Reclassification of Delftia lacustris Jørgensen et al. 2009 as a Later Heterotypic Synonym of Delftia tsuruhatensis Shigematsu et al. 2003
Kong Fanqun §, Wang Xinxia §, Manik Prabhu Narsing Rao, Wang Xinya, Wang Qingfan, Xue Yuchen, Syed Raziuddin Quadri, Cui Jingjing* and Cheng Mei** Author for corresponding; e-mail address: byfycjj@126.com, chm790217@126.com
ORCID ID: https://orcid.org/0000-0003-1259-1728
Volume: Vol.53 No.4 (July 2026)
Research Article
DOI: https://doi.org/10.12982/CMJS.2026.069
Received: 4 April 2026, Revised: 28 May 2026, Accepted: 15 June 2026, Published: 7 July 2026
Citation: Fanqun K., Xinxia W., Narsing Rao M.P., Xinya W., Qingfan W., Yuchen X., et al., Reclassification of Delftia lacustris Jørgensen et al. 2009 as a later heterotypic synonym of Delftia tsuruhatensis Shigematsu et al. 2003. Chiang Mai Journal of Science, 2026; 53(4): e2026069. DOI 10.12982/CMJS.2026.069.
Graphical Abstract
Abstract
In the present study, the taxonomic position of Delftia lacustris and Delftia tsuruhatensis was evaluated through genome analysis. The genome size of Delftia lacustris DSM 21246ᵀ was 7,267,296 bp with a G+C content of 66.1%, whereas the genome size of Delftia tsuruhatensis NBRC 16741ᵀ was 6,607,932 bp with a G+C content of 66.5%. The 16S rRNA gene sequence extracted from the genome of D. lacustris DSM 21246ᵀ showed 100% similarity to that of D. tsuruhatensis NBRC 16741ᵀ, exceeding the species delineation threshold (98.65%). In the phylogenetic and phylogenomic trees, both clustered within the same clade, indicating close evolutionary relatedness. The average nucleotide identity (ANIb) between the genomes was 97.7%, and the digital DNA–DNA hybridization (dDDH) value was 85.6%, both exceeding the accepted species delineation thresholds (95–96% for ANI and 70% for dDDH). These results support the reclassification of Delftia lacustris Jørgensen et al. 2009 as a later heterotypic synonym of Delftia tsuruhatensis Shigematsu et al. 2003.
1. INTRODUCTION
The genus Delftia, with Delftia acidovorans as a type species, was proposed by Wen et al. [1] by the transfer of Comamonas acidovorans as a novel genus and combination novel. At the time of writing, this genus consists of six species with validly published species names (accessed on 14/03/2026) [2] isolated from various ecological niches like rhizosphere [3], soil enriched with acetamide [1, 4], desert soil [5], freshwater [6], freshwater shrimp culture pond [7], and activated sludge [8]. They were reported to be aerobic, Gram-negative, rod-shaped, motile, poly-β-hydroxybutyrate-accumulating, chemotaxonomically, having hexadecanoic acid (C16 : 0), hexadecenoic acid (C16 : 1) and octadecenoic acid (C18 : 1) as predominant fatty acids and Q-8 as the major quinone [1, 5].
Replacement of the traditional DNA–DNA hybridization (DDH) approach in prokaryotic taxonomy with genome-based similarity methods has been enabled by advances in sequencing technologies and bioinformatics tools [9]. In recent years, using genome-based analysis, we have reclassified many prokaryotic species [10, 11]. The recognition of heterotypic synonyms helps to improve taxonomic consistency, reduces redundancy in microbial databases, and enhances the accuracy of species identification.
During the literature survey, we noticed that the type strain of Delftia lacustris was reported to share high 16S rRNA gene sequence similarity with the type strain of Delftia tsuruhatensis, while their DDH value was reported below the threshold value (70 %) for the delineation of novel species [12]. Due to their high 16S rRNA gene sequence similarity, in the present study, we evaluated their taxonomic position through genome analysis.
2. MATERIALS AND METHODS
The genome sequences of Delftia species were downloaded from the GenBank database (https://www.ncbi.nlm.nih.gov/), and their quality was estimated by CheckM (version 1.2.2; marker lineage Comamonadaceae) [13]. The 16S rRNA gene sequence from the genomes was extracted using Barrnap (v. 0.9) [14] and compared using the pairwise alignment feature implemented on the EzBioCloud server (www.ezbiocloud.net/tools/pairAlign). A phylogenetic tree (based on 16S rRNA gene sequence) was constructed with the maximum-likelihood [15] method using MEGA software (version 12.1.2) [16]. Clustal W program [17] was used for multiple alignments of sequences. Kimura’s two-parameter model [18] was used to evaluate the evolutionary distance matrices with 1000 Bootstrap replications [19]. Genomic relatedness was assessed using digital DNA-DNA hybridization (dDDH) with the Genome-to-Genome Distance Calculator (version 3.0; http://ggdc.dsmz.de/ggdc.php) using BLAST+ and formula 2 [20-22], and average nucleotide identity (ANI) was performed using JSpeciesWS [23]. A phylogenomic tree was constructed using the Anvi’o tool [24, 25]. Prodigal was used to identify open reading frames [26], HMMER to identify genes matching bacterial single-copy core gene collections [27, 28], and MUSCLE for multiple sequence alignment [29], and the resulting tree was visualized using MEGA (version 12.1.2) software [16].
3. RESULTS AND DISCUSSION
The genome size of Delftia lacustris DSM 21246T was 7267296 (bp) with 66.1% G+C content, while the genome size of Delftia tsuruhatensis NBRC 16741T was 6607932 (bp) with 66.5% G+C content. The 16S rRNA gene sequence extracted from Delftia lacustris DSM 21246T genome showed 100% similarity with the 16S rRNA gene sequence extracted from Delftia tsuruhatensis NBRC 16741T, which exceeded the species delineation threshold (98.65%) [30], preliminarily indicating they are the same species. In the ML-based phylogenetic tree (Figure 1), the type strains of Delftia lacustris and Delftia tsuruhatensis clade together. During the proposal of Delftia lacustris as a novel species, Jørgensen et al. [6] identified distinguishing characteristics relative to Delftia tsuruhatensis, including chitinase production and the utilization of carbon sources such as D-mannitol and D-malic acid for growth. However, such differential characteristics are commonly observed among closely related bacterial species and even among strains of the same species. These variations may arise due to differences in environmental adaptation, cultivation conditions, and genomic variability affecting metabolic expression.
The genome of Delftia tsuruhatensis NBRC 16741ᵀ showed 99.8% completeness with no detectable contamination, whereas the genome of Delftia lacustris DSM 21246ᵀ exhibited 100.0% completeness with 0.5% contamination [13]. In the phylogenomic tree, Delftia lacustris and Delftia tsuruhatensis clade together (Figure 2).
Genome relatedness between Delftia lacustris DSM 21246ᵀ and Delftia tsuruhatensis NBRC 16741ᵀ was calculated using ANI and dDDH (Table 1). The ANIb value between Delftia lacustris DSM 21246ᵀ and Delftia tsuruhatensis NBRC 16741ᵀ was 97.6%, and the dDDH value was 85.6%, both of which were above the established cut-off thresholds (95–96% for ANI and 70% for dDDH) for species delineation [31-33], indicating they are similar species. Based on the above results, we propose to reclassify Delftia lacustris Jørgensen et al. 2009 as a later heterotypic synonym of Delftia tsuruhatensis Shigematsu et al. 2003.
4. CONCLUSIONS
Comparative genomic and phylogenetic analyses consistently demonstrated that Delftia lacustris DSM 21246ᵀ and Delftia tsuruhatensis NBRC 16741ᵀ represent the same taxonomic entity. Multiple independent lines of evidence, including genome similarity indices and phylogenomic clustering, clearly support their close relationship beyond the accepted thresholds used for bacterial species delineation. These findings highlight the importance of genome-based approaches for improving taxonomic resolution within the genus Delftia. Based on the overall genomic relatedness and phylogenetic consistency, Delftia lacustris Jørgensen et al. 2009 should be reclassified as a later heterotypic synonym of Delftia tsuruhatensis Shigematsu et al. 2003.
ACKNOWLEDGEMENTS
This research was funded by the Natural Science Foundation of Yantai, China (grant no. ZR2025Z041). The author, Syed Raziuddin Quadri, extends his appreciation to the Deanship of Scientific Research at Northern Border University, Arar, Kingdom of Saudi Arabia, for funding this research work through the project number NBU-FFR-2026-2046-05.
AUTHOR CONTRIBUTIONS
Kong Fanqun, Wang Xinxia, Wang Xinya, Wang Qingfan and Xue Yuchen: conceptualization, methodology, and data curation. Manik Prabhu Narsing Rao: data curation and preparation of the original draft. Syed Raziuddin Quadri: revising the manuscript. Cui Jingjing and Cheng Mei: Supervision and Funding acquisition.
CONFLICT OF INTEREST STATEMENT
The authors declared that they have no conflict of interest that is relevant to the contents of this article.
REFERENCES
[1] Wen A., Fegan M., Hayward C., Chakraborty S., and Sly L.I., Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987) gen. nov., comb. nov. International Journal of Systematic Bacteriology, 1999; 49(2): 567-576. DOI 10.1099/00207713-49-2-567.
[2] Parte A.C., Sardà Carbasse J., Meier-Kolthoff J.P., Reimer L.C., and Göker M., List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 2020; 70(11): 5607-5612. DOI 10.1099/ijsem.0.004332.
[3] Carro L., Mulas R., Pastor-Bueis R., Blanco D., Terrón A., González-Andrés F., et al., Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer. International Journal of Systematic and Evolutionary Microbiology, 2017; 67(6): 1957-1960. DOI 10.1099/ijsem.0.001892.
[4] den Dooren de Jong L.E., Bijdrage Tot De Kennis Van Het Mineralisatieproces, Proefschrift, Technische Hogeschool, Delft, 1926.
[5] Li C.T., Yan Z.F., Chu X., Hussain F., Xian W.D., Yunus Z., et al., Delftia deserti sp. nov., isolated from a desert soil sample. Antonie van Leeuwenhoek, 2015; 107(6): 1445-1450. DOI 10.1007/s10482-015-0440-4.
[6] Jørgensen N.O.G, Brandt K.K., Nybroe O. and Hansen M., Delftia lacustris sp. nov., a peptidoglycan-degrading bacterium from fresh water, and emended description of Delftia tsuruhatensis as a peptidoglycan-degrading bacterium. International Journal of Systematic and Evolutionary Microbiology, 2009; 59(9): 2195-2199. DOI 10.1099/ijs.0.008375-0.
[7] Chen W.M., Lin Y.S., Sheu D.S. and Sheu S.Y., Delftia litopenaei sp. nov., a poly-β-hydroxybutyrate-accumulating bacterium isolated from a freshwater shrimp culture pond. International Journal of Systematic and Evolutionary Microbiology, 2012; 62(10): 2315-2321. DOI 10.1099/ijs.0.037507-0.
[8] Shigematsu T., Yumihara K., Ueda Y., Numaguchi M., Morimura S. and Kida K. Delftia tsuruhatensis sp. nov., a terephthalate-assimilating bacterium isolated from activated sludge. International Journal of Systematic and Evolutionary Microbiology, 2003; 53(5): 1479-1483. DOI 10.1099/ijs.0.02285-0.
[9] Chun J., Oren A., Ventosa A., Christensen H., Arahal D.R., da Costa M.S., et al., Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 2018; 68(1): 461-466. DOI 10.1099/ijsem.0.002516.
[10] Quadri S.R., Sathish M., Quach N.T., Li W.J. and Narsing Rao M.P., Reclassification of Salinisphaera halophila Zhang et al. 2012 as a later heterotypic synonym of Salinisphaera orenii Park et al. 2012. Current Microbiology, 2025; 82(3): 100. DOI 10.1007/s00284-024-04059-z.
[11] Quadri S.R. and Narsing Rao M.P., Reclassification of Gulbenkiania indica Jyoti et al. 2010 as a later heterotypic synonym of Gulbenkiania mobilis Vaz-Moreira et al. 2007. Chiang Mai Journal of Science, 2025; 52(6): e2025083. DOI 10.12982/CMJS.2025.083.
[12] Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., et al., Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic Bacteriology, 1987; 37(4): 463-464. DOI 10.1099/00207713-37-4-463.
[13] Parks D.H., Imelfort M., Skennerton C.T., Hugenholtz P. and Tyson G.W., CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 2015; 25(7): 1043-1055. DOI 10.1101/gr.186072.114.
[14] Seemann T., barrnap 0.9: Rapid ribosomal RNA prediction; Available at: https://github.com/tseemann/barrnap. (Accessed on 14/03/2026).
[15] Felsenstein J., Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 1981; 17(6): 368-376. DOI 10.1007/bf01734359.
[16] Kumar S., Stecher G., Suleski M., Sanderford M., Sharma S. and Tamura K., MEGA12: Molecular evolutionary genetic analysis version 12 for adaptive and green computing. Molecular Biology and Evolution, 2024; 41(12): msae263. DOI 10.1093/molbev/msae263.
[17] Thompson J.D., Higgins D.G. and Gibson T.J., CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 1994; 22(22): 4673-4680. DOI 10.1093/nar/22.22.4673.
[18] Kimura M., A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 1980; 16(2): 111-120. DOI 10.1007/BF01731581.
[19] Felsenstein J., Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 1985; 39(4): 783-791. DOI 10.1111/j.1558-5646.1985.tb00420.x
[20] Meier-Kolthoff J.P., Auch A.F., Klenk H.P. and Göker M., Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics, 2013; 14: 60. DOI 10.1186/1471-2105-14-60.
[21] Meier-Kolthoff J.P., Carbasse J.S., Peinado-Olarte R.L. and Göker M., TYGS and LPSN: A database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Research, 2022; 50(D1): D801-D807. DOI 10.1093/nar/gkab902.
[22] Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., et al., BLAST+: Architecture and applications. BMC Bioinformatics, 2009; 10: 421. DOI 10.1186/1471-2105-10-421.
[23] Richter M., Rosselló-Móra R., Oliver Glöckner F. and Peplies J., JSpeciesWS: A web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics, 2015; 32(6): 929-931. DOI 10.1093/bioinformatics/btv681.
[24] Eren A.M., Esen Ö.C., Quince C., Vineis J.H., Morrison H.G., Sogin M.L., et al., Anvi'o: An advanced analysis and visualization platform for 'omics data. PeerJ, 2015; 3: e1319. DOI 10.7717/peerj.1319.
[25] Eren A.M., Kiefl E., Shaiber A., Veseli I., Miller S.E., Schechter M.S., et al., Community-led, integrated, reproducible multi-omics with anvi'o. Nature Microbiology, 2021; 6(1): 3-6. DOI 10.1038/s41564-020-00834-3.
[26] Hyatt D., Chen G.L., Locascio P.F., Land M.L., Larimer F.W. and Hauser L.J., Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 2010; 11: 119. DOI 10.1186/1471-2105-11-119.
[27] Eddy S.R., Accelerated profile HMM searches. PLoS Computational Biology, 2011; 7(10): e1002195. DOI 10.1371/journal.pcbi.1002195.
[28] Lee M.D., GToTree: A user-friendly workflow for phylogenomics. Bioinformatics, 2019; 35(20): 4162-4164. DOI 10.1093/bioinformatics/btz188.
[29] Edgar R.C., MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 2004; 32(5): 1792-1797. DOI 10.1093/nar/gkh340.
[30] Kim M., Oh H.S., Park S.C. and Chun J., Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 2014; 64(2): 346-351. DOI 10.1099/ijs.0.059774-0.
[31] Auch A.F., von Jan M., Klenk H.P. and Göker M., Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Standards in Genomic Sciences, 2010; 2(1): 117-134. DOI 10.4056/sigs.531120.
[32] Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P. and Tiedje J.M., DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. International Journal of Systematic and Evolutionary Microbiology, 2007; 57(1): 81-91. DOI 10.1099/ijs.0.64483-0.
[33] Richter M., and Rosselló-Móra R., Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences of the United States of America, 2009; 106(45): 19126-19131. DOI 10.1073/pnas.0906412106.