Bioplastic (poly-3-hydroxybutyrate)-producing Massilia endophytica sp. nov., isolated from Cannabis sativa L. 'Cheungsam'

A rod-shaped, motile, Gram-negative bacterial strain named DM-R-R2A-13T was isolated from the plant Cannabis sativa L. 'Cheungsam'. The phylogenetic analysis of the 16S rRNA gene sequence revealed that strain DM-R-R2A-13T belongs to the family Oxalobacteraceae and is closely related to members of the genus Massilia, with Massilia flava (97.58% sequence similarity) and Massilia armeniaca (97.37% sequence similarity) being the closest members. The digital DNA-DNA hybridization (dDDH) values between strain DM-R-R2A-13T and Massilia flava CGMCC 1.10685T and Massilia armeniaca ZMN-3Twere 22.2% and 23.3%, while the average nucleotide identity (ANI) values were 78.85% and 79.63%, respectively. The DNA G+C content was measured to be 64.6 mol%. Moreover, the bacterium was found to contain polyhydroxyalkanoate (PHA) granules based on transmission electron microscopy, indicating its potential to produce bioplastic. Genome annotation revealed the presence of PHA synthase genes (phaC, phaR, phaP, and phaZ), and the biopolymer was identified as poly-3-hydroxybutyrate (PHB) based on nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR) analyses. Using maltose as a carbon source, the strain produced PHB of up to 58.06% of its dry cell weight. Based on the phenotypic, chemotaxonomic, and phylogenetic characteristics, it has been determined that DM-R-R2A-13T represents a novel species belonging to the genus Massilia. As such, the name Massilia endophytica sp. nov. is proposed for this newly identified species. The type strain is DM-R-R2A-13T (= KCTC 92072T = GDMCC 1.2920T).

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

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.

Massilia puerhi sp. nov., isolated from soil of Pu-erh tea cellar

A Gram-reaction-negative, yellow-pigmented, non-spore-forming rod, aerobic, motile bacterium, designated SJY3^T, was isolated from soil samples collected from a Pu-erh tea cellar in Bolian Pu-erh tea estate Co. Ltd. in Pu'er city, Yunnan, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Massilia. The closest phylogenetic relative was Massilia arenae CICC 24458^T (99.5 %), followed by M. timonae CCUG45783^T (97.9 %), M. oculi CCUG43427A^T (97.8 %), and M. aurea DSM 18055^T (97.8 %). The major fatty acids were C_16 : 0 and C_16 : 1  ω7c and/or C_16 : 1  ω6c. The major respiratory quinone was ubiquinone Q-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Genome sequencing revealed a genome size of 5.97 M bp and a G+C content of 65.4 mol%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA-DNA hybridization (dDDH) values were all below the threshold. Although the 16S rRNA gene similarity of stain SJY3^T and Massilia arenae CICC 24458^T was more than 99 %, the gANI, dDDH values and genomic tree clearly indicated that they were not of the same species. In summary, strain SJY3^T represents a new species, for which we propose the name Massilia puerhi sp. nov. with the type strain SJY3^T (=CGMCC 1.17158^T=KCTC 82193^T).

Massilia atriviolacea sp. nov., a dark purple-pigmented bacterium isolated from soil

A bacterial strain, designated SOD^T, with Gram-stain-negative and motile rod-shaped cells, was isolated from soil in Hefei, PR China, and was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SOD^T belonged to the genus Massilia and showed the highest similarities to Massilia violaceinigra B2^T (99.3 %), followed by Massilia glaciei B448-2^T (98.7 %), Massilia eurypsychrophila CGMCC 1.12828^T (98.6 %) and Rugamonas rubra CCM3730^T (97.8 %). Average nucleotide identity and digital DNA-DNA hybridization values between genome sequences of strain SOD^T and the closely related species ranged from 77.1 to 89.3% and from 22.2 to 34.7 %. The DNA G+C content of strain SOD^T was 65.4 mol%. Strain SOD^T contained Q-8 as the major ubiquinone and the dominant fatty acids were summed feature 3 (C16 : 1ω7c and/or C15 : 0iso 2-OH; 58.5 %), C16 : 0 (26.8 %) and C18 : 1ω7c (5.0 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. On the basis of the evidence presented in this study, strain SOD^T represents a novel species of the genus Massilia, for which the name Massiliaatriviolacea sp. nov. is proposed. The type strain is SOD^T (=KCTC 62720^T=LMG 30840^T).

Massilia buxea sp. nov., isolated from a rock surface

A Gram-stain-negative, rod-shaped and motile bacterial strain, designated A9^T, was isolated from the surface of rock collected from the shore of Nvshan lake in Mingguang, Anhui province, China. Phylogenetic analysis based on 16S rDNA sequence data showed that strain A9^T was affiliated with the genus Massilia and showed the highest sequence similarities to Massilia plicata KCTC 12344^T (98.8 %) and Massilia lurida CGMCC 1.10822^T (97.9 %). The major fatty acids (>5 %) were summed feature 3 (C16 : 1ω7c and/or C15 : 0 iso 2-OH), C16 : 0 and C18 : 1ω7c. Strain A9^T contained Q-8 as the predominant ubiquinone and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid as the predominant polar lipids. The DNA G+C content was 69.9 mol%. Mean DNA-DNA relatedness values between strain A9^T and its closest phylogenetic relatives, M. plicata KCTC 12344^T and M. lurida CGMCC 1.10822^T, were 38.8 % and 23.23 %, respectively. On the basis of the results obtained in this study, strain A9^T is considered to represent a novel species of the genus Massilia, for which the name Massilia buxea sp. nov. is proposed. The type strain is A9^T (=DSM 103547^T=CGMCC 1.15931^T=KCTC 52429^T).

Massilia phosphatilytica sp. nov., a phosphate solubilizing bacteria isolated from a long-term fertilized soil

A Gram-stain-negative and rod-shaped bacterial strain, 12-OD1T, with rock phosphate solubilizing ability was isolated from agricultural soil in Hailun, Heilongjiang, PR China. The isolate was affiliated to the genus Massilia, based on 16S rRNA gene sequence alignments, having the highest similarities with Massilia putida6 NM-7T (98.67 %), Massilia kyonggiensis TSA1T (98.28 %), and Massilia norwichensis NS9T (98.07 %), respectively. The DNA G+C content was 67.72 mol% and DNA-DNA hybridization showed low relatedness values (less than 47 %) between strain 12-OD1T and other phylogenetically related species of the genus Massilia. The predominant isoprenoid quinone was Q-8 and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C17 : 0 cyclo (25.4 %), C16 : 0 (23.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1 ω6c) (22.5 %), which differentiates it from close relatives within the genus Massilia. Combined genetic, physiological and biochemical properties indicate that strain 12-OD1T is a novel species of the genus Massilia, for which the name Massilia phosphatilytica sp. nov., is proposed, with the type strain 12-OD1T (=CCTCC AB 2016251T=LMG 29956T=KCTC 52513T).

Massilia varians Isolated from a Clinical Specimen

We report a case of Massilia varians isolated from a deep finger wound following orthopedic surgery on an immunocompetent patient. The bacterium was identified by 16S rDNA sequence analysis. This is the first case of M. varians isolated from a clinical specimen since the first report in 2008.

Massilia psychrophila sp. nov., isolated from an ice core

A Gram-stain-negative, aerobic, rod-shaped, motile bacterium, strain B1555-1T, was isolated from an ice core drilled from Ulugh Muztagh Glacier, China. The optimum growth temperature of strain B1555-1T was 15 °C and optimum pH was 7. The major fatty acids of strain B1555-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The predominant respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain B1555-1T was 66.0 mol%. In 16S rRNA gene sequence comparisons, strain B1555-1T was affiliated to the genus Massilia and shared 98.30 and 97.13 % similarity with Massilia eurypsychrophila B528-3T and Massilia niabensis 5420S-26T, respectively. The results of DNA-DNA hybridization revealed that strain B1555-1T showed 49.8 % relatedness with M. eurypsychrophila B528-3T and 38.5 % with M. niabensis 5420S-26T. Based on the genotypic and phenotypic evidence presented in this study, strain B1555-1T represents a novel species of the genus Massilia, for which the name Massilia psychrophila sp. nov. is proposed. The type strain is B1555-1T (=CGMCC 1.15196T=JCM 30813T).

Massilia eurypsychrophila sp. nov. a facultatively psychrophilic bacteria isolated from ice core

Strain B528-3T, a Gram-stain-negative, rod-shaped, aerobic, facultatively psychrophilic bacterium with polar flagella, was isolated from an ice core drilled from Muztagh Glacier, Xinjiang, China. The novel isolate was classified into the genus Massilia. The 16S rRNA gene sequence of the novel isolate shares a pairwise similarity of less than 97 % with those of all the type strains of the genus Massilia. The major fatty acids of strain B528-3T were summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) (57.31 %), C16:0 (11.46 %) and C18:1ω7c (14.72 %). The predominant isoprenoid quinone was Q-8. The DNA G+C content was 62.2 mol% (T m). The major polar lipids of this bacterium were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. From the genotypic and phenotypic data, it is evident that strain B528-3T represents a novel species of the genus Massilia, for which the name Massilia eurypsychrophila sp. nov. is proposed. The type strain is B528-3T ( = JCM 30074T = CGMCC 1.12828T).

Massilia norwichensis sp. nov., isolated from an air sample

A Gram-negative, rod-shaped and motile bacterial isolate, designated strain NS9(T), isolated from air of the Sainsbury Centre for Visual Arts in Norwich, UK, was subjected to a polyphasic taxonomic study including phylogenetic analyses based on partial 16S rRNA, gyrB and lepA gene sequences and phenotypic characterization. The 16S rRNA gene sequence of NS9(T) identified Massilia haematophila CCUG 38318(T), M. niastensis 5516S-1(T) (both 97.7% similarity), M. aerilata 5516S-11(T) (97.4%) and M. tieshanensis TS3(T) (97.4%) as the next closest relatives. In partial gyrB and lepA sequences, NS9(T) shared the highest similarities with M. haematophila CCUG 38318(T) (94.5%) and M. aerilata 5516-11(T) (94.3%), respectively. These sequence data demonstrate the affiliation of NS9(T) to the genus Massilia. The detection of the predominant ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a polyamine pattern containing 2-hydroxyputrescine and putrescine were in agreement with the assignment of strain NS9(T) to the genus Massilia. Major fatty acids were summed feature 3 (C16:1ω7c and/or iso-C15 : 0 2-OH), C16:0, C18: 1ω7c and C10:0 3-OH. Dissimilarities in partial lepA and gyrB gene sequences as well as results from DNA-DNA hybridizations demonstrate that strain NS9(T) is a representative of an as-yet undescribed species of the genus Massilia that is also distinguished from its close relatives based on physiological and biochemical traits. Hence, we describe a novel species, for which we propose the name Massilia norwichensis sp. nov., with the type strain NS9(T) ( = CCUG 65457(T) =LMG 28164(T)).

Massilia umbonata sp. nov., able to accumulate poly-β-hydroxybutyrate, isolated from a sewage sludge compost-soil microcosm

A bacterial strain, designated strain LP01(T), was isolated from a laboratory-scale microcosm packed with a mixture of soil and sewage sludge compost designed to study the evolution of microbial biodiversity over time. The bacterial strain was selected for its potential ability to store polyhydroxyalkanoates (PHAs) as intracellular granules. The cells were aerobic, Gram-stain-negative, non-endospore-forming motile rods. Phylogenetically, the strain was classified within the genus Massilia, as its 16S rRNA gene sequence had similarity of 99.2 % with respect to those of Massilia albidiflava DSM 17472(T) and M. lutea DSM 17473(T). DNA-DNA hybridization showed low relatedness of strain LP01(T) to the type strains of other, phylogenetically related species of the genus Massilia. It contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acid(s). It was found to contain small amounts of the fatty acids C18 : 0 and C14 : 0 2-OH, a feature that served to distinguish it from its closest phylogenetic relatives within the genus Massilia. The DNA G+C content was 66.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data obtained in this study suggest that strain LP01(T) represents a novel species of the genus Massilia, for which the name Massilia umbonata sp. nov. is proposed. The type strain is LP01(T) ( = CECT 7753(T) = DSM 26121(T)).