1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 8

sp. nov., from earthworm soil biofertilizer with the potential to degrade oil palm empty fruit bunch No Access

Abstract

Oil palm empty fruit bunch (OPEFB) is lignocellulosic waste from the palm oil industry in Southeast Asia. It is difficult to degrade because of its complex matrix and recalcitrant structure. To decompose OPEFB, highly efficient micro-organisms and robust enzymatic systems are required. A bacterium with high degradation ability against untreated OPEFB was isolated from earthworm soil biofertilizer and designated as strain EW123. Cells were Gram-stain-positive, rod-shaped and catalase-positive. In tests, the strain was negative for mycelium formation, motility, nitrate reductase and urease. The 16S rRNA gene analysis of the isolate showed 98.21 % similarity to NBRC 3747, whereas similarity to other species was below 98 %. The genome of strain EW123 was 3 834 009 bp long, with 73.97 mol% G+C content. Polar lipid analysis of strain EW123 indicated phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and aminophospholipid as the lipid components of the cell wall. The major cellular fatty acid was anteiso-C (41.26 %) and the isomer of 2,6-diaminopimelic acid (DAP) was -DAP. The average nucleotide identity value between the genome sequences of EW123 and NBRC 3747 was 88.6 %. In addition, the digital DNA–DNA hybridization and genome average amino acid between those strains were 36.1 and 89.68 %, respectively. The ORF number (186) of carbohydrate-active enzymes, including cellulases, xylanases, mannanase, lipase and lignin-degrading enzymes, was higher than those of related strains. These results indicate that the polyphasic characteristics of EW123 differ from those of other related species in the genus . We therefore propose a novel species of the genus , namely sp. nov. (type strain TBRC 11805=NBRC 114552), with the ability to effectively degrade untreated OPEFB.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): carbohydrate-active enzyme , Cellulomonas , Cellulomonas palmilyticum sp. nov. , EW123 and oil palm empty fruit bunch degradation
Funding
This study was supported by the:
  • Petchra Pra Jom Klao Ph.D. Research Scholarship year 2018, King Mongkut’s University of Technology Thonburi, Thailand, under financial supported number 32/2561.
    • Principle Award Recipient: Ake-kavitchSiriatcharanon
© 2022 The Authors

Erratum

An erratum has been published for this content:
Erratum: sp. nov. from earthworm soil biofertilizer with potential to degrade oil palm empty fruit bunch
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005494
2022-08-12
2024-04-19
Loading full text...

Full text loading...

References

  1. Stackebrandt E, Schumann P. The family Cellulomonadaceae. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. eds The Prokaryotes: Actinobacteria Berlin, Heidelberg: Springer; 2014 pp 163–184
     [Google Scholar]
  2. Wakarchuk WW, Brochu D, Foote S, Robotham A, Saxena H et al. Proteomic analysis of the secretome of Cellulomonas fimi ATCC 484 and Cellulomonas flavigena ATCC 482. PLoS One 2016; 11:e0151186 [View Article] [PubMed]
     [Google Scholar]
  3. Taylor EC. Role of aerobic microbial populations in cellulose digestion by desert millipedes. Appl Environ Microbiol 1982; 44:281–291 [View Article] [PubMed]
     [Google Scholar]
  4. Galkiewicz JP, Kellogg CA. Cross-kingdom amplification using bacteria-specific primers: complications for studies of coral microbial ecology. Appl Environ Microbiol 2008; 74:7828–7831 [View Article] [PubMed]
     [Google Scholar]
  5. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 2011; 7:539 [View Article] [PubMed]
     [Google Scholar]
  6. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  7. Seemann T. Rapid haploid variant calling and core genome alignment updated 3.2. n.d https://github.com/tseemann/snippy
  8. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  9. 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]
  10. Vanlaere E, Baldwin A, Gevers D, Henry D, De Brandt E et al. Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. Int J Syst Evol Microbiol 2009; 59:102–111 [View Article]
     [Google Scholar]
  11. Martens M, Dawyndt P, Coopman R, Gillis M, De Vos P et al. Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). Int J Syst Evol Microbiol 2008; 58:200–214 [View Article] [PubMed]
     [Google Scholar]
  12. De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 2018; 34:2666–2669 [View Article] [PubMed]
     [Google Scholar]
  13. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
     [Google Scholar]
  14. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  15. Loman NJ, Quick J, Simpson JT. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 2015; 12:733–735 [View Article] [PubMed]
     [Google Scholar]
  16. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  17. Horiguchi T, Yoshii H, Mizuno S, Shiraishi H. Decline in intertidal biota after the 2011 Great East Japan earthquake and tsunami and the Fukushima nuclear disaster: field observations. Sci Rep 2016; 6:20416 [View Article] [PubMed]
     [Google Scholar]
  18. Wingett SW, Andrews S. FastQ Screen: a tool for multi-genome mapping and quality control. F1000Res 2018; 7:1338 [View Article] [PubMed]
     [Google Scholar]
  19. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  20. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
     [Google Scholar]
  21. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  22. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  25. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
     [Google Scholar]
  26. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  27. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
     [Google Scholar]
  28. Holt JG. Group 20. irregular, non sporing Gram-positive rods. In Holt JG, Krieg NR, Sneath PH, Staley JT, Williams ST. eds Bergey’s Manual of Determinative Bacteriology, 9th edn. Baltimore, MD: Williams & Wilkins Co; 1994 pp 571–596
     [Google Scholar]
  29. Schumann P. Peptidoglycan structure. Methods Microbiology 2011; 38:101–129
     [Google Scholar]
  30. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  31. Kaláb M, Yang A-F, Chabot D. Eastern Cereal and Oilseed Research Centre Conventional scanning electron microscopy of bacteria. Infocus Magazine 2008; 10:42–61 [View Article]
     [Google Scholar]
  32. Parte A, Whitman WB, Goodfellow M, Kämpfer P, Busse H-J et al. Genus Cellulomonas. In Bergey’s Manual of Systematic Bacteriology: Volume 5: The Actinobacteria Berlin: Springer; 2012 pp 702–710
     [Google Scholar]
  33. Elberson MA, Malekzadeh F, Yazdi MT, Kameranpour N, Noori-Daloii MR et al. Cellulomonas persica sp. nov. and Cellulomonas iranensis sp. nov., mesophilic cellulose-degrading bacteria isolated from forest soils. Int J Syst Evol Microbiol 2000; 50 Pt 3:993–996 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005494
Loading
Cellulomonas palmilyticum sp. nov., from earthworm soil biofertilizer with the potential to degrade oil palm empty fruit bunch
Int J Syst Evol Microbiol 72, 005494 (2022); https://doi.org/10.1099/ijsem.0.005494
/content/journal/ijsem/10.1099/ijsem.0.005494
/content/journal/ijsem/10.1099/ijsem.0.005494
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