Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov

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 Paraburkholderiaaspalathi, Paraburkholderiamadseniana, Paraburkholderiasediminicola, Paraburkholderiacaffeinilytica, Paraburkholderiasolitsugae and Paraburkholderiaelongata 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; comparative genomics; lignin; microdiversity.

Figure 1

Phylogenetic tree based on recA gene sequences. Sequences (633–1074 bp) were aligned based on their amino acid sequences and phylogeny was inferred using the Maximum Likelihood method and GTRGAMMA substitution model in RAxML. The percentage of trees in which the associated taxa clustered together (1000 bootstrap replicates) is shown next to the branches. Burkholderia cepacia LMG 1222^T was used as outgroup. The scale bar indicates the number of substitutions per site. Isolates in bold character type were selected for whole genome sequence analysis. Sequence accession numbers are shown in parentheses.

Figure 2

Phylogenomic tree based on 107 single-copy core genes. BcgTree was used to extract the nucleotide sequence of 107 single-copy core genes and to construct their phylogeny by partitioned maximum-likelihood analysis. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. Eighteen isolates of the present study, the type strains of their nearest phylogenetic neighbor species and a selection of other Paraburkholderia type strains were included. Burkholderia cenocepacia J2315^T was used as outgroup. Strains reported in the present study are marked in bold character type. Bar, 0.01 changes per nucleotide position.

Figure 3

Degradation pathways of benzoic acid, 3-hydroxybenzoic acid and the lignin derived compounds ferulic acid and p-coumaric acid. (a) Ortho-cleavage pathway; (b) meta-cleavage pathway. Chemical structures were drawn with ChemDraw 19.

Figure 4

MALDI-TOF MS profiles of strains LMG 31832^T, LMG 31836^T, LMG 31837^T and their closest phylogenetic neighbor type strains, ordered conform to genomic relatedness. Asterisks indicate peaks that allow differentiation of the strain from its closest neighbors.