Introduction

2,4-Dinitrophenol (2,4-DNP) is a derivative of phenol with two nitrogen groups at the 2 and 4 positions of the benzene ring. This aromatic compound is widely used for the manufacturing of dyes, drugs, pesticides, herbicides, fungicides, paints and explosives (Badeen et al. 2011). Due to its high toxicity to all forms of living organisms and its widespread occurrence in the environment, 2,4-DNP is included on the “U.S. Environmental Protection Agency” “Priority Pollutant List” (http://www.epa.gov/waterscience/methods/pollutants.htm).

Microbes play an important role in transforming these recalcitrant contaminants by recycling carbon and nitrogen in nature. A few bacterial strains have been isolated for their ability to degrade 2,4-DNP, such as Burkholderia sp strain KU-46, Nocardioides sp JS1661 (Karthikeyan and Spain 2016), Rhodococcus imtechensis RKJ300, Rhodococcus sp RB1, and Rhodococcus erythropolis HL PM-1. Bacterial degradation of 2,4-DNP mainly occurrs via three routes: (i) the 4-nitrophenol and 1,2,4-benzenetriol pathways in Burkholderia sp strain KU-46 (Iwaki et al. 2007; Yamamoto et al. 2019); (ii) the 3-nitroadipic acid pathway in Rhodococcus sp strain RB1 (Timmis et al. 1999); and (iii) the 4,6-dinitrohexanoate pathway in Rhodococcus erythropolis HL 24 − 1/HL 24 − 2 (Lenke et al. 1992) and Rhodococcus imtechensis strain RKJ300 (Ghosh et al. 2010). These studies not only enrich our understanding of the diversity of 2,4-DNP biodegradation pathways but also provide theoretical knowledge for bioremediating 2,4-DNP-contaminated environments.

Herein, we report a newly isolated strain, XM24D, which has the ability to utilize 2,4-dinitrophenol as the sole source of carbon, nitrogen and energy to grow. Analogs of 2,4-DNP, including 4-nitrophenol (PNP) and 2-chloro-4-nitrophenol (2C4NP), can also be degraded by XM24D. To reveal the genome features and nitrophenol degradation pathways in XM24D, we sequenced its genome and transcriptom. Genomic and transcriptomic information on XM24D is expected to provide a valuable reference for further investigations the evolutionary characteristics of nitrophenol degradation pathways in microorganisms.

Materials and methods

Isolation of the XM24D strain

The XM24D strain was isolated from 2,4-DNP-contaminated soil (Fujian, China) by the enrichment technique. Minimum mineral salt media (MM) (Liu et al. 2005) supplemented with 0.2 mM analogs of 2,4-DNP were used to test the degradation ability of XM24D. Cultures were incubated in a rotary shaker (200 rpm) at 30 °C. Growth was monitored by measuring the increasing optical density at 600 nm (OD600). HPLC with a C18 reversed-phase column (5 μm; 4.6 by 250 mm; Agilent Technologies, Palo Alto, CA) was performed at a column temperature of 30 °C on an Agilent series 1260 system (Agilent Technologies) to detect the degradation of aromatic compounds. The mobile phase consisted of methanol (60 %) and 0.1 %(v/v) acetic acid (40 %) at a flow rate of 1 ml/min. Aromatic compounds were quantified at 280 nm.

Genome sequencing, assembly and annotation

Strain XM24D was cultured in LB medium supplemented with 0.2 mM 2,4-DNP at 30 °C and 200 rpm and collected when the OD600 reached approximately 0.5. Whole-genome shotgun sequencing was performed using a PacBio RS II platform and Illumina HiSeq 4000 platform at the Beijing Genomic Institute (BGI, Shenzhen, China). Pbdagcon was used for subread self-correction (https://github.com/PacificBiosciences/pbdagcon). Celera Assembler was used to assemble the genome sequence (Denisov et al. 2008). Glimmer3 was used to predict genes (Delcher et al. 2007). Predicted genes were annotated by alignment to the nonredundant protein sequence (Nr), Kyoto Encyclopedia of Genes and Genomes (KEGG), SwissProt, TrEMBL and InterPro databases using the Basic Local Alignment Search Tool (BLAST) -v2.7.1+ (Altschul et al. 1990), with an E-value cutoff of 1E-5. Gene Ontology (GO) terms were assigned to the genes using the BLAST2GO pipeline (Conesa et al. 2005).

RNA sequencing and differential expression analysis

Strain XM24D was cultured in LB medium at 30 °C and 200 rpm, when the OD600 reached approximately 0.5, three samples were induced by 0.2 mM nitrophenol, and three unsupplemented samples served as the control. After 3 h, all samples were collected. Total RNA was extracted from induced and uninduced cells and sequencing of each sample was performed on the Illumina platform (PE150) at the Beijing Genomic Institute (BGI, Shenzhen, China). Data were analyzed using the HISAT2-StringTie pipeline (Pertea et al. 2016).

Results and discussion

Isolation and genome sequening of strain XM24D

The XM24D strain was originally isolated by an enrichment technique on minimal medium with the addition of 0.2 mM 2,4-dinitrophenol (2,4-DNP). Growth profiles showed that XM4D has the ability to utilize 2,4-DNP as the sole source of carbon, nitrogen and energy (Fig. 1a). Other analogs of 2,4-DNP, such as 4-nitrophenol (PNP) (Fig. 1b) and 2-chloro-4-nitrophenol (2C4NP) (Fig. 1c), can also be degraded by XM24D. However, 2,6-dinitrophenol, 2-nitrophenol, 3-nitrophenol, 4-nitrocatechol, hydroxyquinol, catechol and hydroquinone cannot be degraded by XM24D.

Fig. 1
figure 1

Time courses of XM24D growth and 2,4-DNP/PNP/2C4NP degradation

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To reveal the genome features of XM24D and further improve the understanding of the nitrophenol degradation pathways in XM24D, we performed de novo whole-genome assembly and annotation. Using 5.9 Gb of PacBio data (approximately 649× genome coverage) and 1.1 G of Illumina PE150 data (approximately 122× genome coverage), a genome with a size of 9,083,441 bp and 67.07 % GC content containing 2 chromosomes (Chr1, 7,849,285 bp and Chr2, 1,234,156 bp) was obtained. In contrast to other toxicant-degrading Rhodococcus spp that reportedly possess plasmid sequences encoding the genes of aromatic degrading proteins (Na et al. 2005; Sekine et al. 2006; Takeda et al. 2010), no plasmids were detected in XM24D. A total of 9081 protein-coding genes and 69 RNAs-coding genes (51 tRNA, 12 rRNA, and 16 ncRNA genes) were predicted in the XM24D genome. Of the 9081 predicted proteins, 8614 (94.85 %) were classified into families according to their putative functions. The numbers and percentages determined by each database were as follows: SwissProt (2863, 31.52 %), TrEMBL (8344 91.88 %), Nr (8400, 92.5 %), KEGG (4239, 46.67 %) and GO (5,121, 56.39 %). Detailed information regarding the assembled genome and the general physiology of XM24D are shown in Table 1.

Table 1 General physiological and assembled genome information for XM2D
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Strain XM24D belongs to Rhodococcus imtechensis

16S rRNA gene sequence analysis indicated that XM24D belonged to the genus Rhodococcus and showed 100 % sequence similarity to Rhodococcus wratislaviensi. Comparisons of average nucleotide identity (ANI) values between the genome of XM24D and those of 390 other Rhodococcus spp revealed that Rhodococcus imtechensis RKJ300 (GCA_000260815.1) (99.4 %) was the most closely related strain to XM24D, followed by Rhodococcus jostii RHA1 (GCA_000014565.1) (95.14 %). According to the standards proposed by Chun et al. (Chun et al. 2018), ANI values above 96 % can be assumed to confirm that two organisms belong to the same species. Thus, the XM24D strain most likely belongs to the same family as Rhodococcus imtechensis RKJ300.

2,4-DNP/PNP/2C4NP degradation pathway

To improve the understanding of the 2,4-DNP/PNP/2C4NP degradation pathways in XM24D, comparative transcriptomic sequencing and HISAT2-StringTie pipeline analysis (Pertea et al. 2016) were employed to gain insight into the gene clusters related to 2,4-DNP/PNP/2C4NP degradation. Based on the comparative transcriptomic results, the 2,4-DNP/PNP/2C4NP degradation pathway was predicted.

2,4-DNP degradation pathway A gene cluster containing 17 genes was found to be associated with 2,4-DNP degradation. Twelve of 17 genes were significantly upregulated (|fold change|>= 2 and adjusted p-value = < 0.001) when XM24D was exposed to 2,4-DNP (a heatmap of these differentially expressed genes involved in 2,4-DNP degradation are shown in Fig. 2a). These significantly expressed genes included a hydride transferase I gene (dnpA1), a hydride transferase II gene (dnpA2), an NADPH-dependent F420 oxidoreductase gene (dnpB), a hydrolase gene (dnpC) and seven coenzyme F420 biosynthesis pathway genes (Table 2). As shown in Fig. 3a, the 2,4-DNP degradation pathway in XM24D shares high degrees of protein identity (> 96 %) and similar organizations with the 2,4-DNP degradation pathway in Rhodococcus opacus HL PM-1 (Hofmann et al. 2004), suggesting that 2,4-DNP is degraded via the “Meisenheimer complex of 2,4-DNP/2,4-dinitrocyclohexanone” in XM24D, with F420 as the co-factor (Fig. 3a, b).

Fig. 2
figure 2

Heatmap of differentially expressed 2,4-DNP/PNP/2C4NP degradation pathway genes when XM24D was exposed to 2,4-DNP (a), PNP (b), and 2C4NP (c)

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Table 2 Description of genes related to 2,4-DNP/PNP/2C4NP degradation pathways
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Fig. 3
figure 3

Organization structure of 2,4-DNP/PNP/2C4NP degradation pathway genes and the proposed 2,4-DNP/PNP/2C4NP degradation pathway (b, d) in XM24D. Solid arrows show significantly upregulated genes when XM24D was exposed to 2,4-DNP or PNP or 2C4NP. “%” indicates the degree of protein identity

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 PNP degradation pathway A gene cluster including 5 genes was found to be associated with PNP degradation. This gene cluster encodes an oxygenase component of 4-nitrophenol 2-monooxygenase/4-nitrocatechol 4-monooxygenase (PnpA), a reductase component of 4-nitrophenol 2-monooxygenase/4-nitrocatechol 4-monooxygenase(PnpB), a hydroxyquinol 1,2-dioxygenase (PnpC), a maleylacetate reductase (PnpD) and a LysR family transcriptional regulator (Table 2). All of these genes were significantly upregulated (|fold change|>= 2 and adjusted p-value = < 0.001) when XM24D was exposed to PNP (a heatmap of these significantly upregulated genes involved in PNP degradation is shown in Fig. 2b). Further analysis showed that these genes exhibit high degrees of protein identity (> 99 %) and similar organizations with the PNP degradation pathway genes in Rhodococcus opacus SAO101 (Kitagawa et al. 2004) and Rhodococcus imtechensis RKJ300 (Ghosh et al. 2010), indicating that PNP is degraded via the 4-nitrocatechol/hydroxyquinol pathway in XM24D (Fig. 3c, d).

2C4NP degradation pathway According to Min et al., the PNP degradation pathway in Rhodococcus imtechensis RKJ300 is also responsible for 2C4NP degradation (Min et al. 2016), suggesting that 2C4NP can aslo be mineralized via the PNP degradation pathway in XM24D and that hydroxyquinol is the intermediate compound (Fig. 3d). However, a transcriptomic analysis indicated that both 2,4-DNP degradation pathway genes (16 of 17) and PNP degradation pathway genes (5 of 5) were significantly upregulated (|fold change|>= 2 and adjusted p value = < 0.001) when XM24D was exposed to 2C4NP (a heatmap of these differentially expressed genes is shown in Fig. 2c). Therefore, more experimental evidence is needed to determine whether 2C4NP can be degraded via the 2,4-DNP degradation pathway.

Nucleotide sequence accession numbers

The genome sequences of Rhodococcus imtechensis XM24D have been deposited in DDBJ/EMBL/GenBank under accession numbers CP051855-CP051856. The sequencing reads used for genome assembly and comparative transcriptome analysis have been deposited in the Sequence Read Archive (SRA) database under BioProject ID PRJNA627025 and PRJNA627856, respectively.