Extensimonas perlucida sp. nov., a Novel Bacterium Isolated from Sludge

A bacterium, designated HX2-24 ^T, was isolated from activated sludge treating pesticide-manufacturing wastewater. Colonies of the strain on nutrient agar were circular, transparent, and colorless. Strain HX2-24 ^T shared 98.1% 16S rRNA gene sequence similarity with Extensimonas vulgaris S4^T, and less than 97% similarities with other type strains. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain formed a clade with E. vulgaris S4^T. The major cellular fatty acids were C_16:0, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) and C_17:0 cyclo, the major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), aminophospholipid (APL), glycophospholipid (GPL), and aminoglycolipid (AGL). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between HX2-24 ^T and E. vulgaris S4^T were 92% and 41%, respectively. The G + C content of strain HX2-24 ^T was 64.4 mol%. Thus, based on the phenotypic, chemotaxonomic, and genotypic characteristics, strain HX2-24 ^T represents a novel species in the genus Extensimonas, for which the name Extensimonas perlucida HX2-24 ^T sp. nov. is proposed. The type strain is HX2-24 ^T (= KCTC 72472 ^T = CCTCC AB 2019178 ^T).

Multidisciplinary characterization of U(VI) sequestration by Acidovorax facilis for bioremediation purposes

The contamination of the environment by U may affect plant life and consequently may have an impact on animal and human health. The present work describes U(VI) sequestration by Acidovorax facilis using a multidisciplinary approach combining wet chemistry, transmission electron microscopy, and spectroscopy methods (e.g. cryo-time resolved laser-induced fluorescence spectroscopy, extended X-ray absorption fine structure spectroscopy, and in-situ attenuated total reflection Fourier transform infrared spectroscopy). This bacterial strain is widely distributed in nature including U-contaminated sites. In kinetic batch experiments cells of A. facilis were contacted for 5 min to 48 h with 0.1 mM U(VI). The results show that the local coordination of U species associated with the cells depends upon time contact. U is bound mainly to phosphate groups of lipopolysaccharide (LPS) at the outer membrane within the first hour. And, that both, phosphoryl and carboxyl functionality groups of LPS and peptidoglycan of A. facilis cells may effectuate the removal of high U amounts from solution at 24-48 h of incubation. It is clearly demonstrated that A. facilis may play an important role in predicting the transport behaviour of U in the environment and that the results will contribute to the improvement of bioremediation methods of U-contaminated sites.

[Curvibacter sp. strain HJ-1 induced the formation of aragonite under the condition of low Mg/Ca ratio]

OBJECTIVE

To study the effects of bacteria on the species and morphology of carbonate minerals.

METHODS

We conducted a series of cultural experiments in the medium with initial Mg/Ca ratio of 2 but without carbonate ion using Curvibacter sp. strain HJ-1 for 50 days. During the cultivation, bacterial density, precipitate quantities, calcium and magnesium concentration were determined. The morphologies of precipitated carbonates were observed using scanning electron microscopy, and mineral species of carbonate were determined by X-ray diffraction.

RESULTS

Strain HJ-1 could induce the precipitation of carbonate minerals, the quality of carbonate gradually increased with the incubation time. XRD patterns showed that the mineral precipitates consisted of high-Mg calcite and aragonite. The percentage of aragonite in the precipitates was up to 86%. The morphology of carbonate minerals was multiform, including rod-shaped, dumbbell-shaped, spherical, tabular, as well as irregular and flake.

CONCLUSION

The formation of aragonite under the condition of low Mg/Ca ratio has a close correlation with extracellular polysaccharide secreted by Curvibacter sp. strain HJ-1.

Synchrotron-based chemical nano-tomography of microbial cell-mineral aggregates in their natural, hydrated state

Chemical nano-tomography of microbial cells in their natural, hydrated state provides direct evidence of metabolic and chemical processes. Cells of the nitrate-reducing Acidovorax sp. strain BoFeN1 were cultured in the presence of ferrous iron. Bacterial reduction of nitrate causes precipitation of Fe(III)-(oxyhydr)oxides in the periplasm and in direct vicinity of the cells. Nanoliter aliquots of cell-suspension were injected into custom-designed sample holders wherein polyimide membranes collapse around the cells by capillary forces. The immobilized, hydrated cells were analyzed by synchrotron-based scanning transmission X-ray microscopy in combination with angle-scan tomography. This approach provides three-dimensional (3D) maps of the chemical species in the sample by employing their intrinsic near-edge X-ray absorption properties. The cells were scanned through the focus of a monochromatic soft X-ray beam at different, chemically specific X-ray energies to acquire projection images of their corresponding X-ray absorbance. Based on these images, chemical composition maps were then calculated. Acquiring projections at different tilt angles allowed for 3D reconstruction of the chemical composition. Our approach allows for 3D chemical mapping of hydrated samples and thus provides direct evidence for the localization of metabolic and chemical processes in situ.

Differentiation in MALDI-TOF MS and FTIR spectra between two closely related species Acidovorax oryzae and Acidovorax citrulli

BACKGROUND

Two important plant pathogenic bacteria Acidovorax oryzae and Acidovorax citrulli are closely related and often not easy to be differentiated from each other, which often resulted in a false identification between them based on traditional methods such as carbon source utilization profile, fatty acid methyl esters, and ELISA detection tests. MALDI-TOF MS and Fourier transform infrared (FTIR) spectra have recently been successfully applied in bacterial identification and classification, which provide an alternate method for differentiating the two species.

RESULTS

Characterization and comparison of the 10 A. oryzae strains and 10 A. citrulli strains were performed based on traditional bacteriological methods, MALDI-TOF MS, and FTIR spectroscopy. Our results showed that the identity of the two closely related plant pathogenic bacteria A. oryzae and A. citrulli was able to be confirmed by both pathogenicity tests and species-specific PCR, but the two species were difficult to be differentiated based on Biolog and FAME profile as well as 16 S rRNA sequence analysis. However, there were significant differences in MALDI-TOF MS and FTIR spectra between the two species of Acidovorax. MALDI-TOF MS revealed that 22 and 18 peaks were specific to A. oryzae and A. citrulli, respectively, while FTIR spectra of the two species of Acidovorax have the specific peaks at 1738, 1311, 1128, 1078, 989 cm(-1) and at 1337, 968, 933, 916, 786 cm(-1), respectively.

CONCLUSIONS

This study indicated that MALDI-TOF MS and FTIR spectra may give a new strategy for rapid bacterial identification and differentiation of the two closely related species of Acidovorax.

Environmental fate, toxicity, characteristics and potential applications of novel bioemulsifiers produced by Variovorax paradoxus 7bCT5

The aims of this work were the characterisation and the evaluation of potential environmental applications of the bioemulsifiers produced by Variovorax paradoxus 7bCT5. V. paradoxus 7bCT5 produces a mixture of high molecular weight polysaccharides. The extracellular bioemulsifiers were able to produce a thick stable oil/water emulsion and maintained the emulsification activity after boiling and at low temperatures. Environmental behavior and impact of bioemulsifiers release were assessed by evaluating biodegradability, toxicity and soil sorption. Respirometric tests showed that moderate biodegradability occurred by soil bacterial inoculum. Furthermore, the produced compounds did not show any toxic properties through different ecotoxicological tests. The K(d) values ranged from 1.3 to 7.3 L/kg indicating a high sorption affinity of the bioemulsifier molecules to soil particles. The soil sorption affinity likely affected the bioemulsifier ability to remove hydrocarbons from contaminated soils. In fact, V. paradoxus 7bCT5 bioemulsifiers significantly increased the removal of crude-oil from sandy soil compared to water.

Diaphorobacter oryzae sp. nov., isolated from a thiosulfate-oxidizing enrichment culture

A taxonomic study was performed on two isolates, strains RF3(T) and RF21, recovered from a thiosulfate-oxidizing enrichment culture. Comparative 16S rRNA gene sequence analysis showed that these isolates were clearly affiliated with the class Betaproteobacteria. Strains RF3(T) and RF21 were most closely related to Diaphorobacter nitroreducens NA10B(T) (97.9 and 98.2 % 16S rRNA gene sequence similarity, respectively). The level of 16S rRNA gene sequence similarity between strains RF3(T) and RF21 was 99.8 %. The two isolates were Gram-negative, aerobic and denitrifying. Growth was observed at 7-35 degrees C. Physiological and biochemical properties of strains RF3(T) and RF21 were different from those of D. nitroreducens NA10B(T) in that strains RF3(T) and RF21 were able to utilize l-histidine, 2-ketogluconate and caprate, but unable to utilize suberate. The G+C contents of the genomic DNA of strains RF3(T) and RF21 were 62.9 and 62.8 mol%, respectively, and the predominant quinone was ubiquinone-8. Strains RF3(T) and RF21 possessed C(16 : 0), C(17 : 0) cyclo, and C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH as major fatty acids. DNA-DNA relatedness data indicated that strains RF3(T) and RF21 represent a genomic species separate from D. nitroreducens. On the basis of the evidence presented from this polyphasic analysis, it is suggested that strains RF3(T) and RF21 represent a novel species of the genus Diaphorobacter, for which the name Diaphorobacter oryzae sp. nov. is proposed. The type strain is RF3(T) (=KCTC 22225(T)=LMG 24467(T)).

Hydrogenophaga caeni sp. nov., isolated from activated sludge

A Gram-negative bacterium, designated strain EMB71T, was isolated from activated sludge used for enhanced biological phosphorus removal in a sequencing batch reactor. The cells of the isolate were facultatively aerobic, motile rods with single polar flagella. Growth was observed to occur at 15–35 °C (optimally at 30 °C) and at pH 6.0–9.0 (optimally at pH 7.0–8.0). The predominant fatty acids of strain EMB71T were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), and the polar lipids comprised a large amount of phosphatidylethanolamine and a small amount of diphosphatidylglycerol. The G+C content of the genomic DNA was 61.6 mol % and the major quinone was Q-8. Comparative 16S rRNA gene sequence analyses showed that strain EMB71T formed a phyletic lineage with the genus Hydrogenophaga within the family Comamonadaceae. The levels of 16S rRNA gene sequence similarity with respect to the type strains of Hydrogenophaga species ranged from 95.1 to 96.9 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB71T represents a novel species of the genus Hydrogenophaga, for which the name Hydrogenophaga caeni sp. nov. is proposed. The type strain is EMB71T (=KCTC 12613T=DSM 17962T).

Simplicispira limi sp. nov., isolated from activated sludge

A Gram-negative, motile, rod-shaped bacterium, designated strain EMB325T, was isolated from activated sludge that performed enhanced biological phosphorus removal in a sequencing batch reactor. The predominant fatty acids of strain EMB325T were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1 ω7c and C18 : 1 ω7c 11-methyl. The strain contained phosphatidylethanolamine and diphosphatidylglycerol as polar lipids. The G+C content of the genomic DNA was 63.3 mol%. The major quinone was Q-8. Phylogenetic analysis of 16S rRNA gene sequences showed that strain EMB325T formed a phyletic lineage with members of the genus Simplicispira and was most closely related to Simplicispira psychrophila LMG 5408T and Simplicispira metamorpha DSM 1837T with similarities of 98.1 and 97.9 %, respectively. Levels of DNA–DNA relatedness between strain EMB325T and S. psychrophila LMG 5408T and S. metamorpha DSM 1837T were 28 and 23 %, respectively. On the basis of chemotaxonomic data and molecular characteristics, strain EMB325T is considered to represent a novel species within the genus Simplicispira, for which the name Simplicispira limi sp. nov. is proposed. The type strain is EMB325T (=KCTC 12608T=DSM 17964T).

Identification of bacterial N-acylhomoserine lactones (AHLs) with a combination of ultra-performance liquid chromatography (UPLC), ultra-high-resolution mass spectrometry, and in-situ biosensors

N-Acylated homoserine lactones (AHLs) are produced by Gram-negative bacteria as communication signals and are frequently studied as mediators of the "quorum sensing" response of bacterial communities. Several reports have recently been published on the identification of AHLs from different species and attempts have been made to study their role in natural habitats, for example the surface of plant roots in the rhizosphere. In this article, different analytical methods, including bacterial biosensors and chromatographic techniques, are reviewed. A concept for assignment of the structures of AHLs is also presented. The retention behaviour of derivatives of AHLs containing beta-keto or hydroxyl groups and/or double bonds has been evaluated in relation to the separation behaviour of AHLs with saturated and unsubstituted alkanoyl chains. Samples have also been analysed by high resolution mass spectrometry (Fourier-transform ion-cyclotron-resonance mass spectrometry, FTICR-MS), nano liquid chromatography-electrospray ionization ion trap mass spectrometry (nano-LC-MS) and by the aid of a biosensor. The results obtained from ultra performance liquid chromatography (UPLC), FTICR-MS, nano-LC-MS, and bioassays have been compared to attempt structural characterisation of AHL without chemical synthesis of analytical standards. The method was used to identify the major AHL compound produced by the rhizosphere bacterium Acidovorax sp. N35 as N-(3-hydroxydecanoyl)homoserine lactone.

Variovorax soli sp. nov., isolated from greenhouse soil

A Gram-negative, rod-shaped, non-spore-forming bacterium, strain GH9-3T, isolated from greenhouse soil, was investigated in a polyphasic study. The novel organism grew at 10–35 °C, 0–3 % NaCl and pH 5–9. It had ubiquinone 8 (Q-8) as the predominant isoprenoid quinone and possessed C16 : 0, summed feature 3, C17 : 0 cyclo and C18 : 1 ω7c as the major fatty acids (together representing 87.4 % of the total). The DNA G+C content was 67.1 mol%. 16S rRNA gene sequence analysis of strain GH9-3T showed that it grouped within the Variovorax cluster, with highest sequence similarities to Variovorax paradoxus IAM 12373T (98.3 %) and Variovorax dokdonensis DS-43T (98.0 %). DNA–DNA hybridization values between strain GH9-3T and V. paradoxus DSM 30034T and V. dokdonensis DS-43T were 38 and 29 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic features, it is proposed that strain GH9-3T represents a novel species of the genus Variovorax with the name Variovorax soli sp. nov. The type strain is GH9-3T (=KACC 11579T=DSM 18216T).

Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov

Two strains of curved bacteria, 7-1(T) and 7-2(T), isolated from well water, were phylogenetically examined to determine their taxonomic position. Strain 7-1(T) is a Gram-negative, slightly curved rod. Analysis of the 16S rRNA gene sequence showed that strain 7-1(T) formed a cluster with [Aquaspirillum] delicatum and [Pseudomonas] lanceolata. It has some similar characteristics to [A.] delicatum and [P.] lanceolata, but has sufficient distance to separate it from other genera. DNA-DNA hybridization analysis, as well as chemotaxonomic and morphological studies, demonstrated that strain 7-1(T), [A.] delicatum and [P.] lanceolata belong to a new genus, Curvibacter gen. nov. Strain 7-1(T) (=IAM 15033(T)=ATCC BAA-807(T)) is classified as the type strain of Curvibacter gracilis gen. nov., sp. nov., and [A.] delicatum and [P.] lanceolata are classified as Curvibacter delicatus comb. nov. and Curvibacter lanceolatus comb. nov., respectively. Strain 7-2(T) is a Gram-negative spirillum. Phylogenetic study based on the 16S rRNA gene sequences showed that it formed a cluster with the members of the genus Herbaspirillum, [Pseudomonas] huttiensis and [Aquaspirillum] autotrophicum. The classification is therefore proposed of strain 7-2(T) (=IAM 15032(T)=ATCC BAA-806(T)) as the type strain of Herbaspirillum putei sp. nov., and [P.] huttiensis and [A.] autotrophicum are transferred to the genus Herbaspirillum as Herbaspirillum huttiense comb. nov. and Herbaspirillum autotrophicum comb. nov., respectively.

Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge

Two Gram-negative, oxidase-positive rods (strains BSB 9.5T and BSB 41.8T) isolated from wastewater were studied using a polyphasic approach. 16S rRNA gene sequence comparisons demonstrated that both strains cluster phylogenetically within the family Comamonadaceae: the two strains shared 99·9 % 16S rRNA gene sequence similarity and were most closely related to the type strains of Hydrogenophaga palleronii (98·5 %) and Hydrogenophaga taeniospiralis (98·0 %). The fatty acid patterns and substrate-utilization profiles displayed similarity to the those of the five Hydrogenophaga species with validly published names, although clear differentiating characteristics were also observed. The two strains showed DNA–DNA hybridization values of 51 % with respect to each other. No close similarities to any other Hydrogenophaga species were detected in hybridization experiments with the genomic DNAs. On the basis of these results, two novel Hydrogenophaga species, Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov. are proposed, with BSB 9.5T (=DSM 15341T=CIP 108119T) and BSB 41.8T (=DSM 15342T=CIP 108118T) as the respective type strains.