Novel exported fusion enzymes with chorismate mutase and cyclohexadienyl dehydratase activity: Shikimate pathway enzymes teamed up in no man's land

Chorismate mutase (CM) and cyclohexadienyl dehydratase (CDT) catalyze two subsequent reactions in the intracellular biosynthesis of l-phenylalanine (Phe). Here, we report the discovery of novel and extremely rare bifunctional fusion enzymes, consisting of fused CM and CDT domains, which are exported from the cytoplasm. Such enzymes were found in only nine bacterial species belonging to non-pathogenic γ- or β-Proteobacteria. In γ-proteobacterial fusion enzymes, the CM domain is N-terminal to the CDT domain, whereas the order is inverted in β-Proteobacteria. The CM domains share 15% to 20% sequence identity with the AroQγ class CM holotype of Mycobacterium tuberculosis (∗MtCM), and the CDT domains 40% to 60% identity with the exported monofunctional enzyme of Pseudomonas aeruginosa (PheC). In vitro kinetics revealed a Km <7 μM, much lower than for ∗MtCM, whereas kinetic parameters are similar for CDT domains and PheC. There is no feedback inhibition of CM or CDT by the pathway's end product Phe, and no catalytic benefit of the domain fusion compared with engineered single-domain constructs. The fusion enzymes of Aequoribacter fuscus, Janthinobacterium sp. HH01, and Duganella sacchari were crystallized and their structures refined to 1.6, 1.7, and 2.4 Å resolution, respectively. Neither the crystal structures nor the size-exclusion chromatography show evidence for substrate channeling or higher oligomeric structure that could account for the cooperation of CM and CDT active sites. The genetic neighborhood with genes encoding transporter and substrate binding proteins suggests that these exported bifunctional fusion enzymes may participate in signaling systems rather than in the biosynthesis of Phe.

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.

Duganella dendranthematis sp. nov. and Massilia forsythiae sp. nov., isolated from flowers

Two aerobic, Gram-stain-negative, motile, mesophilic, rod-shaped and catalase-positive bacterial strains designated AF9R3T and GN2-R2T were isolated from flowers collected in the Republic of Korea. Strain AF9R3T grew at 4–33 °C, pH 4.0–9.0 and with 0–1 % NaCl (w/v), and strain GN2-R2T grew at 10–33 °C, pH 4.0–9.0 and with 0–1 % NaCl (w/v). Phylogenetic analysis on the basis of 16S rRNA gene sequences indicated that strains AF9R3T and GN2-R2T belonged to the genera Duganella and Massilia , respectively, showing high sequence similarity to Duganella levis CY42WT (99.4 %) and Massilia putida 6 NM-7T (98.0 %), respectively. Both strains contained summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and C16 : 0 as the major fatty acids, and ubiquinone Q-8 as the predominant quinone. Strain AF9R3T had diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and strain GN2-R2T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Orthologous average nucleotide identity and digital DNA–DNA hybridization values of strain AF9R3T to its closest relative D. levis CY42WT were 92.6 and 56.5 %, and those of strain GN2-R2T to its closest relative M. putida 6 NM-7T were 81.4 and 24.8 %. Based on genotypic and phenotypic data, strains AF9R3T and GN2-R2T are considered to represent novel species of the genus Duganella and Massilia , respectively, for which the names Duganella dendranthematis sp. nov. (type strain AF9R3T=KACC 21258T=NBRC 114510T) and Massilia forsythiae sp. nov. (type strain GN2-R2T=KACC 21261T=NBRC 114511T) have been proposed.

Effect of the Manufacturing Process on the Microbiota, Organoleptic Properties and Volatilome of Three Salmon-Based Products

Lightly preserved seafood products, such as cold-smoked fish and fish gravlax, are traditionally consumed in Europe and are of considerable economic importance. This work aimed to compare three products that were obtained from the same batch of fish: cold-smoked salmon (CSS) stored under vacuum packaging (VP) or a modified atmosphere packaging (MAP) and VP salmon dill gravlax (SG). Classical microbiological analyses and 16S rRNA metabarcoding, biochemical analyses (trimethylamine, total volatile basic nitrogen (TVBN), biogenic amines, pH, volatile organic compounds (VOCs)) and sensory analyses (quantitative descriptive analysis) were performed on each product throughout their storage at a chilled temperature. The three products shared the same initial microbiota, which were mainly dominated by Photobacterium, Lactococcus and Lactobacillus genera. On day 28, the VP CSS ecosystem was mainly composed of Photobacterium and, to a lesser extent, Lactococcus and Lactobacillus genera, while Lactobacillus was dominant in the MAP CSS. The diversity was higher in the SG, which was mainly dominated by Enterobacteriaceae, Photobacterium, Lactobacillus and Lactococcus. Although the sensory spoilage was generally weak, gravlax was the most perishable product (slight increase in amine and acidic off-odors and flavors, fatty appearance, slight discoloration and drop in firmness), followed by the VP CSS, while the MAP CSS did not spoil. Spoilage was associated with an increase in the TVBN, biogenic amines and spoilage associated VOCs, such as decanal, nonanal, hexadecanal, benzaldehyde, benzeneacetaldehyde, ethanol, 3-methyl-1-butanol, 2,3-butanediol, 1-octen-3-ol, 2-butanone and 1-octen-3-one. This study showed that the processing and packaging conditions both had an effect on the microbial composition and the quality of the final product.

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

A Gram-reaction-negative, strictly aerobic, betaproteobacterial strain, designated SAP-35^T, 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-35^T 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-35^T 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, C_16:0 and C_17:0 cyclo. The G + C content of genome was 64.9%. The average nucleotide identity and dDDH values between strain SAP-35^T and the members of the genera Rugamonas and Duganella were < 85.1% and < 49%, respectively. Based on the combined data presented here, strain SAP-35^T (= KCTC 72227^T = NBRC 113903^T) 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.

Duganella callida sp. nov., a novel addition to the Duganella genus, isolated from the soil of a cultivated maize field

A Gram-negative, rod-shaped bacterium, strain Duganella callida DN04^T, was isolated from the soil of a maize field in North Carolina, USA. Based on the 16S rRNA gene sequence, the most similar Duganella species are D. sacchari Sac-22^T, D. ginsengisoli DCY83^T, and D. radicis Sac-41^T with a 97.8, 97.6, or 96.9 % sequence similarity, respectively. We compared the biochemical phenotype of DN04^T to D. sacchari Sac-22^T and D. zoogloeoides 115^T and other reference strains from different genera within the Oxalobacteraceae and while the biochemical profile of DN04^T is most similar to D. sacchari Sac-22^T and other Duganella and Massilia strains, there are also distinct differences. DN04^T can for example utilize turanose, N-acetyl-d-glucosamine, inosine, and l-pyroglutamic acid. The four fatty acids found in the highest percentages were C_15 : 0 iso (24.6 %), C_15 : 1 isoG (19.4 %), C_17 : 0 iso3-OH (16.8 %), and summed feature 3 (C_16:1 ⍵7c and/or C_16:1 ⍵6c) (12.5 %). We also applied whole genome sequencing to determine if DN04^T is a novel species. The most similar AAI (average amino acid identity) score was 70.8 % (Massilia plicata NZ CP038026^T), and the most similar ANI (average nucleotide identity) score was 84.8 % (D. radicis KCTC 22382^T), which indicates that DN04^T is a novel species. The genome-to-genome-distance calculation (GGDC) revealed a DDH of 28.3 % to D. radicis KCTC 22382^T, which is much lower than the new species threshold. Based on the morphological, phenotypic, and genomic differences, we propose Duganella callida sp. nov. as a novel species within the Duganella genus (type strain DN04^T=NRRL B-65552^T=LMG 31736^T).

Duganella lactea sp. nov., Duganella guangzhouensis sp. nov., Duganella flavida sp. nov. and Massilia rivuli sp. nov., isolated from a subtropical stream in PR China and proposal to reclassify Duganella ginsengisoli as Massilia ginsengisoli comb. nov

Five Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT50W^T, FT80W^T, FT92W^T, FT94W and FT135W^T) were isolated from a subtropical stream in PR China. Comparisons based on 16S rRNA gene sequences showed that strains FT50W^T, FT94W and FT135W^T take strain Duganella sacchari Sac-22^T, and strains FT80W^T and FT92W^T take strain Duganella ginsengisoli DCY83^T as their closest neighbour in the phylogenetic trees, respectively. The G+C contents of strains FT50W^T, FT80W^T, FT92W^T, FT94W and FT135W^T were 63.3, 62.4, 62.8, 63.8 and 60.8 %, respectively. The reconstructed phylogenomic tree based on concatenated 92 core genes showed that strains FT50W^T, FT80W^T, FT94W and FT135W^T clustered together with species of the genus Duganella, but strains FT92W^T and D. ginsengisoli KCTC 42409^T were located in the clades of the genus Massilia. The calculated pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among strains FT50W^T, FT80W^T, FT92W^T, FT94W, FT135W^T and related strains were in the ranges of 75.6-87.8% and 20.3-33.8% except that the values between strains FT50W^T and FT94W were 98.7 and 89.2%, respectively. The respiratory quinone of these five strains was Q-8. The major fatty acids were C_16 : 1  ω7c, C_16 : 0, C_18 : 1  ω7c and C_12 : 0. The polar lipids included phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. Considering the distinct phylogenetic relationships of D. ginsengisoli with species of the genus Massilia in the phylogenomic tree, it was reasonable to transfer D. ginsengisoli to the genus Massilia as Massilia ginsengisoli comb. nov. Combining the results of phylogenomic analysis, ANI and dDDH data, and a range of physiological and biochemical characteristics together, strains FT50W^T and FT94W should belong to the same species and be assigned to genus Duganella with strains FT80W^T and FT135W^T together, and strain FT92W^T should be assigned to the genus Massilia, for which the names Duganella lactea sp. nov. (type strain FT50W^T=GDMCC 1.1674^T=KACC 21466^T), Duganella guangzhouensis sp. nov. (FT80W^T=GDMCC 1.1678^T=KACC 21470^T), Duganella flavida sp. nov. (FT135W^T=GDMCC 1.1745^T=KACC 21659^T) and Massilia rivuli sp. nov. (FT92W^T=GDMCC 1.1682^T=KACC 21474^T) are proposed.

Physiological change alters endophytic bacterial community in clubroot of tumorous stem mustard infected by Plasmodiophora brassicae

BACKGROUND

Endophytic bacteria are considered as symbionts living within plants and are influenced by abiotic and biotic environments. Pathogen cause biotic stress, which may change physiology of plants and may affect the endophytic bacterial communiy. Here, we reveal how endophytic bacteria in tumorous stem mustard (Brassica juncea var. tumida) are affected by plant physiological changes caused by Plasmodiophora brassicae using 16S rRNA high-throughput sequencing.

RESULTS

The results showed that Proteobacteria was the dominant group in both healthy roots and clubroots, but their abundance differed. At the genus level, Pseudomonas was dominant in clubroots, whereas Rhodanobacter was the dominant in healthy roots. Hierarchical clustering, UniFrac-weighted principal component analysis (PCA), non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) indicated significant differences between the endophytic bacterial communities in healthy roots and clubroots. The physiological properties including soluble sugar, soluble protein, methanol, peroxidase (POD) and superoxide dismutase (SOD) significantly differed between healthy roots and clubroots. The distance-based redundancy analysis (db-RDA) and two-factor correlation network showed that soluble sugar, soluble protein and methanol were strongly related to the endophytic bacterial community in clubroots, whereas POD and SOD correlated with the endophytic bacterial community in healthy roots.

CONCLUSIONS

Our results illustrate that physiologcial changes caused by P. brassicae infection may alter the endophytic bacterial community in clubroots of tumorous stem mustard.

Duganella alba sp. nov., Duganella aquatilis sp. nov., Duganella margarita sp. nov. and Duganella levis sp. nov., isolated from subtropical streams in China

Six Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT9W^T, FT25W, FT26W^T, FT109W^T, FT134W and CY42W^T) were isolated from subtropical streams in China. Comparisons based on 16S rRNA gene sequences showed that the six strains shared similarities of less than 98.1 % with other species within the family Oxalobacteraceae and formed two separately distinct clades in phylogenetic trees. The 16S rRNA gene sequence similarities between strains FT9W^T and FT25W, and between strains FT109W^T and FT134W were both 99.7 %. The genome sizes of strains FT9W^T, FT25W, FT26W^T, FT109W^T, FT134W and CY42W^T were 6.45, 6.45, 6.54, 6.43, 6.52 and 6.74 Mbp with G+C contents of 64.0, 64.0, 63.8, 63.2, 63.2 and 62.5 %, respectively. The calculated pairwise average nucleotide (ANI) values among the six strains and other related species were less than 93.9 %, except that the values were 99.9 % between strains FT9W^T and FT25W, 98.2 % between strains FT109W^T and FT134W, and 95.0 and 95.1 % between strain FT26W^T and strains FT9W^T and FT25W, respectively. However, strain FT26W^T shared 16S rRNA gene sequence similarities of only 98.3 and 98.2 % with FT9W^T and FT25W, respectively. The respiratory quinone of the six strains was determined to be Q-8. The major fatty acids were C_16 : 1 ω7c, C_16 : 0 and C_12 : 0. The predominant polar lipids included phosphatidylethanolamine and phosphatidylglycerol. Considering the phenotypic, biochemical, genotypic and ANI data, strains FT9W^T and FT25W, and FT109W^T and FT134W may belong to the same species, respectively. Although the pairwise ANI values between strain FT26W^T and each of strains FT9W^T and FT25W were located in the transition region of species demarcation, the dissimilarities among them indicated that strain FT26W^T could represent an independent novel species. The reconstructed phylogenomic tree based on a concatenation of 92 core genes showed that the six strains clustered closely with Duganella sacchari Sac-22^T and Duganella radicis KCTC 22382^T, and supported that these six strains belong to the genus Duganella. The names Duganella albus sp. nov. (type strain FT9W^T=GDMCC 1.1637^T=KACC 21313^T), Duganella aquatilis sp. nov. (type strain FT26W^T=GDMCC 1.1641^T=KACC 21315^T), Duganella pernnla sp. nov. (type strain FT109W^T=GDMCC 1.1688^T=KACC 21480^T) and Duganella levis sp. nov. (type strain CY42W^T=GDMCC 1.1673^T=KACC 21465^T) are proposed.

Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil

Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, ¹³ C-CO₂ labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in ¹³ C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in ¹³ C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear ¹³ C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.

Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality

The aim of this study was to determine the impacts of anthropogenic disturbances on bacterial community composition in an urban river (Mooi River). Physico-chemical analysis, bacterial enumeration and 454-pyrosequencing were conducted on the Mooi River system upstream and downstream of an urban settlement in the North West Province, South Africa. Pyrosequencing and multivariate analysis showed that nutrient inputs and faecal pollution strongly impacted the physico-chemical and microbiological quality at the downstream sites. Also, bacterial communities showed higher richness and evenness at the downstream sites. Multivariate analysis suggested that the abundances of Betaproteobacteria, Epsilonproteobacteria, Acidobacteria, Bacteroidetes and Verrucomicrobia are related to temperature, pH, dissolved oxygen (DO), sulphate and chlorophyll-a levels. These results suggest that urbanisation caused the overall water quality of this river to deteriorate, which in turn affected the bacterial community composition. In addition, our work identified potential indicator groups that may be used to track faecal and organic pollution in freshwater systems.

Se (IV) triggers faster Te (IV) reduction by soil isolates of heterotrophic aerobic bacteria: formation of extracellular SeTe nanospheres

Background

Selenium and Tellurium have many common chemical properties as both belong to group 16 of the periodic table. High toxicities of Se and Te oxyanions cause environmental problems in contaminated soils and waters. Three strains (C4, C6 and C7) of selenite reducing and nanoparticle forming aerobic bacteria which were isolated from agricultural soils of India containing high concentrations of Se were investigated after 3.5 months of freeze-storage for their resistance against the toxic oxyanion tellurite and its reduction to non toxic elemental form Te⁰ as well as nanoparticles formation.

Results

Strains C4, C6 and C7 reduced tellurite at maximum reduction rates of 2.3, 1.5 and 2.1 mg Te (IV)/L/d, respectively and produced extracellular Te⁰ nanospheres as revealed from SEM-EDX analysis. Production of extracellular Te nanospheres has been described seldom. Further, concurrent reduction of both selenite and tellurite by bacteria was examined as these toxic oxyanions are often present together in natural environments, mine tailings or wastewater from copper refining. Interestingly, bioreduction of 100 mg/L selenite in shake flasks was not much affected by the presence of 10 mg/L tellurite but tellurite reduction rate increased 13 fold with selenite in the medium. The concurrent reduction of these oxyanions resulted in rarely described bioformation of extracellular nanoparticles composed of both Se and Te, reported first time for aerobically growing heterotrophic non-halophilic bacterial cultures. Duganella violacienigra, the closely related strain to C4 was also found to be resistant to oxyanions of Se and Te.

Conclusions

Selenite reducing heterotrophic non-halophilic aerobic bacteria revived from 3.5 months freeze storage could successfully reduce toxic tellurite to non toxic elemental form and produced extracellular nanospheres during detoxification. Presence of relatively less toxic selenite in the medium triggers bioreduction of more toxic tellurite leading to formation of extracellular SeTe nanospheres which are sought by solar and optical recording media industry because of their excellent photovoltaic and optical properties. The bacterial cultures investigated in this study could be exploited commercially to remediate not only selenite and tellurite-contaminated soil and water but also for green synthesis of extracellular Se, Te and Se + Te nanospheres.

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)).