Abstract
A novel bacterium capable of utilizing metamitron as the sole source of carbon and energy was isolated from contaminated soil and identified as Rhodococcus sp. MET based on its morphological characteristics, BIOLOG GP2 microplate profile, and 16S rDNA phylogeny. Genome sequencing and functional annotation of the isolate MET showed a 6,340,880 bp genome with a 62.47% GC content and 5,987 protein-coding genes. In total, 5,907 genes were annotated with the COG, GO, KEGG, Pfam, Swiss-Prot, TrEMBL, and nr databases. The degradation rate of metamitron by the isolate MET obviously increased with increasing substrate concentrations from 1 to 10 mg/l and subsequently decreased at 100 mg/l. The optimal pH and temperature for metamitron biodegradation were 7.0 and 20–30 °C, respectively. Based on genome annotation of the metamitron degradation genes and the metabolites detected by HPLC-MS/MS, the following metamitron biodegradation pathways were proposed: 1) Metamitron was transformed into 2-(3-hydrazinyl-2-ethyl)-hydrazono-2-phenylacetic acid by triazinone ring cleavage and further mineralization; 2) Metamitron was converted into 3-methyl-4-amino-6(2-hydroxy-muconic acid)-1,2,4-triazine-5(4H)-one by phenyl ring cleavage and further mineralization. The coexistence of diverse mineralization pathways indicates that our isolate may effectively bioremediate triazinone herbicide-contaminated soils.
Highlights
Metamitron (4-amino-3-methyl-6-phenyl-1,2,4-triazin-5(4H)-one) is a selective systemic triazinone herbicide used as pre- and/or post-emergence in sugar beet, onion, and bean crops to control turf grass and broadleaf weeds[1]
MET; and 4) to reveal the potential biodegradation pathway of metamitron based on functional annotation of its genome and HPLC-MS/MS analysis
To confirm the validity of the metamitron extraction method, recovery studies were performed at three spiking levels of 1, 10, and 100 mg/l in 20 ml of sterile mineral salts medium (MSM)
Summary
Genome functional annotation of the isolate MET against GO database is shown in Fig. 1b and Table S3. The functional classification of the isolate MET genome based on the COG database revealed 25 function classes including energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, lipid transport and metabolism, and transcription These sequence data can be used to predict genes for xenobiotic biodegradation and metabolism[16]. The degradation rates of metamitron at levels of 1, 10, and 100 mg/l by the isolate MET after 6 h of incubation were 0.14, 1.22, and 0.97 mg/l/h, respectively (Table 2). The results showed that the degradation of metamitron by the isolate MET was significantly (p ≤ 0.05) faster at Property Raw reads size (bp) Clean reads size (bp) Genome size (bp) Fold coverage Scaffold number Scaffold N50 (bp) Contig number (> 500 bp) Contig length (bp) Contig N50 (bp) GC content (%) COG annotation GO annotation KEGG annotation Pfam annotation Swiss-Prot annotation TrEMBL annotation nr annotation
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