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Lu H, Song D, Deng T, Mei C, Xu M. Duganella vulcania sp. nov., Rugamonas fusca sp. nov., Rugamonas brunnea sp. nov. and Rugamonas apoptosis sp. nov., isolated from subtropical streams, and phylogenomic analyses of the genera Janthinobacterium, Duganella, Rugamonas, Pseudoduganella and Massilia. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT81WT, FT82W, FT107W, FT3ST, LX20WT and LX47WT) sharing high 16S rRNA gene sequence similarities with species of the genera
Janthinobacterium
(97.0–98.3 %),
Duganella
(96.3–98.8 %),
Rugamonas
(97.8–98.6 %),
Pseudoduganella
(96.8–97.5 %) and
Massilia
(94.5–98.6 %) were isolated from subtropical streams in PR China. The phylogenetic trees reconstructed using the 16S rRNA gene sequences indicated that the species of above five genera often mix together, indicating that the taxonomic statuses of some species were questionable. Phylogenomic reconstruction based on 369 single-copy orthologous clusters indicated that the species of the genus
Janthinobacterium
form a distinct cluster, strains FT81WT, FT82W and FT107W form a tight cluster with the species of the genus
Duganella
, and strains FT3ST, LX20WT and LX47WT form a tight cluster with the species of genus
Rugamonas
, and the species of genus
Pseudoduganella
form a tight cluster with
Massilia guangdongensis
,
Massilia ginsengisoli
,
Massilia rivuli
,
Massilia namucuonensis
,
Massilia aquatica
sensu Lu et al.,
Massilia buxea
,
Massilia armeniaca
,
Massilia plicata
,
Massilia flava
,
Massilia lurida
,
Massilia dura
,
Massilia lutea
,
Massilia umbonata
,
Massilia albidiflava
and
Massilia violacea
. It should be noted that
Massilia aquatica
Lu et al. 2020 non
Massilia aquatica
Holochová et al. 2020 is a later homonym and an illegitimate name. The GTDB Release 202 also supported the proposal that
M. guangdongensis
,
M. ginsengisoli
,
M. rivuli
,
M. namucuonensis
,
M. aquatica
sensu Lu et al.,
M. buxea
,
M. armeniaca
,
M. plicata
,
M. flava
,
M. lurida
,
M. dura
,
M. lutea
,
M. umbonata
,
M. albidiflava
and
M. violacea
should be transferred into the genus
Pseudoduganella
. The calculated pairwise orthologous average nucleotide identity by usearch (OrthoANIu) values were between 95.0 % and 95.6 % among strains FT81WT, FT82W and FT107W, but were less than 91.5 % among strains FT3ST, LX20WT, LX47WT and other related strains. Combining the results of phylogenomic analyses, phenotypic, biochemical and genotypic characteristics, strains FT81WT, FT82W and FT107W should represent a novel species of the genus
Duganella
, and strains FT3ST, LX20WT and LX47WT should represent three novel species of the genus
Rugamonas
, for which the names Duganella vulcania sp. nov. (type strain FT81WT=GDMCC 1.1679T =KACC 21471T), Rugamonas fusca sp. nov. (type strain FT3ST=GDMCC 1.1907T =KACC 21952T), Rugamonas brunnea sp. nov. (type strain LX20WT=GDMCC 1.1911T =KACC 21956T) and Rugamonas apoptosis sp. nov. (type strain LX47WT=GDMCC 1.1914T =KACC 21959T) are proposed.
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Affiliation(s)
- Huibin Lu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, PR China
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, School of Tourism and Geography, Yunnan Normal University, Kunming, PR China
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
| | - Da Song
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, PR China
| | - Tongchu Deng
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, PR China
| | - Chengfang Mei
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, PR China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, PR China
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Duganella aceris sp. nov., isolated from tree sap and proposal to transfer of Rugamonas aquatica and Rugamonas rivuli to the genus Duganella as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas. Arch Microbiol 2021; 203:2843-2852. [PMID: 33748874 DOI: 10.1007/s00203-021-02191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 12/12/2020] [Accepted: 02/04/2021] [Indexed: 10/21/2022]
Abstract
A Gram-reaction-negative, strictly aerobic, betaproteobacterial strain, designated SAP-35T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea, and its taxonomic status was examined by a polyphasic approach. Cells of the organism were non-sporulating, motile rods and grew at 4-30 °C, pH 6-7 and in the absence of NaCl. 16S rRNA gene- and whole genome-based phylogenetic analyses showed that strain SAP-35T belonged to the family Oxalobacteraceae and was closely related to Rugamonas rivuli (98.9% 16S rRNA gene sequence similarity) and Rugamonas aquatica (98.4%). The phylogenomic clustering and average amino acid identity values supported that strain SAP-35T belonged to the genus Duganella and two Rugamonas species should be transferred to the genus Duganella. The major isoprenoid quinone of the isolate was Q-8. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The predominant fatty acids were summed feature 3, C16:0 and C17:0 cyclo. The G + C content of genome was 64.9%. The average nucleotide identity and dDDH values between strain SAP-35T and the members of the genera Rugamonas and Duganella were < 85.1% and < 49%, respectively. Based on the combined data presented here, strain SAP-35T (= KCTC 72227T = NBRC 113903T) represents a novel species of the genus Duganella, for which the name Duganella aceris sp. nov. is proposed. Also, Rugamonas aquatica Lu et al. (Int J Syst Evol Microbiol 70: 3328-3334, 2020) and Rugamonas aquatica Lu et al. 2020 are reclassified as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas.
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