Four Gram-stain-negative, catalase-positive, rod-shaped and motile strains (FT55WT, FT93WT, CY13WT and DS3T) were isolated from subtropical streams in China. Comparisons based on 16S rRNA gene sequences indicated that strains FT55WT, FT93WT and CY13WT take strain Pseudoduganella danionis E3/2T, and strain DS3T takes strain Pseudoduganella eburnea 10R5-21T as their closest neighbour, respectively. The genome sizes of strains FT55WT, FT93WT, CY13WT and DS3T were 6.15, 5.10, 5.31 and 5.72 Mbp with G+C contents of 61.7, 60.9, 60.6 and 64.0%, respectively. The reconstructed phylogenomic tree based on concatenated 92 core genes showed that strain FT55WT clusters closely with Duganella radicis KCTC 22382T and Duganella sacchari Sac-22T, strains FT93WT and CY13WT form a distinct clade with P. danionis DSM 103461T and this clade clusters with the clades of genus Duganella together, and strain DS3T forms a distinct clade with P. eburnea JCM 31587T and Pseudoduganella violaceinigra DSM 15887T and this clade clusters closely with the clades of genus Massilia, respectively. The calculated pairwise OrthoANIu values and digital DNA–DNA hybridization (DDH) values among strains FT55WT, FT93WT, CY13WT, DS3T and related strains were in the ranges of 75.6–94.2% and 20.6–56.2%, respectively. Q-8 was the sole respiratory quinone of these four strains. The major fatty acids were C16:1 ω7c, C16:0 and C12:0. The polar lipids included phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid. Considering the similar fatty acids and polar lipids profiles of species within genus Pseudoduganella, Massilia and Duganella, there is currently no justification for assigning the species of genus Pseudoduganella into the Massilia and Duganella clades in the phylogenomic tree. It is reasonable to transfer P. violaceinigra and P. eburnea to the genus Massilia as Massilia violaceinigrum comb. nov. and Massilia eburnea comb. nov., and transfer P. danionis to the genus Duganella as Duganella danionis comb. nov. Considering phylogenomic analysis, OrthoANIu data, digital DDH data and a range of physiological and biochemical characteristics, strains FT55WT, FT93WT and CY13WT should be assigned to genus Duganella, and strain DS3T should be classified as a novel species within genus Massilia, for which the names Duganella rivus sp. nov. (type strain FT55WT = GDMCC 1.1675T = KACC 21467T), Duganella fentianensis sp. nov. (type strain FT93WT = GDMCC 1.1683T = KACC 21475T), Duganella qianjiadongensis sp. nov. (type strain CY13WT = GDMCC 1.1669T = KACC 21461T) and Massilia guangdongensis sp. nov. (type strain DS3T = GDMCC 1.1636T = KACC 21312T) are proposed.
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Tax calculation will be finalised during checkout.
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
Tax calculation will be finalised during checkout.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Baldani JI, Rouws L, Cruz LM, Olivares FL, Schmid M, Hartmann A (2014) The Family Oxalobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes: Alphaproteobacteria and Betaproteobacteria. Springer, Berlin Heidelberg, pp 919–974
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD et al (2012) SPAdes: a new genome assembly algorithm and its applications to single cell sequencing. J Comput Biol 19:455–477
Dong XZ, Cai MY (2001) Determinative manual for routine bacteriology. Beijing Scientific Press, Beijing
Durán N, Justo GZ, Ferreira CV, Melo PS, Cordi L, Martins D (2007) Violacein: properties and biological activities. Biotechnol Appl Biochem 48:127–133
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
Hiraishi A, Shin YK, Sugiyama J (1997) Proposal to reclassify Zoogloea ramigera IAM 12670 (P. R. Dugan 115) as Duganella zoogloeoides gen. nov., sp. nov. Int J Syst Bacteriol 47:1249–1252
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P (2017) Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol 34:2115–2122
Jin DH, Subhash Y, Lee SS (2017) Pseudoduganella eburnea sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 67:5268–5272
Kämpfer P, Lodders N, Martin K, Falsen E (2011) Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov. Int J Syst Evol Microbiol 61:1528–1533
Kämpfer P, Wellner S, Lohse K, Martin K, Lodders N (2012) Duganella phyllosphaerae sp. nov., isolated from the leaf surface of Trifolium repens and proposal to reclassify Duganella violaceinigra into a novel genus as Pseudoduganella violceinigra gen. nov., comb. nov. Syst Appl Microbiol 35:19–23
Kämpfer P, Irgang R, Busse HJ, Mathías PM, Kleinhagauer T, Glaeser SP, Ruben AH (2016) Pseudoduganella danionis sp. nov., isolated from zebrafish (Danio rerio). Int J Syst Evol Microbiol 66:4671–4675
Kanehisa M, Sato Y, Morishima K (2015) BlastKOALA and GhostKOALA: KEGG tools for functional characterisation of genome and metagenome sequences. J Mol Biol 428:726–731
Kimura M (1979) The neutral theory of molecular evolution. Sci Am 241:98–100, 102, 108
Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of Anurans. Syst Zool 18:1–32
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870
Kuykendall LD, Roy MA, O’Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 38:358–361
La Scola B, Birtles RJ, Mallet MN, Raoult D (1998) Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions. J Clin Microbiol 36:2847–2852
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid sequencing techniques in bacterial systematics. Wiley, New York, pp 115–175
Li WJ, Zhang YQ, Park DJ, Li CT, Xu LH, Kim CJ, Jiang CL (2004) Duganella violaceinigra sp. nov., a novel mesophilic bacterium isolated from forest soil. Int J Syst Evol Microbiol 54:1811–1814
Lu HB, Xue XF, Phurbu D, Xing P, Wu QL (2018) Roseovarius tibetensis sp. nov., a halophilic bacterium isolated from Lake LongmuCo on Tibetan Plateau. J Microbiol 56:783–789
Madhaiyan M, Poonguzhali S, Saravanan VS, Hari K, Lee KC, Lee JS (2013) Duganella sacchari sp. nov. and Duganella radicis sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane. Int J Syst Evol Microbiol 63:1126–1131
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60
Michael R, Ramon RM (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J (2018) UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285
Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sasser M (1990) Identification of bacteria through fatty acid analysis. In: Klement Z, Rudolph K, Sands DC (eds) Methods in phytobacteriology. Akademiai Kaido, Budapest, pp 199–204
Singh H, Du J, Won K, Yang JE, Yin C, Kook M, Yi TH (2015) Massilia arvi sp. nov., isolated from fallow-land soil previously cultivated with Brassica oleracea, and emended description of the genus Massilia. Int J Syst Evol Microbiol 65:3690–3696
Tatiana T, Michael D, Azat B, Vyacheslav C, Eric PN, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882
Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202
Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A (1982) Numerical taxonomy of moderately halophilic Gram-negative rods. J Gen Microbiol 128:1959–1968
Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E et al (1987) Report of the Ad Hoc Committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2016) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617
Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1–6
Zhang JL, Kim YJ, Hoang VA, Nguyen NL, Wang C, Kang JP, Wang DD, Yang DC (2016) Duganella ginsengisoli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 66:56–61
Zhong ZP, Liu Y, Wang F, Zhou YG, Liu HC, Liu ZP (2016) Lacimicrobium alkaliphilum gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from a salt lake. Int J Syst Evol Microbiol 66:422–429
This work was funded by Key-Area Research and Development Program of Guangdong Province, China (No. 2018B020205003), National Natural Science Foundation of China (91851202, 51678163), Guangdong Provincial Programs for Science and Technology Development (2019B110205004; 2018B030324002), GDAS’ Special Project of Science and Technology Development (2018GDASCX-0916; 2019GDASYL-0301002) and Guangdong MEPP Fund (NO. GDOE(2019)A34).
Conflict of interest
The authors declare that they have no direct or indirect conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
About this article
Cite this article
Lu, HB., Cai, ZP., Yang, YG. et al. Duganella rivus sp. nov., Duganella fentianensis sp. nov., Duganella qianjiadongensis sp. nov. and Massilia guangdongensis sp. nov., isolated from subtropical streams in China and reclassification of all species within genus Pseudoduganella. Antonie van Leeuwenhoek 113, 1155–1165 (2020). https://doi.org/10.1007/s10482-020-01422-5
- Digital DDH