Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4

Introduction

The taxonomy and phylogeny of the genus Agrobacterium has proven to be complex and controversial. Bacteria of the genus Agrobacterium have been grouped into six species based on the disease phenotype associated, in part, with the resident disease-inducing plasmid. Among those six species are Agrobacterium tumefaciens causing crown gall on dicotyledonous plants, stone fruit and nut trees and Agrobacterium radiobacter that is not known to cause plant diseases of any kind (Bouzar & Jones, 2001; Conn, 1942; Kerr & Panagopoulos, 1977; Panagopoulos, Psallidas & Alivizatos, 1978; Riker et al., 1930; Starr & Weiss, 1943; Süle, 1978). An alternative classification approach grouped Agrobacterium organisms into three biovars based on physiological and biochemical properties without consideration of disease phenotype (Keane, Kerr & New, 1970; Kerr & Panagopoulos, 1977; Panagopoulos, Psallidas & Alivizatos, 1978). The species and biovar classification schemes do not coincide well, in a large part, because of the disease-inducing plasmids, tumor-inducing (pTi) and hairy root-inducing (pRi), are readily transmissible plasmids (Young et al., 2001).

Many widely used approaches for bacterial species definition include composition of peptidoglycan, base composition of DNA, fatty acid and 16S rDNA sequence (Stackebrandt et al., 2002) in addition to newer methods based on the whole-genome analysis (Coutinho et al., 2016; Jain et al., 2018), horizontal gene transfer analysis (Bobay & Ochman, 2017) or the core genome analysis (Moldovan & Gelfand, 2018) which is used in the present study. The genus Agrobacterium is a prime example with many proposals and oppositions regarding the amalgamation of Agrobacterium and Rhizobium over the last three or four decades (Farrand, Van Berkum & Oger, 2003; Gaunt et al., 2001; Young et al., 2001, 2003). However, more recent studies appear to favor the preservation of the genus Agrobacterium backed by strong genetic and genomic evidence (Gan & Savka, 2018; Ramírez-Bahena et al., 2014). Within the genus Agrobacterium, the taxonomic status of Agrobacterium radiobacter and Agrobacterium tumefaciens remains contentious (Sawada et al., 1993; Young, 2008; Young, Pennycook & Watson, 2006). Agrobacterium radiobacter (originally proposed as Bacillus radiobacter) is a non-pathogenic soil bacterium associated with nitrogen utilization isolated more than a century ago in 1902 (Beijerinck & Van Delden, 1902; Conn, 1942). On the other hand, Agrobacterium tumefaciens (previously Bacterium tumefaciens) is a plant pathogen capable of inducing tumorigenesis (Smith & Townsend, 1907). However, the descriptive assignment for Agrobacterium tumefaciens was later found to be contributed by a set of genes located on the large Ti plasmid that can be lost (Gordon & Christie, 2014). In other words, the curing of Ti plasmid in Agrobacterium tumefaciens will change its identity to the non-pathogenic species, Agrobacterium radiobacter. Furthermore, comparative molecular analysis based on single-copy housekeeping genes also supports the close relatedness of Agrobacterium radiobacter and Agrobacterium tumefaciens, blurring the taxonomic boundaries between these species (Mousavi et al., 2015; Shams et al., 2013). As taxa are reclassified into different populations that do not conform to the characteristics of the original description, the given names lose their significant and descriptive importance. Consistent with the Judicial Commission according to the Rules of the International Code of Nomenclature of Bacteria, Tindall (2014) concluded that the combination of Agrobacterium radiobacter has priority over the combination Agrobacterium tumefaciens when the two are treated as members of the same species since Agrobacterium radiobacter was the first proposed and described in 1902 whereas Agrobacterium tumefaciens was first proposed and described in 1907) (Tindall, 2014). However, given that Agrobacterium tumefaciens has been more widely studied than Agrobacterium radiobacter due to its strong relevance to agriculture (Bourras, Rouxel & Meyer, 2015), it remains unclear but interesting to see if the broader scientific community will obey this rule by adopting the recommended species name change in future studies.

To our knowledge, a detailed comparative genomics analysis of Agrobacterium radiobacter and Agrobacterium tumefaciens type strains has not been reported despite their genome availability (Zhang et al., 2014). The high genomic relatedness of both type strains was briefly mentioned by Kim & Gan (2017) through whole genome alignment and pairwise nucleotide identity calculation from homologous regions. However, evidence is now mounting that the Agrobacterium radiobacter DSM 30147^T reported by Zhang et al. (2014) is contaminated, warranting immediate investigation (Jeong, Pan & Park, 2016). The assembled genome is nearly 7 megabases, the largest among Agrobacterium currently sequenced at that time with up to 6,853 predicted protein-coding genes contained in over 600 contigs. At sequencing depth of nearly 200×, its genome assembly is unusually fragmented even for a challenging microbial genome (Utturkar et al., 2017). Furthermore, the phylogenomic placement of Agrobacterium radiobacter DSM 30147^T based on this genome assembly has been questionable as evidenced by its basal position and substantially longer branch length relative to other members of the species (Gan & Savka, 2018). The overly fragmented nature of this assembly also precludes fruitful comparative genomics focusing on gene synteny analysis. More importantly, analysis done on a contaminated assembly but with the assumption that it is not, will likely lead to incorrect biological interpretations (Allnutt et al., 2018).

In this study, we sequenced the whole genome of Agrobacterium radiobacter using a type strain that was sourced from the National Collection of Plant Pathogenic Bacteria (NCPPB). We produced a contiguous genome assembly exhibiting genomic statistics that are more similar to other assembled Agrobacterium genomes. We show here, through comparative genomics and phylogenetics, that the previously assembled Agrobacterium radiobacter DSM 30147^T genome contains substantial genomic representation from another Agrobacterium sp. isolated and sequenced by the same lab, consistent with our initial suspicion of strain contamination. Using the newly assembled genome for subsequent comparative analysis, we provide genomic evidence that Agrobacterium radiobacter DSM 30147^T and Agrobacterium tumefaciens B6^T are the same species. However, strain DSM 30147^T should not be considered as a merely non-tumorigenic strain of Agrobacterium tumefaciens as substantial genomic variation exists between these two type strains notably in the nucleotide sugar metabolism pathway that may contribute to their ecological niche differentiation.

Materials and Methods

Results

The inflated genome size of Agrobacterium radiobacter DSM 30147(T) is due to technical errors

Instead of sharing a recent common ancestor as would be expected for a recently duplicated gene, the duplicated single copy genes coding for seryl-tRNA synthetase in Agrobacterium radiobacter DSM 30147^T were placed in two distinct clusters with one affiliated to genomospecies 4 and the other affiliated to genomospecies 7 (Fig. 1A). Such an unexpected clustering pattern raises the suspicion of genome assembly from two or more non-clonal bacterial strains. In addition, by performing comparison at the genome-scale based on whole proteome clustering of Agrobacterium radiobacter DSM 30147^T/NCPPB 3001^T (Previous study, GCF_000421945; This study, GCF_001541305), A. sp. TS43 (unpublished, GCF_001526605) and Agrobacterium tumefaciens B6 (GCF_001541315), we observed a high number of proteins that were exclusively shared between Zhang et al. Agrobacterium radiobacter DSM 30147 and A. sp. TS43 belonging to genomospecies 7 (Fig. 1B). Coincidentally, despite not sharing the same Bioproject ID, the whole genomes of strains DSM 30147^T and TS43 were sequenced by the Zhang et al., and submitted to NCBI on the same date, 30 May 2013, hinting strain contamination during sample processing in the lab.

Genome-scale average nucleotide identity calculation supports the amalgamation of Agrobacterium radiobacter and Agrobacterium tumefaciens into a single genomospecies

Single gene tree shows that Agrobacterium radiobacter NCPPB 3001^T and Agrobacterium tumefaciens B6^T belong to the genomospecies 4 clade (Fig. 1A), corroborating with the PhyloPhlAN phylogenomic tree that was constructed based on the alignment of 400 universal single-copy proteins (Fig. S1). The pairwise average nucleotide identity (ANI) among strains within this clade is consistently more than 95% further supporting their affiliation to the same genomospecies (Fig. 2) (Coutinho et al., 2016; Jain et al., 2018). As expected, pairwise ANI of less than 92% was observed when they were compared with strains from genomospecies 7 (strains RV3 and Zutra 3/1). A 100% pairwise ANI was observed between Agrobacterium radiobacter type strains that were sourced from NCPPB and LMG. In addition, non-type strains B140/95 and CFBP5621 also exhibit a strikingly high pairwise ANI (>99%) to the type strains of Agrobacterium tumefaciens and Agrobacterium radiobacter, respectively, leading to the formation of sub-clusters within genomospecies 4 (Fig. 2).

Is Agrobacterium radiobacter a non-tumorigenic strain of Agrobacterium tumefaciens?

A majority of the currently sequenced strains from genomospecies 4 are non-tumorigenic as evidenced by the near complete lack of genomic region with significant nucleotide similarity to the octopine-type Ti reference plasmid (Fig. 3). Of the 14 genomes analyzed, only strains B6^T and B140/95 exhibit a complete coverage of the Ti plasmid with near 100% sequence identity while strain 186 shows hits mainly to the essential gene clusters of a Ti plasmid such as the vir gene cluster (black rings and gene labels in Fig. 3) at a substantially lower sequence identity (50% < x < 90%) (Fig. 3), suggesting that it may be harboring a dissimilar variant of Ti plasmid, for example, different opine type. In addition, although lacking hits to the virulence gene of the Ti plasmid, the tra and trb clusters involved in plasmid conjugal transfer are present in strains Kerr 14, CCNWGS0286 and UNC420CL41Cvi. Despite belonging to the same genomospecies, core genome alignment and phylogenomic analysis indicates that Agrobacterium radiobacter NCPPB3001^T is sufficiently divergent from Agrobacterium tumefaciens B6^T leading to their separation into two distinct sub-clusters (Fig. 4A). This is also resonated by their different sub-cluster placement in the pairwise ANI heatplot (Fig. 2). Furthermore, strains from both subclades could be broadly differentiated by the set of core accessory genes that they harbor (Fig. 4B). Therefore, even though Agrobacterium radiobacter does not harbor a Ti plasmid, it cannot be considered as a non-tumorigenic strain of Agrobacterium tumefaciens given multiple lines of evidence indicating its substantial genomic divergence from Agrobacterium tumefaciens.

Agrobacterium genomospecies 4 strains differ in their genomic potential for nucleotide sugar metabolism

Individual comparison of the reconstructed KEGG pathways in Agrobacterium tumefaciens (Fig. 5A) and Agrobacterium radiobacter (Fig. 5B) revealed stark contrast in the anabolism of dTDP-L-rhamnose which is commonly found in the O-antigen of lipopolysaccharide (LPS) in gram-negative bacteria. Surprisingly, the entire enzyme set required for the generation of dTDP-L-rhamnose from D-glucose-phosphate (Table 2) is absent in Agrobacterium tumefaciens B6, suggesting that this common nucleotide sugar may be absent from the LPS O-antigen of strain B6. A manual inspection of the accessory genes uniquely shared by Agrobacterium tumefaciens strains B6 and B140/95 identified a homolog cluster containing GDP-L-fucose synthase (EC 1.1.1.271) that is involved in the enzymatic production of GDP-L-fucose from GDP-4-dehydro-6-deoxy-D-mannose and NADH (Table 2; Fig. 5C). As expected, the genes coding for this enzyme and GDP-mannose 4,6-dehydratase involved in the conversion of GDP-alpha-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose, are absent in the Agrobacterium radiobacter NCPPB3001 genome (Fig. 5D). Intriguingly, HMMsearch scan revealed the presence of two protein hits to the TIGR01479 HMM profile in Agrobacterium tumefaciens B6 that corresponds to D-mannose 1,6-phosphomutase (EC 5.4.2.8) required for the synthesis of D-mannose 6-phosphate. In addition to strain B6, its close relative, strain B140/95, and a more distantly related strain Kerr14 also harbor two copies of this gene. However, one of the D-mannose 1,6-phosphomutases in strain Kerr14 is more divergent with a lower TIGRFAM HMM sequence score (Table 2). Furthermore, it exhibits less than 70% protein identity to the Agrobacterium tumefaciens B6 and B140/95 homologs, forming a private protein cluster in the pan-genome (data not shown).

Table 2:

Identification of Agrobacterium proteins with TIGRFAM domains involved in the biosynthesis of nucleotide sugar.

Assembly ID	Strain	TIGR01479 (EC 5.4.2.8)		TIGR01472 (EC 4.2.1.47)	TIGR01207 (EC 2.7.7.24)	TIGR01181 (EC 4.2.1.46)	TIGR01221 (EC 5.1.3.13)	TIGR01214 (EC 1.1.1.133)
		1st hit	2nd hit
GCF_900045375	B6	690.2	566.6	589.5
GCF_001541315	B6	690.2	566.6	589.5
GCF_001692245	B140/95	690.2	566.6	589.5
GCF_900011755	Kerr14	691.3	690.2	428.6*
GCF_001541305	NCPPB3001	690.2			494.6	488.5	215.4	331.5
GCF_002008215	LMG140	690.2			494.6	488.5	215.4	331.5
GCF_900012605	CFBP5621	689.3			494.6	489.5	215.4	331.5
GCF_002591665	186	689.3			494.6	488.5	215.4	331.8
GCF_003031125	LAD9	688.5			494.4	487.9	215.4	329.9
GCF_000233975	CCNWGS	644.8			494.6	487.5	215.4	331.8
GCF_002179795	LMG215	690.2
GCF_000384555	224MFTsu31	644.8
GCF_000482285	UNC420CL41Cvi	644.8
GCF_900188475	719_389	687.5

DOI: 10.7717/peerj.6366/table-2

Notes:

Numbers indicate bit scores calculated based on protein alignment to the model with higher scores indicating stronger and more significant hits.

* Formed a separate protein cluster from the rest of genomospecies 4 GDP-mannose-4,6-dehydratase orthologs (<70% pairwise protein identity).

Discussion

We re-sequenced the genome of Agrobacterium radiobacter type strain using strain directly obtained from NCPPB. The assembled Agrobacterium radiobacter genome reported in this study exhibits assembly statistics that are consistent with a high-quality draft genome such as high genome completeness and contiguity, near-zero contamination/duplication and comparable genome size to other closely related strains (Gan, Lee & Savka, 2018; Parks et al., 2015). Furthermore, given the improved contiguity and dramatic reduction in the number of contigs of this newly assembled draft genome, we recommend using this genome in place of the previously published draft genome for future Agrobacterium comparative studies.

The distinct separation of Agrobacterium genomospecies 4 and 7 at 95% ANI cutoff corroborates with the previously established “genomic yardstick” for species differentiation (Konstantinidis & Tiedje, 2005; Richter & Rosselló-Móra, 2009). Using this percentage cutoff, the ANI approach has been successfully used to provide a near “black-and-white” pattern of species separation in even some of the most diverse bacterial genera such as Pseudomonas, Arcobacter and Stenotrophomonas (Pérez-Cataluña et al., 2018; Tran, Savka & Gan, 2017; Vinuesa, Ochoa-Sánchez & Contreras-Moreira, 2018). Given the increasing evidence highlighting the robustness and reliability of the ANI approach in species delineation, the pairwise ANI between Agrobacterium tumefaciens and Agrobacterium radiobacter type strains that is at least 2.5% higher than the 95% cutoff value is rigorous evidence that they belong to the same genomospecies, effectively serving as the final nail in the coffin for the decade-long debate on their taxonomic status. The amalgamation of Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species have been repeatedly suggested in the past few years but was complicated by the special status of Agrobacterium tumefaciens as the type species of the genus Agrobacterium despite the priority that Agrobacterium radiobacter has over Agrobacterium tumefaciens as it was isolated and described 3 years before Agrobacterium tumefaciens (Young et al., 2001, 2003). Despite sharing numerous morphological and biochemical features, differences in genomic features such as pairwise ANI, phylogenomic clustering and core accessory gene contents do exist among members in Agrobacterium genomospecies 4 that can facilitate the identification of genotypic and phenotypic variants to accurately delimit sub-species relationships in the future (Brenner, Staley & Krieg, 2000; Jezbera et al., 2011; Meier-Kolthoff et al., 2014; Tan et al., 2013).

To date the LPS for both type strains have been determined (De Castro et al., 2002, 2004). In stark contrast to Agrobacterium radiobacter, the Agrobacterium tumefaciens LPS consists of D-arabinose and L-fucose that have yet been reported to date in another members of the genus Agrobacterium (De Castro et al., 2002). The presence of the L configuration of fucose is considered to be rare even among plant pathogenic bacteria but may be associated with the ability of Agrobacterium tumefaciens to colonize or bind to wounded plant cell (Lippincott, Whatley & Lippincott, 1977; Whatley et al., 1976; Whatley & Spiess, 1977). It has been previously shown that the LPS of Agrobacterium tumefaciens but not Agrobacterium radiobacter can bind to the plant cells thus providing protection against subsequent infection by pathogenic strains (Whatley et al., 1976). The presence and absence of nucleotide sugars in the O-chain constituent of LPS in both type strains corroborates with their observed genomic potential in the nucleotide sugar metabolism pathway thus underscoring the utility of comparative genomics in facilitating the prediction of microbial host range and ecological niche (Klosterman et al., 2011). For example, the absence of L-rhamnose and L-fucose in the LPS of Agrobacterium tumefaciens B6 and Agrobacterium radiobacter DSM30147, respectively, is consistent with the lack of genes coding for enzymes involved with the particular nucleotide sugar metabolism. Generation of Agrobacterium tumefaciens B6 LPS mutant via targeted gene deletion (Kaczmarczyk, Vorholt & Francez-Charlot, 2012) or the classical but more laborious transposon mutagenesis approach followed by characterization of the LPS mutant host-range and phytopathogenicity will be instructive (Gan et al., 2011; Reuhs et al., 2005).

Our current genomic sampling indicates that the Ti plasmid appears to be restricted to the Agrobacterium tumefaciens subclade. The maintenance of the Ti plasmid is metabolically taxing given its large size (Barker et al., 1983; Glick, 1995). Even if the Ti plasmid was conjugally transfer, for example, to Agrobacterium radiobacter, the inability of Agrobacterium radiobacter to colonize plant host as evidenced by its LPS incompatibility will not confer an advantage to the new plasmid host in a natural environment (Thomashow et al., 1980). Furthermore, in the absence of high density Acyl-homoserine lactone (AHL) signals which is required to trigger Ti plasmid conjugation (Fuqua & Winans, 1994; Pappas, 2008; Zhang, Wang & Zhang, 2002), the newly acquired Ti plasmid in Agrobacterium radiobacter may be cured in its natural soil habitat after a few generations. Although the spontaneous transfer of the Ti plasmid from tumorigenic Agrobacterium tumefaciens to Agrobacterium radiobacter K84 has been reported previously, strain K84 was re-classified based on a recent core gene analysis to Rhizobium rhizogenes K84 (Velázquez et al., 2010; Vicedo et al., 1996), reiterating the pervasive taxonomic inconsistency within the genus Agrobacterium that may have confound previous biological interpretations (De Ley et al., 1966; Lindström et al., 1995; Young, 2008). Given that a large majority of Agrobacterium genetics was performed during the pre-NGS era (Gan & Savka, 2018), it remains unknown as to how many Agrobacterium tumefaciens and Agrobacterium radiobacter strains have been molecularly misclassified due to their high genomic relatedness.

The inability to accurately identify plasmid and chromosomal-derived contigs among the draft genomes means that some of the core accessory genes among tumorigenic strains may be plasmid-derived and should be treated with caution as the low-copy-number Ti-plasmid is prone to curing in the absence of AHL signals. Despite the value of complete genome assembly in enabling the accurate partitioning of plasmid and chromosomal genomic region (Arredondo-Alonso et al., 2017), the representation of complete Agrobacterium genomes in current database is still very low as a majority of the genomes were assembled from short Illumina reads that cannot effectively span repetitive region (Wibberg et al., 2011; Wood et al., 2001). Furthermore, most Agrobacterium strains harbor multiple large plasmids that further complicate short-read-only assembly graph (Kado & Liu, 1981; Lowe et al., 2009; Shao et al., 2018). Given the currently available genomic resources for Agrobacterium, defining subspecies within the Agrobacterium genomospecies 4 based on the identification of lineage-specific gene set (Moldovan & Gelfand, 2018) will be challenging. However, we anticipate that the advent of high throughput long-read sequencing that can span large repetitive region in recent years is likely going to overcome this limitation allowing a more accurate depiction of microbial pangenome (Gan et al., 2012; Gan, Lee & Austin, 2017; Schmid et al., 2018a, 2018b). Future hybrid genome assemblies (Illumina and Nanopore/PacBio reads) of members from genomospecies 4 with comprehensive metadata and reliable phenotypic information, will be instructive.

Conclusions

Despite belonging to the same genomospecies, Agrobacterium tumefaciens and Agrobacterium radiobacter are by no means clonal at the chromosomal level and instead demonstrate sufficient genomic characters that qualify their separation into two sub-species. In addition, the difference in the LPS profile among two type strains will have implications to host specificity leading to geographical separation. In the spirit of preserving the naming of both species but at the same time respecting the taxonomic jurisdiction for strain priority, we propose Agrobacterium tumefaciens to be reclassified as Agrobacterium radiobacter subsp. tumefaciens and for Agrobacterium radiobacter to retains its species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter.

Supplemental Information