Genome Organization and Adaptive Potential of Archetypal Organophosphate Degrading Sphingobium fuliginis ATCC 27551

Abstract

Sphingobium fuliginis ATCC 27551, previously classified as Flavobacterium sp. ATCC 27551, degrades neurotoxic organophosphate insecticides and nerve agents through the activity of a membrane-associated organophosphate hydrolase. This study was designed to determine the complete genome sequence of S. fuliginis ATCC 27551 to unravel its degradative potential and adaptability to harsh environments. The 5,414,624 bp genome with a GC content of 64.4% is distributed between two chromosomes and four plasmids and encodes 5,557 proteins. Of the four plasmids, designated as pSF1, pSF2, pSF3, and pSF4, only two (pSF1 and pSF2) are self-transmissible and contained the complete genetic repertoire for a T4SS. The other two plasmids (pSF3 and pSF4) are mobilizable and both showed the presence of an oriT and relaxase-encoding sequences. The sequence of plasmid pSF3 coincided with the previously determined sequence of pPDL2 and included an opd gene encoding organophosphate hydrolase as a part of the mobile element. About 15,455 orthologous clusters were identified from among the cumulatively annotated genes of 49 Sphingobium species. Phylogenetic analysis done using the core genome consisting of 802 orthologous clusters revealed a close relationship between S. fuliginis ATCC 27551 and bacteria capable of degradation of polyaromatic hydrocarbon compounds. Genes coding for transposases, efflux pumps conferring resistance to heavy metals, and TonR-type outer membrane receptors are selectively enriched in the genome of S. fuliginis ATCC 27551 and appear to contribute to the adaptive potential of the organism to challenging and harsh environments.

Introduction

Agricultural soils contain high amounts of insecticide residues due to repeated and indiscriminate use of insecticides. Microorganisms living in soils gain access to these xenobiotic compounds, hitherto unknown to the native environment. Some of the microbial enzymes show promiscuous activity toward the accumulated residues due to the existence of structural similarities with their cognate substrates (Guzman et al. 2019). Such promiscuity contributes to the evolution of new enzymes/degradation pathways required for the degradation/mineralization of these toxic substances (Kolvenbach et al. 2014).

Organophosphate (OP) insecticides, which are used as substitutes for the most persistent organochloride insecticides, have potentially neurotoxic effects and adversely impact on human and animal health (Bouchard et al. 2011). Sphingobium fuliginis ATCC 27551, previously classified as Flavobacterium sp. ATCC 27551, degrades a wide range of OP insecticides due to the existence of a plasmid-encoded triesterase, designated as organophosphate hydrolase (OPH) (Sethunathan and Yoshida 1973; Mulbry et al. 1986; Mulbry and Karns 1989; Kawahara 2010). Sphingobiumfuliginis ATCC 27551 contains four indigenous plasmids, of which only plasmid pPDL2 carries the opd gene. The physiological significance of the other three plasmids is unknown. Although the ability of S. fuliginis ATCC 27551 to degrade OP pesticides is known, due to the lack of genome information its potential has not yet been fully exploited to remediate OP-polluted environments. The present study reports the complete genome sequence of S. fuliginis ATCC 27551 and its adaptive potential to harsh environments.

Materials and Methods

The whole genome of S. fuliginis ATCC 27551 was sequenced using Pacific Biosciences (Pacbio RSII) and Illumina platforms (MiSeq). PacBio reads were assembled using Canu, HGAP2, and HGAP3 pipelines and circularized by circlator v1.4.0 (Hunt et al. 2015). Processed MiSeq data were mapped onto assemblies using bowtie2 (Langmead and Salzberg 2012) and Canu assembly was chosen for the final assembly. The RAST server (Brettin et al. 2015) was used for structural and functional annotation. COG (Cluster of Orthologous Groups) profiles were assigned to the genes using RPS-BLAST v2.4.1. Only genes with at least 25% identity, 70% alignment length, and an e-value cut-off of 0.01 were taken into consideration while assigning COG functional groups. Proteins coded by these genes and the proteome of 48 species of the Sphingobium genus downloaded from PATRIC database were used for orthology analysis using Orthomcl v1.4 (Li et al. 2003). The phylogenetic tree was constructed using RAxML (Stamatakis 2014). Plasmid pPDL2 (NCBI: JX312671.1) of S. fuliginis ATCC27551 (Pandeeti et al. 2012) was compared with the in-house assembled plasmids using the Mummer3 package (Kurtz et al. 2004). The detailed methodology is given in the Supplementary Material online.

Results and Discussion

The 796 Mb data generated through a single SMRT cell of PacBio were filtered to select reads with a length of 500 bp and above. After filtration, 133,313 reads were obtained and of these, the largest read was of 48.2 kb. If the approximate size of the S. fuliginis ATCC 27551 genome is assumed to be ∼5 Mb, the total filtered data of 795.2 Mb amounts to a 159-fold coverage.

The filtered data were used to assemble the genome sequence using both the SMRT analysis pipeline and the Canu assembler. The polished assembly generated using the HGAP2 and HGAP3 workflows of the SMRT pipeline was then compared with the assembly data obtained from Canu to gain a clear picture as to the quality of sequence assembly (supplementary table S1, Supplementary Material online). Out of 795.2 Mb of data, the HGAP3 workflow produced seven contigs, while HGAP2 and Canu produced six contigs. After the circularization of the contigs, the total size of the assembled genome from HGAP3, HGAP2, and Canu was determined to be 5,428,378, 5,413,947, and 5,414,624 bp, respectively.

After assembling the single SMRT cell of the PacBio-generated sequence, the 4.36 million paired-end (PE), preprocessed reads of MiSeq were used to map onto different assemblies. Overall, about 99.32% of MiSeq reads could be aligned with the assembled sequence. However, the best alignment was seen with the Canu assembly, where 97.38% of reads were aligned concordantly and uniquely, whereas only 1.7% of the reads aligned to more than one position. Therefore, the Canu circulated assembly, which gave a very high-quality reference genome without any gaps or ambiguous nucleotides is taken as a final genome assembly of S. fuliginis ATCC 27551 (GCA_006363875.1). The complete genome contains six contigs, consisting of two chromosomes and four plasmids. The sizes of the largest contigs named as chromosome I and chromosome II are 3,844,607 and 1,213,992 bp, respectively. Of four plasmids, only three were circularized successfully, the fourth plasmid remained open-ended. These four indigenous plasmids are named pSF1 (224,736 bp), pSF2 (60,848 bp), pSF3 (43,234 bp), and pSF4 (27,207 bp).

After generating the high-quality genome sequence of S. fuliginis ATCC 27551 it was compared with the draft genome sequences of two more strains of S. fuliginis available in the NCBI database (supplementary table S2, Supplementary Material online). The genome of S. fuliginis DSM 18781 (GCA_004152845.1) is available as 21 contigs. Of these 21 contigs, 10 contigs showed similarity with chromosome 1, and 5 contigs aligned with chromosome 2 of S. fuliginis ATCC 27551. Only one contig aligned with the largest plasmid, pSF1, and no sequence information from strain DSM 18781 showed any similarity with the other three indigenous plasmids of strain ATCC 27551.

In contrast, the sequence of S. fuliginis ATCC 27551 failed to align properly with the sequence of S. fuliginis OMI, which is available as 34 scaffolds (GCA_002723855.1). When we blasted the largest contig of OMI with the genome sequence of ATCC 27551 it matched with the chromosome 1, chromosome 2, and one of the indigenous plasmids, pSF1, indicating erroneous assembly of the sequence of S. fuliginis OMI. Since there is no raw data, we could not make use the available sequence to perform comparative genomics.

Genome Annotation

The two chromosomes of S. fuliginis ATCC 27551 are annotated with 5,164 genes, of which chromosome I contains 4,030 genes and chromosome II 1,134 genes (supplementary table S3, Supplementary Material online). Of the 5,164 genes, 5,100 are protein-coding genes and the remaining 64 genes code for tRNA (55) and rRNA (9) molecules. Chromosome I includes 51 tRNA genes and 3 rRNA genes, whereas chromosome II has only 4 tRNA and 6 rRNA genes. The coding density of the genome is 86.72% and the GC content is 64.37%. The distribution of various features of the sequenced genome, such as functionally assigned genes, hypothetical genes, GC content, GC skew, VNTRs are shown in figures 1A and 1B.

Fig. 1.

—Circular maps of the chromosomes (A and B) and plasmids (C- F) of Sphingobium fuliginis ATCC 27551. The innermost circle depicts the GC-skew of the reverse and forward strands in dodger blue and dark green, respectively. The second innermost circle represents the GC-content of the reverse and forward strands represented in violet and dark yellow, respectively. The third innermost (in pink) represents VNTRs. The fourth circle represents RNA genes (rRNAs in dark blue and tRNAs in light blue). Hypothetical and annotated proteins of the reverse strand are shown in blue and dark orange, respectively, in the fifth circle. The hypothetical (in red) and annotated proteins (in vivid green) of the forward strand are shown in the sixth circle. Island patches have been shown in pink color in the outermost circle. VNTRs are not shown in plasmids. The fourth circle is absent in plasmids(C- F) as the genes coding rRNAs and tRNAs are not present.

Annotation of the four indigenous plasmids pSF1, pSF2, pSF3, and pSF4 identified 393 genes. Among them, plasmid pSF1 contains 239 genes. The other 154 genes are distributed among pSF2 (66), pSF3 (51), and pSF4 (37) (supplementary table S3, Supplementary Material online). All annotated genes code for proteins and no RNA-coding genes were found in any of the four plasmids. The GC content of the plasmids varied from 61.18% to 63.17%, whereas the coding density varied from 81.38% to 84.94% (fig. 1C–F).

The functional characterization of the proteome of S. fuliginis ATCC 27551 was done by performing Clusters of Orthologous Groups (COG) analysis. Out of 5,100 annotated proteins, 2,679 could be grouped into 23 COG categories (supplementary fig. S1, Supplementary Material online). Protein clustered with general cellular functions (R), lipid transport and metabolism (I), energy production and conversion (C), and transcription (K) were enriched in S. fuliginis ATCC27551, along with a COG cluster consisting of proteins of unknown function (S). In contrast, just one predicted gene-product was found in the COG cluster related to chromatin structure and dynamics (B) and <50 proteins were allocated to the COG groups W (extracellular structure), D (cell cycle control), N (cell motility), and X (Mobilome).

Orthology and Phylogenetic Analysis

The orthologous genes were identified in the Sphingobium genus by taking 223,547 cumulatively annotated genes found in the genomes of 49 species. Of 15,455 orthologous groups, only 802 were present in all 49 species and hence were designated as a core genome of the Sphingobium genus. Sphingobium sp. 22B was represented in the highest number of orthologous groups (4,799), whereas the lowest number (2,916) of orthologous groups was found in Sphingobium sp. SYK-6. Of 4,786 genes of S. fuliginis ATCC 27551, only 4,502 existed as part of known orthologous groups. The remaining 449 genes did not cluster with any of these orthologous groups and hence were considered as singletons. However, six orthologous groups comprising a total number of 13 genes were specific to only S. fuliginis ATCC 27551 and were not found in any of the other 49 genomes analyzed. Therefore, these 13 genes and 449 singletons are considered as unique to the genome of S. fuliginis ATCC 27551.

A significant proportion of the unique genome of the Sphingobium genus codes for transposases and it was found to be the largest orthologous group with 283 genes. The top 15 largest orthologous groups of Sphingobium genus are highly enriched and contain a number of paralogous sequences. These orthologous groups code for efflux pumps and membrane transporters.

The phylogenetic inferences of the Sphingobium genus were drawn by taking the core genome into consideration. Of 802 orthologous groups, 251 were found to be multicopy orthologs. Thus, only 551 single-copy orthologs were used while constructing the phylogenetic tree for the genus. The phylogenetic tree thus constructed contains three clades. The clade where S. fuliginis ATCC 27551 is grouped contains Sphingobium sp. kk22, Sphingobium sp. YBL2, Sphingobium sp. AM, and Sphingobium sp. 22B. All of them are involved in degradation of rare and recalcitrant aromatic compounds, such as polyaromatic hydrocarbons (PAHs) and herbicides (Gu et al. 2013; Maeda et al. 2013, 2015; Madueño et al. 2016; Festa et al. 2017). The clustering of S. fuliginis ATCC 27551 with PAH-degraders appears to have functional and evolutionary significance. This clade apparently shows considerable distance with hexachlorocyclohexane (HCH)-degrading Sphingobiumjaponicum and Sphingobiumindicum (supplementary fig. S2, Supplementary Material online).

Indigenous Plasmids

The plasmids of S. fuliginis ATCC 27551 have received considerable attention because they possess the genetic repertoire required for the degradation of OP insecticides and they play a critical role in the horizontal mobility of the opd (OP-degradation) gene. Sphingobiumfuliginis ATCC 27551 has four plasmids (Mulbry et al. 1986, 1987) and their sizes were previously determined by electrophoretic mobility to be 51 kb (pPDL1), 43 kb (pPDL2), 27 kb (pPDL3), and 23 kb (pPDL4). Among these plasmids, only pPDL2 carries the opd gene and plays a role in transferring the opd gene to other soil bacteria (Siddavattam et al. 2003, 2019; Pandeeti et al. 2012). Our genome sequence analysis of S. fuliginis ATCC 27551 also identified these four plasmids; however, surprisingly, their sizes did not match those determined by electrophoretic mobility (Mulbry et al. 1986, 1987). Based on our sequence analysis, these four plasmids have now been renamed as pSF1 (224,736 bp), pSF2 (60,848 bp), pSF3 (43,234 bp), and pSF4 (27,207 bp) to indicate the source of isolation and to maintain uniformity. Plasmid pSF1 codes for 239 proteins, and of these 89 are hypothetical proteins. All genes required for coding a Type 4 secretory system (T4SS), a typical feature required for mediating horizontal gene transfer (HGT) are found on plasmid pSF1. Interestingly, pSF1 also includes a complete set of genes required for copper uptake and codes for efflux pumps, which are predicted to confer resistance to cobalt–zinc–cadmium. Likewise, plasmid pSF2 also contains genes coding for a functional T4SS. Most of the other predicted genes of plasmid pSF2 code for hypothetical proteins. Interestingly, genes encoding the T4SS are absent on both pSF3 and pSF4. However, these two plasmids have well-conserved oriT (origin of transfer) sequences and encode relaxase, which is required for initiating HGT.

The sequence of plasmid pPDL2 was manually determined and coincided with the sequence of pSF3. Both of the sequences showed exact synteny, except in the region spanning 12,680–18,619 bp. This region hits twice to the SMRT assembled sequence of pSF3 indicating the existence of a 5,939 bp duplication in the sequence of pSF3 (fig. 2A). The duplication is seen near the opd element. In this region, the opd and mfhA genes coding for an esterase, are flanked by IS21 and a duplicated Tn3 (fig. 2B). Plasmid pSF3 also contains a functional integration module that can integrate at an attachment (attB) site such as those typically found in integrative mobilizable elements. These two unique structural features of plasmid pSF3 strongly suggest it involvement in the lateral transfer of the opd gene among soil bacteria.

Fig. 2.

—Graphical representation of the pair-wise alignment of SMRT-generated pSF3 sequence with pPDL2 is shown along with ∼6 kb duplicated region in panel (A). The genetic organization of the duplication region is shown in panel (B).

The genus Sphingobium plays a critical role in the mineralization of toxic and recalcitrant organic compounds. Species belonging to this genus have gained prominence due to their bioremediation potential, especially of agricultural soils and dump sites contaminated with HCH. Genome sequences of S. japonicum, Sphingobiumchlorophenolicum, and S. indicum are available in the database (Nagata et al. 2010; Anand et al. 2012; Copley et al. 2012). As we have shown here for S. fuliginus ATCC 27551, all of them have two chromosomes. Orthology analysis revealed high pressure on the species to adapt to various environmental conditions. Genes that are under selective pressure are often duplicated and present in high copy-number. Such multicopy genes play a critical role in the adaptability of the species to a particular environment (Wagner 2002). The genes encoding efflux pumps, which confer resistance to heavy metals such as cadmium, zinc, and mercury, are found in multiple copies suggesting the species has the ability to survive in environments polluted with heavy metals (Nies 2003; Ojuederie and Babalola 2017). Another interesting feature of the species is the existence of a high number of outer membrane-associated TonB-dependent receptors (TonRs). TonR are an integral part of TonB-dependent transport (TonBDT) system and are specialized for the transport of nutrients through the energy-deprived outer membrane (Noinaj et al. 2010). Vitamin B12, nickel complexes, and ferric-siderophores are substrates of the TonBDT system. In addition to TonR, the TonBDT system consists a Ton-complex consisting of the proton-motive-force-dependent pump components (ExbB/ExbD) and the energy transducing TonB protein. The Ton complex is conserved in TonBDT. However, the TonR sequences are variable and appear to be substrate-specific (Noinaj et al. 2010). Limited information is currently available on TonBDT making it somewhat difficult to predict to the potential substrate transported (Schauer et al. 2008). However, the number of TonR copies is proportionate to the complexity of the environment (Schauer et al. 2008). Gram-negative bacteria adapted to a pathogenic lifestyle, living in harsh environmental conditions, and those surviving in the mammalian gut contain the highest number of TonRs (Blanvillain et al. 2007; Schauer et al. 2008). These TonRs are implicated to be important in the transport of rare and unique nutrients available in these particular environments. The genome of S. fuliginis ATCC 27551 contains 87 copies of the TonR-coding genes, compared with three copies of TonB- and two copies of ExbB/ExbD-coding genes. The existence of such a large number of TonRs with structural diversity indicates the presence of novel TonBDT systems among Sphingobium members, perhaps aiding their acquisition of scarce nutrients in soil.

Supplementary Material

Supplementary data are available at Genome Biology and Evolution online.

Data deposition: This project has been deposited at NCBI genbank under accession numbers CP041016-CP041021(GCA_006363875.1).