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Genomic aromatic compound degradation potential of novel Paraburkholderia species : Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.

Sarah Vanwijnsberghe (UGent) , Charlotte Peeters (UGent) , Emmelie De Ridder (UGent) , Charles Dumolin (UGent) , Anneleen Wieme (UGent) , Nico Boon (UGent) and Peter Vandamme (UGent)
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Abstract
We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderia aspalathi, Paraburkholderia madseniana, Paraburkholderia sediminicola, Paraburkholderia caffeinilytica, Paraburkholderia solitsugae and Paraburkholderia elongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA-DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia domus with LMG 31832(T) (=CECT 30334) as the type strain, Paraburkholderia nemoris with LMG 31836(T) (=CECT 30335) as the type strain and Paraburkholderia haematera with LMG 31837(T) (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.
Keywords
Paraburkholderia, aromatic compound degradation, microdiversity, comparative genomics, lignin, LIGNIN-DEGRADING BACTERIA, RNA GENE-SEQUENCES, HUMIC ACIDS, BURKHOLDERIA, FOREST, SOIL, IDENTIFICATION, ENZYMES, LITTER, MICRODIVERSITY

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MLA
Vanwijnsberghe, Sarah, et al. “Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species : Paraburkholderia Domus Sp. Nov., Paraburkholderia Haematera Sp. Nov. and Paraburkholderia Nemoris Sp. Nov.” INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 22, no. 13, 2021, doi:10.3390/ijms22137003.
APA
Vanwijnsberghe, S., Peeters, C., De Ridder, E., Dumolin, C., Wieme, A., Boon, N., & Vandamme, P. (2021). Genomic aromatic compound degradation potential of novel Paraburkholderia species : Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 22(13). https://doi.org/10.3390/ijms22137003
Chicago author-date
Vanwijnsberghe, Sarah, Charlotte Peeters, Emmelie De Ridder, Charles Dumolin, Anneleen Wieme, Nico Boon, and Peter Vandamme. 2021. “Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species : Paraburkholderia Domus Sp. Nov., Paraburkholderia Haematera Sp. Nov. and Paraburkholderia Nemoris Sp. Nov.” INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 22 (13). https://doi.org/10.3390/ijms22137003.
Chicago author-date (all authors)
Vanwijnsberghe, Sarah, Charlotte Peeters, Emmelie De Ridder, Charles Dumolin, Anneleen Wieme, Nico Boon, and Peter Vandamme. 2021. “Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species : Paraburkholderia Domus Sp. Nov., Paraburkholderia Haematera Sp. Nov. and Paraburkholderia Nemoris Sp. Nov.” INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 22 (13). doi:10.3390/ijms22137003.
Vancouver
1.
Vanwijnsberghe S, Peeters C, De Ridder E, Dumolin C, Wieme A, Boon N, et al. Genomic aromatic compound degradation potential of novel Paraburkholderia species : Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 2021;22(13).
IEEE
[1]
S. Vanwijnsberghe et al., “Genomic aromatic compound degradation potential of novel Paraburkholderia species : Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.,” INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 22, no. 13, 2021.
@article{8714695,
  abstract     = {{We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderia aspalathi, Paraburkholderia madseniana, Paraburkholderia sediminicola, Paraburkholderia caffeinilytica, Paraburkholderia solitsugae and Paraburkholderia elongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA-DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia domus with LMG 31832(T) (=CECT 30334) as the type strain, Paraburkholderia nemoris with LMG 31836(T) (=CECT 30335) as the type strain and Paraburkholderia haematera with LMG 31837(T) (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.}},
  articleno    = {{7003}},
  author       = {{Vanwijnsberghe, Sarah and Peeters, Charlotte and De Ridder, Emmelie and Dumolin, Charles and Wieme, Anneleen and Boon, Nico and Vandamme, Peter}},
  issn         = {{1422-0067}},
  journal      = {{INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}},
  keywords     = {{Paraburkholderia,aromatic compound degradation,microdiversity,comparative genomics,lignin,LIGNIN-DEGRADING BACTERIA,RNA GENE-SEQUENCES,HUMIC ACIDS,BURKHOLDERIA,FOREST,SOIL,IDENTIFICATION,ENZYMES,LITTER,MICRODIVERSITY}},
  language     = {{eng}},
  number       = {{13}},
  pages        = {{27}},
  title        = {{Genomic aromatic compound degradation potential of novel Paraburkholderia species : Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.}},
  url          = {{http://dx.doi.org/10.3390/ijms22137003}},
  volume       = {{22}},
  year         = {{2021}},
}

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