Draft Genome Sequence of Pandoraea sp. Strain SD6-2, Isolated from Lindane-Contaminated Australian Soil

Abstract

Pandoraea sp. strain SD6-2 is a δ-hexachlorocyclohexane-degrading bacterial strain isolated from lindane-contaminated soil in Queensland, Australia. The genome of SD6-2 was sequenced to investigate its ability to degrade δ-hexachlorocyclohexane. Here we report the annotated genome sequence of this strain.

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

“…The 27 genomes from the present study were compared to all 41 publicly available Pandoraea genomes (GenBank database, January 29, 2019), which included 6 unclassified Pandoraea strains (Pushiri et al, 2013; Chan et al, 2015; Crofts et al, 2017; Kumar et al, 2018a; Liu et al, 2018). Pairwise dDDH and ANI values among the 68 genome sequences were calculated and are listed in Supplementary Tables S3, S4, respectively.…”

“…The phylogenomic analyses also allowed us to identify 4 out of 6 unclassified Pandoraea strains for which genome sequences are publicly available: strain ISTKB (Kumar M. et al, 2016) was assigned to P. capi , strain B-6 (Liu et al, 2018) to P. cepalis , strain SD6-2 (Pushiri et al, 2013) to P. communis , and strain E26 (Chan et al, 2015) to P. pnomenusa (Figure 2 and Table 2). Finally, strains PE-S2R-1 and PE-S2T-3 (Crofts et al, 2017) formed a separate cluster, which represented yet another novel Pandoraea species that remains to be formally classified (Supplementary Tables S3, S4).…”

“…Because many Pandoraea strains participate in the biodegradation of recalcitrant xenobiotics (Uhlik et al, 2012; Pushiri et al, 2013; Shi et al, 2013; Wang et al, 2015; Crofts et al, 2017; de Paula et al, 2017; Sarkar et al, 2017; Tirado-Torres et al, 2017; Kumar et al, 2018b; Yang et al, 2018; Liu et al, 2019; Wu et al, 2019), we specifically looked at the orthogroups in the KEGG pathway Xenobiotics biodegradation and metabolism (Figure 7). Most orthogroups in this pathway were present in multiple species ( n = 28) and some were even present in the core Pandoraea genome ( n = 6).…”

“…The latter suggests they may be important contributors to soil formation, soil fertility and retention, and cycling of elements necessary for plant growth (Sahin, 2003). These free-living Pandoraea bacteria are often enriched in polluted soils and participate in the biodegradation of complex organic substances including lignin (Shi et al, 2013; Kumar et al, 2018b; Liu et al, 2019), biodiesel and petroleum by-products (de Paula et al, 2017; Sarkar et al, 2017; Tirado-Torres et al, 2017), p -xylene (Wang et al, 2015), δ-hexachlorocyclohexane (Pushiri et al, 2013), di- n -butyl phthalate (Yang et al, 2018), biphenyl, benzoate and naphthalene (Uhlik et al, 2012), and tetracycline (Wu et al, 2019) and β-lactam antibiotics (Crofts et al, 2017). A particularly well-documented Pandoraea strain, i.e., JB1 T (LMG 31106 T ), was isolated in the 1980s from garden soil (Parsons et al, 1988) and was able to use biphenyl, 2-, 3- and 4-chloro-biphenyl, m -toluate, p -toluate naphthalene, m -hydroxybenzoate and diphenylmethane (Springael et al, 1996).…”

“…The genome sequences of several strains with bioremediation potential have been reported, but a growing number of studies fail to provide species level identification of such strains (Pushiri et al, 2013; Chan et al, 2015; Kumar M. et al, 2016; Crofts et al, 2017; Liu et al, 2018; Wu et al, 2019). In addition, in our studies on the diversity and epidemiology of opportunistic pathogens in persons with cystic fibrosis, we isolated a considerable number of Pandoraea strains that represent novel species (unpublished data).…”