0.006436
/content/journal/ijsem/10.1099/ijsem.0.006436
/content/journal/ijsem/10.1099/ijsem.0.006436
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error