Whole Genome Sequencing and Comparative Genomics Analyses of Pandoraea sp. XY-2, a New Species Capable of Biodegrade Tetracycline

Abstract

Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium Pandoraea sp. XY-2, which could biodegrade 74% tetracycline at pH 7.0 and 30°C within 6 days. Thereafter, we determined the whole genome sequence of Pandoraea sp. XY-2 genome is a single circular chromosome of 5.06 Mb in size. Genomic annotation showed that two AA6 family members-encoding genes and nine glutathione S-transferase (GSTs)-encoding genes could be relevant to tetracycline biodegradation. In addition, the average nucleotide identities (ANI) analysis between the genomes of Pandoraea sp. XY-2 and other Pandoraea spp. revealed that Pandoraea sp. XY-2 belongs to a new species. Moreover, comparative genome analysis of 36 Pandoraea strains identified the pan and specific genes, numerous single nucleotide polymorphisms (SNPs), insertions, and deletion variations (InDels) and different syntenial relationships in the genome of Pandoraea sp. XY-2. Finally, the evolution and the origin analysis of genes related to tetracycline resistance revealed that the six tetA(48) genes and two specificgenes tetG and tetR in Pandoraea sp. XY-2 were acquired by horizontal gene transfer (HGT) events from sources related to Paraburkholderia, Burkholderia, Caballeronia, Salmonella, Vibrio, Proteobacteria, Pseudomonas, Acinetobacter, Flavimaricola, and some unidentified sources. As a new species, Pandoraea sp. XY-2 will be an excellent resource for the bioremediation of tetracycline-contaminated environment.

Comparative characterization and functional genomic analysis of two Comamonas sp. strains for biodegradation of quinoline

“…Similar patterns also were observed in the genomes of tetracycline‐degrader Pandoraea sp. XY‐2, biodrying bacterial strain Bacillus thermoamylovorans and indole‐degrader Acinetobacter sp. JW …”

Construction of a Tetracycline Degrading Bacterial Consortium and Its Application Evaluation in Laboratory-Scale Soil Remediation

“…XY-1 (Accession number provided by the NCBI database: MN428658), and the other is Pandoraea sp. XY-2 (CP030849) [14]. For convenience, the four strains were abbreviated as follows: S1 stands for A. faecalis S-1, S2 stands for A. faecalis S-2, R stands for Raoultella sp.…”

“…TC concentration in soil was detected by HPLC (Hitachi 8DD-0801) with a C18 reversed-phase column (Agilent TC-C18(2) 150 mm × 4.6 mm). Instrument parameter setting, operation, and pretreatment of liquid samples were performed according to the previous study [14]. Besides, soil samples were treated as follows: In a 10 mL centrifuge tube, 5 mL of methanol, and EDTA-McIlvaine (1/1, v/v) buffer were added to 2 g of soil samples, then oscillated at 25 • C for 10 min, ultrasonicated for 10 min, and centrifuged at 4500 rpm/min for 10 min.…”

Phenotypic Modulation of Biofilm Formation in a Staphylococcus epidermidis Orthopedic Clinical Isolate Grown Under Different Mechanical Stimuli: Contribution From a Combined Proteomic Study

“…The aap mediates the biofilm formation process in a PIAindependent manner by supporting the cell-to-cell adhesion and aggregation process (Rohde et al, 2005). Staphylococci have evolved many different defense strategies to survive the presence of both exogenous and endogenous oxidants (Gaupp et al, 2012). Accordingly, the NADPH end product of the up regulated PPP might be exploited by S. epidermidis aggregates to prevent oxidative stress in the reduction of glutathione via glutathione peroxidase (Q5HPN6/SERP0872), confirming the stress response also found in planktonic clinical isolates.…”