Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism

Peeters, Charlotte; Canck, Evelien De; Cnockaert, Margo; Brandt, Evie De; Snauwaert, Cindy; Verheyde, Bart; Depoorter, Eliza; Spilker, Theodore; LiPuma, John J.; Vandamme, Peter

doi:10.3389/fmicb.2019.02556

Cited by 87 publications

(16 citation statements)

References 69 publications

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“…Paired-end 150 bp libraries were sequenced on an Illumina HiSeq4000 sequencer (Oxford Genomics Centre – Wellcome Centre for Human Genetics, Oxford, United Kingdom). Quality control, assembly and annotation were performed as described previously ( Peeters et al, 2019 ). Annotation was performed using Prokka v1.12 ( Seemann, 2014 ) with a genus-specific database based on reference genomes from the Burkholderia Genome Database v8.1 ( Winsor et al, 2008 ).…”

Section: Methodsmentioning

confidence: 99%

Burkholderia cepacia Complex Taxon K: Where to Split?

et al. 2020

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The objective of the present study was to provide an updated classification for Burkholderia cepacia complex (Bcc) taxon K isolates. A representative set of 39 taxon K isolates were analyzed through multilocus sequence typing (MLST) and phylogenomic analyses. MLST analysis revealed the presence of at least six clusters of sequence types (STs) within taxon K, two of which contain the type strains of Burkholderia contaminans (ST-102) and Burkholderia lata (ST-101), and four corresponding to the previously defined taxa Other Bcc groups C, G, H and M. This clustering was largely supported by a phylogenomic tree which revealed three main clades. Isolates of B. contaminans and of Other Bcc groups C, G, and H represented a first clade which generally shared average nucleotide identity (ANI) and average digital DNA-DNA hybridization (dDDH) values at or above the 95-96% ANI and 70% dDDH thresholds for species delineation. A second clade consisted of Other Bcc group M bacteria and of four B. lata isolates and was supported by average ANI and dDDH values of 97.2 and 76.1% within this clade and average ANI and dDDH values of 94.5 and 57.2% toward the remaining B. lata isolates (including the type strain), which represented a third clade. We therefore concluded that isolates known as Other Bcc groups C, G, and H should be classified as B. contaminans, and propose a novel species, Burkholderia aenigmatica sp. nov., to accommodate Other Bcc M and B. lata ST-98, ST-103, and ST-119 isolates. Optimized MALDI-TOF MS databases for the identification of clinical Burkholderia isolates may provide correct species-level identification for some of these bacteria but would identify most of them as B. cepacia complex. MLST facilitates species-level identification of many taxon K strains but some may require comparative genomics for accurate species-level assignment. Finally, the inclusion of Other Bcc groups C, G, and H into B. contaminans affects the phenotype of this species minimally and the proposal to classify Other Bcc group M and B. lata ST-98, ST-103, and ST-119 strains as a novel Burkholderia species is supported by a distinctive phenotype, i.e., growth at 42 • C and lysine decarboxylase activity.

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Section: Methodsmentioning

confidence: 99%

Burkholderia cepacia Complex Taxon K: Where to Split?

et al. 2020

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“…As numerous studies have reported that this genus is dominant in the degradation of xenobiotics in bio lter systems (Portune et al, 2015, Allievi et al, 2018, this indicated a shift in degrading contribution away from Rhodococcus and more toward ASVs from the genera Devosia, Aquamicrobium, and Rhizobiales, which had high positive correlation with performance. The genus Pandoreae was reported to be highly enriched in species capable of effective degradation of xenobiotics (Peeters et al, 2019), and was positively correlated with r>0.7 in both bio lters as shown in Fig. 6.…”

Section: Discussionmentioning

confidence: 90%

Low-dosage Ozonation in Gas-phase Biofilter Promotes Community Diversity and Robustness.

Yeung

Saingam

Yang

et al. 2020

Preprint

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BackgroundThe ozonation of biofilters is known to alleviate clogging and pressure drop issues while maintaining removal performances in biofiltration systems treating gaseous volatile organic compounds (VOCs). The effects of ozone on the biofilter microbiome in terms of biodiversity, community structure, metabolic abilities, and dominant taxa correlated with performance remain largely unknown.MethodsThis study investigated two biofilters treating high-concentration toluene operating in parallel, with one acting as control and the other exposed to low-dosage (200 mg/m3) ozonation. The microbial community diversity, metabolic rates of different carbon sources, functional predictions, and microbial co-occurrence networks of both communities were examined.ResultsConsistently higher biodiversity of over 30% was observed in the microbiome after ozonation, with increased overall metabolic abilities for amino acids and carboxylic acids. The relative abundance of species with reported stress-tolerant and biofilm-forming abilities significantly increased, with a consortium of changes in predicted biological pathways, including shifts in degradation pathways of intermediate compounds, while the correlation of top ASVs and genus with performance indicators showed diversifications in microbiota responsible for toluene degradation. A co-occurrence network of the community showed a decrease in average path distance and average betweenness with ozonation.ConclusionMajor degrading species highly correlated with performance shifted after ozonation. Increases in microbial biodiversity, coupled with improvements in metabolizing performances of multiple carbon sources including organic acids could explain the consistent performance commonly seen in the ozonation of biofilters despite the decrease in biomass, while avoiding acid buildup in long term operation. The increased presence of stress-tolerant microbes in the microbiome coupled with the decentralization of the co-occurrence network suggested that ozonation could not only ameliorate clogging issues but also provide a microbiome more robust to loading shock seen in full-scale biofilters.

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“…As numerous studies have reported that this genus is dominant in the degradation of xenobiotics in biofilter systems [ 41 , 46 ], this indicated a shift in degrading contribution away from Rhodococcus and more toward ASVs from the genera Devosia , Aquamicrobium , and Rhizobiales , which had high positive correlation with performance. The genus Pandoraea was reported to be highly enriched in species capable of effective degradation of xenobiotics [ 47 ] and was positively correlated with r > 0.7 in both biofilters as shown in Fig. 6.…”

Section: Discussionmentioning

confidence: 99%

Low-dosage ozonation in gas-phase biofilter promotes community diversity and robustness

Yeung

Saingam

et al. 2021

Microbiome

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Background The ozonation of biofilters is known to alleviate clogging and pressure drop issues while maintaining removal performances in biofiltration systems treating gaseous volatile organic compounds (VOCs). The effects of ozone on the biofilter microbiome in terms of biodiversity, community structure, metabolic abilities, and dominant taxa correlated with performance remain largely unknown. Methods This study investigated two biofilters treating high-concentration toluene operating in parallel, with one acting as control and the other exposed to low-dosage (200 mg/m3) ozonation. The microbial community diversity, metabolic rates of different carbon sources, functional predictions, and microbial co-occurrence networks of both communities were examined. Results Consistently higher biodiversity of over 30% was observed in the microbiome after ozonation, with increased overall metabolic abilities for amino acids and carboxylic acids. The relative abundance of species with reported stress-tolerant and biofilm-forming abilities significantly increased, with a consortium of changes in predicted biological pathways, including shifts in degradation pathways of intermediate compounds, while the correlation of top ASVs and genus with performance indicators showed diversifications in microbiota responsible for toluene degradation. A co-occurrence network of the community showed a decrease in average path distance and average betweenness with ozonation. Conclusion Major degrading species highly correlated with performance shifted after ozonation. Increases in microbial biodiversity, coupled with improvements in metabolizing performances of multiple carbon sources including organic acids could explain the consistent performance commonly seen in the ozonation of biofilters despite the decrease in biomass, while avoiding acid buildup in long-term operation. The increased presence of stress-tolerant microbes in the microbiome coupled with the decentralization of the co-occurrence network suggest that ozonation could not only ameliorate clogging issues but also provide a microbiome more robust to loading shock seen in full-scale biofilters.

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Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism

Cited by 87 publications

References 69 publications

Burkholderia cepacia Complex Taxon K: Where to Split?

Burkholderia cepacia Complex Taxon K: Where to Split?

Low-dosage Ozonation in Gas-phase Biofilter Promotes Community Diversity and Robustness.

Low-dosage ozonation in gas-phase biofilter promotes community diversity and robustness

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