Isolation and characterization of a moderate thermophilic Paenibacillus naphthalenovorans strain 4B1 capable of degrading dibenzofuran from dioxin-contaminated soil in Vietnam

• Published in: Journal of bioscience and bioengineering 2019-11, Vol.128 (5), p.571-577
• Main Authors: Thanh, Le Thi Ha, Thi, Tran Vu Ngoc, Shintani, Masaki, Moriuchi, Ryota, Dohra, Hideo, Loc, Nguyen Hoang, Kimbara, Kazuhide
• Format: Article
• Language: English
• Subjects: Base Sequence; Biodegradation; dbf genes; Dibenzofuran; Dibenzofurans - metabolism; Dioxins - analysis; Genome, Bacterial; Moderate thermophilic; Multigene Family; Open Reading Frames; Paenibacillus; Paenibacillus - drug effects; Paenibacillus - genetics; Paenibacillus - isolation & purification; Paenibacillus - metabolism; RNA, Ribosomal, 16S - genetics; Soil; Soil Microbiology; Vietnam
• ISSN: 1389-1723; 1347-4421
• DOI: 10.1016/j.jbiosc.2019.05.006

A moderate thermophilic dibenzofuran (DF) degrader, strain 4B1, was isolated from dioxin-contaminated soil in Vietnam under thermophilic condition. A 16S rRNA gene sequence analysis assigned the strain to genus Paenibacillus. The optimum growth temperature of strain 4B1 was 45°C with a doubling time of 2.7 h in the presence of DF as a sole carbon and energy source. The rate of its growth and DF-degradation were approximately 3-fold higher than those of a reference Paenibacillus sp. strain. The 4B1 strain degraded 89% of 1000 mg L−1 DF within 48 h cultivation at the optimum temperature. TBLASTN analysis based on its draft genome sequence revealed that this strain possessed a dbf gene cluster. The open reading frames (dbfA1A2RBC) in the cluster shared 99–100% identity with those of Paenibacillus sp. YK5, indicating that DF was likely degraded by an angular dioxygenation pathway in strain 4B1. Four genes in the dbf gene cluster (dbfA1A2BC) were partially induced by DF, which was observed by semi-quantitative RT-PCR. Quantitative PCR analysis of dbfA1 transcripts, encoding the alpha subunit of DF dioxygenase, indicated that dbfA1 was expressed 4-times higher than that of strain YK5 at 45°C. These results suggest that the faster growth and degradation of DF in strain 4B1 could be due to differences in transcriptional regulation of dbf cluster genes. •A moderate thermophilic dibenzofuran degrader, Paenibacillus naphthalenovorans strain 4B1, was isolated from Vietnamese soil.•The isolate showed higher growth rate and dibenzofuran-degradation than a reference Paenibacillus sp. strain YK5.•The dibenzofuran-degradative gene (dbf) clusters were highly conserved between 4B1 and YK5.•The transcriptional levels of the dbf gene were higher in 4B1 than those of YK5.