Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales

• Published in: Environmental microbiology 2012-05, Vol.14 (5), p.1091-1117
• Main Authors: Pérez-Pantoja, Danilo, Donoso, Raúl, Agulló, Loreine, Córdova, Macarena, Seeger, Michael, Pieper, Dietmar H., González, Bernardo
• Format: Article
• Language: English
• Subjects: Betaproteobacteria - classification; Betaproteobacteria - enzymology; Betaproteobacteria - genetics; Betaproteobacteria - metabolism; Biodegradation, Environmental; Catechols - metabolism; Comamonadaceae; Genome, Bacterial - genetics; Genomics; Humans; Hydrocarbons, Aromatic - metabolism; Oxygenases - genetics; Phylogeny
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/j.1462-2920.2011.02613.x

Summary The relevance of the β‐proteobacterial Burkholderiales order in the degradation of a vast array of aromatic compounds, including several priority pollutants, has been largely assumed. In this review, the presence and organization of genes encoding oxygenases involved in aromatics biodegradation in 80 Burkholderiales genomes is analysed. This genomic analysis underscores the impressive catabolic potential of this bacterial lineage, comprising nearly all of the central ring‐cleavage pathways reported so far in bacteria and most of the peripheral pathways involved in channelling of a broad diversity of aromatic compounds. The more widespread pathways in Burkholderiales include protocatechuate ortho ring‐cleavage, catechol ortho ring‐cleavage, homogentisate ring‐cleavage and phenylacetyl‐CoA ring‐cleavage pathways found in at least 60% of genomes analysed. In general, a genus‐specific pattern of positional ordering of biodegradative genes is observed in the catabolic clusters of these pathways indicating recent events in its evolutionary history. In addition, a significant bias towards secondary chromosomes, now termed chromids, is observed in the distribution of catabolic genes across multipartite genomes, which is consistent with a genus‐specific character. Strains isolated from environmental sources such as soil, rhizosphere, sediment or sludge show a higher content of catabolic genes in their genomes compared with strains isolated from human, animal or plant hosts, but no significant difference is found among Alcaligenaceae, Burkholderiaceae and Comamonadaceae families, indicating that habitat is more of a determinant than phylogenetic origin in shaping aromatic catabolic versatility.