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Unrooted tree showing the phylogenetic relationships of strain YT T and representative species of Sphingomonas sensu stricto, Sphingobium, Novosphingobium and Sphingopyxis. Escherichia coli was used as the outgroup. The tree, constructed using the neighbour-joining method, was based on a comparison of a region corresponding to E. coli 16S rDNA positions 37-1417. Bootstrap values, expressed as percentages of 1000 replications, are given at branching points. Bar, 0?05 nucleotide substitution rate (K nuc ) units.
Source publication
A nonylphenol-degrading bacterial strain (YT(T)) was isolated previously from a river sediment sample obtained in Ami-machi, Ibaraki, Japan, and identified as a Sphingomonas species. In this study, the taxonomic relationship between strain YT(T), a recently described nonylphenol-degrading strain, Sphingomonas cloacae, and Sphingobium yanoikuyae, wh...
Context in source publication
Context 1
... phylogenetic tree, based on 16S rDNA sequences, shows that strain YT T belongs to the genus Sphingobium (Fig. 2). In addition, the nucleotide signatures specific to the 16S rRNA of Sphingobium, i.e. a U : A pair at position 52 : 359, the presence of U at position 593 and a U : G pair at posi- tion 987 : 1218 ( Takeuchi et al., 2001), were all found in the sequence of strain YT T . Takeuchi et al. (2001) have shown that polyamine patterns and ...
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Biochemical and molecular genetic studies were performed on an unknown Gram-stain-positive, catalase-negative, coccus-shaped organism isolated from clinical samples of a Pyrenean chamois. The micro-organism was identified as a streptococcal species based on its cellular morphological and biochemical tests. 16S rRNA gene sequence comparison studies...
Citations
... Additionally, Ueshiba et al. identified Sphingobium amiense sp., a rare bacterium capable of digesting nonylphenol [20]. Schwien and Schmidt's research in 1982 revealed that aerobic bacteria can convert mono-and dichlorophenols into chlorocatechol through hydroxylation [21]. ...
... Wang et al. 2009, Wang et al. 2011. Sphingobium amiense, isolated from river sediment, can degrade nonylphenol (Ushiba et al. 2003). Additionally, Sphingobium sp. ...
Background
Continuous cropping challenges constrain the development of agriculture. Three main obstacles limit continuous cropping: autotoxicity of plant allelochemicals, deterioration of physicochemical characteristics of soil, and microflora imbalance. Plant-derived phenolic acids can cause autotoxicity, which is considered the main factor mediating continuous cropping obstacles. Reducing the phenolic acids in continuous cropping soils can decrease the autotoxicity of phenolic acids and ameliorate continuous cropping obstacles. Therefore, it is important to study the microbial resources that degrade allelochemical phenolic acids. Thus, the bacterial strain V4 that can degrade phenolic acids was isolated, identified, and genomically analyzed.
Results
Strain V4 isolated from strawberry soil using vanillic acid-mineral agar was identified as a Gram-negative short rod bacterium. Subsequent 16S rRNA phylogenetic analysis revealed that V4 clustered with members of the genus Sphingobium . The most closely related species were Sphingobium lactosutens DS20 T (99% similarity) and Sphingobium abikonense NBRC 16140 T (97.5% similarity). V4 also shared > 95% sequence similarity with other members of Sphingobium , so Sphingobium sp. V4 was named accordingly. Biochemical tests revealed that the biochemical characteristics of Sphingobium sp. V4 were similar to its most similar strains except for some properties. Sphingobium sp. V4 effectively degraded vanillic acid, ferulic acid, p -coumaric acid, p -hydroxybenzoic acid, and syringic acid. V4 grew best at the conditions of 30 °C, pH 6.0–7.0, and 0–0.05% NaCl. 500 mg/L vanillic acid was completely degraded by V4 within 24 h under the optimal conditions. Whole genome analysis showed that Sphingobium sp. V4 contained one chromosome and three plasmids. Two genes involved in vanillic acid degradation were found in the V4 genome: the gene encoding vanillate O -demethylase oxidoreductase VanB on the chromosome and the gene encoding vanillate monooxygenase on a large plasmid. The organization of vanillate catabolic genes differed from the adjacent organization of the genes, encoding vanillate o-demethylase VanA and VanB subunits, in Pseudomonas and Acinetobacter .
Conclusions
The isolated bacterium Sphingobium sp. V4 degraded multiple phenolic acids. Its properties and genome were further analyzed. The study provides support for further investigation and application of this phenolic acid-degrading microorganism to alleviate continuous cropping obstacles in agriculture.
... On the basis of morphological, physiological, and biochemical properties, and this phylogenetic analysis of the 16S rRNA gene sequence (Figure 1), strain DI-6 was identified as Sphingobium sp. Members of this genus are found to be saprophytic soil and water bacteria, and many isolates have been shown to engage in the biodegradation of a variety of toxic organic contaminants such as nonylphenol (Ushiba et al., 2003), phenanthrene (Prakash and Lal, 2006), polycyclic aromatic compounds (Wittich et al., 2007), pentachlorophenol (Zilouei et al., 2008), pyrethroids (Guo et al., 2009), isoproturon (Sun et al., 2009), lindane (Zheng et al., 2011), phenanthrene (Wang et al., 2013), organophosphate and organochlorine pesticides (Cao et al., 2013), and a mixture of polycyclic aromatic hydrocarbons (Fu et al., 2014). Sphingobium sp. ...
Diazinon is one of the most widely used organophosphate insecticides, one that is frequently detected in the environment. In this study, a diazinon-degrading bacterium, DI-6, previously isolated from diazinon-contaminated soil in China has been subsequently identified as Sphingobium sp. on the basis of its physiological and biochemical characteristics, as well as by virtue of a comparative analysis of 16S rRNA gene sequences. This strain is capable of using diazinon as its sole carbon source for growth and was able to degrade 91.8% of 100 mg L–1 diazinon over a 60-h interval. During the degradation of diazinon, the following seven metabolites were captured and identified by gas chromatography/mass spectrometry (GC–MS) analysis: diazoxon, diazinon aldehyde, isopropenyl derivative of diazinon, hydroxyethyl derivative of diazinon, diazinon methyl ketone, O-[2-(1-hydroxyethyl)-6-methylpyrimidin-4-yl] O-methyl O-hydrogen phosphorothioate, and O-(6-methyl pyrimidin-4-yl) O,O-dihydrogen phosphorothioate. Based on these metabolites, a novel microbial biodegradation pathway of diazinon by Sphingobium sp. DI-6 is proposed. This research provides potentially useful information for the application of the DI-6 strain in bioremediation of diazinon-contaminated environments.
... Strains were isolated from various habitats such as soil, water, hydrocarbon dump sites, river sediments, activated sludge, plant rhizosphere, cold springs, green algae, and vermicompost. Sphingobium strains capable of degrading nonylphenol (Ushiba et al., 2003) and dibenzofurans (Wittich et al., 2007) were reported as common inhabitants of river sediments. The species S. algicola and S. paulinellae were exclusively reported from the freshwater green alga Paulinella chromatophora (Lee and Jeon, 2017). ...
Sphin.go'bi.um. N.L. neut. n. sphingosinum (from Gr. gen. n. sphingos, of sphinx, and suff. -ine) sphingosine; N.L. pref. sphingo-, pertaining to sphingosine; Gr. masc. n. bios, life; N.L. neut. n. Sphingobium, sphingosine-containing life.
Proteobacteria / Alphaproteobacteria / Sphingomonadales / Sphingomonadaceae / Sphingobium
The genus Sphingobium belongs to the phylum Proteobacteria, class Alphaproteobacteria, order Sphingomonadales, and family Sphingomonadaceae. Members of this genus can be differentiated from other close relatives of the genera Sphingomonas, Sphingopyxis, and Novosphingobium by their cell morphology, mode of nutrition, composition of fatty acids, distribution of polar lipids in the bacterial cell wall, polyamine pattern, respiratory quinones, accumulation of poly-β-hydroxybutyrate (PHB) granules, and degradation of xenobiotics such as hexachlorocyclohexane (HCH). Several members had been isolated from different biological niches such as freshwater bodies, activated sludge, green algae, sediments, seawater, hydrocarbon-contaminated sites, copper mines, rice rhizosphere, lettuce corky root, cold springs, vermicompost, and industrial wastewater treatment systems. Most of the members are slow-growing, motile or nonmotile, nonsporulating, and flagellated or nonflagellated (bear polar or sub-polar flagella). Able to assimilate a wide range of carbohydrates. Broad substrate specificities and diverse enzymatic activities make them promising candidates for the degradation of several environmental pollutants. Exploitation of their metabolic potential could open up new avenues in industrial microbiology. As per the genome taxonomy database, 103 genomes (draft as well as complete) of different strains of the genus Sphingobium are available on EzBioCloud. Such a large number of sequences provides an opportunity for taxonomic researchers to understand this genus in detail.
DNA G + C content (mol%): 58.8–66.8.
Type species: Sphingobium yanoikuyae Takeuchi et al. 2001VP (basonym: Sphingomonas yanoikuyae Yabuuchi et al. 1990, VL34)).
... Our results further showed that AstI and AstII were positively correlated with the relative abundance of Sphingopyxis in the rhizosphere. Sphingopyxis has been isolated from various habitats, including natural soil, underground water, sediments of contaminated rivers, oil-contaminated soil, seawater, landfill soil and ginseng field (Ushiba et al., 2003;Lee et al., 2008;Verma et al., 2015;Chaudhary and Kim, 2016;Chaudhary et al., 2017a,b). Therefore, we speculated that Sphingopyxis was widespread and had a variety of potential functions. ...
Astragalus membranaceus (Fisch.) Bge. var. mongholicus, which is used in traditional Chinese medicine, contains several bioactive ingredients. The root-associated microbial communities play a crucial role in the production of secondary metabolites in plants. However, the correlation of root-associated bacteria and fungi with the bioactive ingredients production in A. mongholicus has not been elucidated. This study aimed to examine the changes in soil properties, root bioactive ingredients, and microbial communities in different cultivation years. The root-associated bacterial and fungal composition was analyzed using high-throughput sequencing. The correlation between root-associated bacteria and fungi, soil properties, and six major bioactive ingredients were examined using multivariate correlation analysis. Results showed that soil properties and bioactive ingredients were distinct across different cultivation years. The composition of the rhizosphere microbiome was different from that of the root endosphere microbiome. The bacterial community structure was affected by the cultivation year and exhibited a time-decay pattern. Soil properties affected the fungal community composition. It was found that 18 root-associated bacterial operational taxonomic units (OTUs) and four fungal OTUs were positively and negatively correlated with bioactive ingredient content, respectively. The abundance of Stenotrophomonas in the rhizosphere was positively correlated with astragaloside content. Phyllobacterium and Inquilinus in the endosphere were positively correlated with the calycosin content. In summary, this study provided a new opportunity and theoretical reference for improving the production and quality of in A. mongholicus, which thus increase the pharmacological value of A. mongholicus.
... Rhizodegradation of alkylphenols, specifically NP and OP, occurs in aerobic conditions in various environments [75][76][77]. Some microorganisms possess the ability to assimilate alkylphenols as a sole carbon and energy source [78,79] and Toyama et al. [80] isolated bacteria with ability to degrade NP and OP from P. australis rhizosphere. In the case of PCP, DʹAngelo and Reddy [81] observed that under laboratory conditions no PCP degradation occurred in wetland soil which had been sterilized but the compound was degraded in nonsterile soil, suggesting that PCP degradation was due to biological activity and that most wetland soils contain microorganisms with capacity to degrade PCP despite no known history of contamination. ...
This study aims to investigate the effect of two different groups of phenolic compounds (the alkylphenols nonylphenol (NP) and octylphenol (OP), and the chlorophenol pentachlorophenol (PCP)) on constructed wetlands (CWs) performance, including on organic matter, nutrients and contaminants removal efficiency, and on microbial community structure in the plant bed substrate. CWs were assembled at lab scale simulating a vertical flow configuration and irrigated along eight weeks with Ribeira de Joane (an urban stream) water not doped (control) or doped with a mixture of NP and OP or with PCP (at a 100 μg L−1 concentration each). The presence of the phenolic contaminants did not interfere in the removal of organic matter or nutrients in CWs in the long term. Removals of NP and OP were >99%, whereas PCP removals varied between 87% and 98%, mainly due to biodegradation. Microbial richness, diversity and dominance in CWs substrate were generally not affected by phenolic compounds, with only PCP decreasing diversity. Microbial community structure, however, showed that there was an adaptation of the microbial community to the presence of each contaminant, with several specialist genera being enriched following exposure. The three more abundant specialist genera were Methylotenera and Methylophilus (methylophilaceae family) and Hyphomicrobium (hyphomicrobiaceae family) when the systems were exposed to a mixture of NP and OP. When exposed to PCP, the three more abundant genera were Denitromonas (Rhodocyclaceae family), Xenococcus_PCC_7305 (Xenococcaceae family) and Rhodocyclaceae_uncultured (Rhodocyclaceae family). To increase CWs efficiency in the elimination of phenolic compounds, namely PCP which was not totally removed, strategies to stimulate (namely biostimulation) or increase (namely bioaugmentation) the presence of these bacteria should be explore. This study clearly shows the potential of vertical flow CWs for the removal of phenolic compounds, a still little explored subject, contributing to promote the use of CWs as nature-based solutions to remediate water contaminated with different families of persistent and/or emergent contaminants.
... Chemosphere 275 (2021) 130013 Tanghe et al., 1999a;Wheeler et al., 1997) and has been reported to undergo moderate degradation under aerobic conditions (Staples et al., 1999;Ying et al., 2002). Nevertheless, there have been some reports of microbes capable of NP removal (Fujii et al., 2001;Gabriel et al., 2005;Tanghe et al., 1999b;Ushiba et al., 2003). The pioneering work on NP degradation was documented by Tanghe et al. (1999b), who reported an NP degrading novel Sphingomonas strain designated as Sphingomonas sp. ...
... TTNP3, Sphingomonas cloacae, and Sphingomonas xenophagastrain Bayram were obtained from municipal wastewater treatment plants. Sphingobium amiense, a TNP utilizing bacteria obtained from river sediment, was reported by Ushiba et al. (2003). The coldadapted bacterial strains of Stenotrophomonas sp., Pseudomonas mandelii, and Pseudomonas veronii were found effective for bioremediation of nonylphenol (Soares et al., 2003). ...
Nonylphenol (NP) is considered a potential endocrine-disrupting chemical affecting humans and the environment. Due to widespread occurrence in the aquatic environment and neuro-, immuno, reproductive, and estrogenic effects, nonylphenol calls for considerable attention from the scientific community, researchers, government officials, and the public. It can persist in the environment, especially soil, for a long duration because of its high hydrophobic nature. Nonylphenol is incorporated into the water matrices via agricultural run-off, wastewater effluents, agricultural sources, and groundwater leakage from the soil. In this regard, assessment of the source, fate, toxic effect, and removal of nonylphenol seems a high-priority concern. Remediation of nonylphenol is possible through physicochemical and microbial methods. Microbial methods are widely used due to ecofriendly in nature. The microbial strains of the genera, Sphingomonas, Sphingobium, Pseudomonas, Pseudoxanthomonas, Thauera, Novosphingonium, Bacillus, Stenotrophomonas, Clostridium, Arthrobacter, Acidovorax, Maricurvus, Rhizobium, Corynebacterium, Rhodococcus, Burkholderia, Acinetobacter, Aspergillus, Pleurotus, Trametes, Clavariopsis, Candida, Phanerochaete, Bjerkandera, Mucor, Fusarium and Metarhizium have been reported for their potential role in the degradation of NP via its metabolic pathway. This study outlines the recent information on the occurrence, origin, and potential ecological and human-related risks of nonylphenol. The current development in the removal of nonylphenol from the environment using different methods is discussed. Despite the significant importance of nonylphenol and its effects on the environment, the number of studies in this area is limited. This review gives an in-depth understanding of NP occurrence, fate, toxicity, and remediation from the environments.
... The genus of Sphingobium has been reported to contain mostly aerobic and facultative anaerobic soil bacteria (Berney et al. 2014;Chaudhary et al. 2017;Esposti and Romero 2017;Singh and Lal 2009;Ushiba et al. 2003). It has also been reported to perform sulfur respiration (Y. ...
... This may be related to the increased abundance of Sphingobium. Members of this genus are mostly found in saprophytic soils and water, and many isolates are involved in the biodegradation of many toxic organic pollutants such as nonylphenol (Ushiba et al., 2003), phenanthrene (Prakash and Lal, 2006), and polycyclic aromatic compounds (Wittich et al., 2007). Environmental pollutants of xylene and dioxins have carcinogenic effects and reproductive toxicity on animals (Bolden et al., 2015;Johnson et al., 2020). ...
Although rising evidence suggests that the gut microbiota is closely related to host health, the effects of gut microbiota on male fertility are still rarely explored. This study was to investigate the gut microbiota composition and function, fecal short-chain fatty acids (SCFA), intestinal permeability, and systemic inflammatory status of Duroc boar with high (H group, 100%) and low (L group, <80%) semen utilization rate. Fecal samples, analyzed by 16S ribosomal RNA gene sequencing, displayed taxonomic and functional changes between boars with high and low semen utilization rates. For the gut microbiota composition of the boars, four genera were different between the two groups. The [Ruminococcus] and Sphingobium were enriched in L group boars, then negatively correlated with the semen utilization rate. While RFN20 and Paludibacter were enhanced in the H group, only RFN20 showed a significantly positive correlation with the semen utilization rate of boars. In addition, changes in the metabolic function of the gut microbiota of the two groups were found, including altered branched-chain fatty acid (BCFA) production. Significant increases in plasma endotoxin, zonulin, diamine oxidase, and lipocalin-2 levels were observed in boars with low semen utilization, and also, a similar trend in IL-6 and TNF-α was found. However, the concentration of IL-10 in plasma of boars with high semen utilization rate showed an increasing tendency. These results indicated increased intestinal permeability and systemic inflammation in boars with low semen utilization. Data showed that the composition and functions of gut microbiota varied between boars with high or low semen utilization rates, while the semen utilization rate is notably correlated with the gut microbiota composition, intestinal permeability, and inflammatory status of the boar.
... In the data obtained from phylogenetic, chemotaxonomic, and physiological analysis, the previously described Sphingomonas sensu stricto is now classified into four genuses: Sphingomonas, Novospingobium, Sphingobium, and Sphopyxis (Takeuchi et al. 2001). It has been reported that Sphingobium members have been isolated from a variety of habitats including oil-contaminated soil, hexachlorocyclo hexane dump site, rhizosphere soil, river sediment, cattle pasture soil, freshwater, copper mine soil, roots, fly ash dumping site, and waste water (Kumari et al. 2009;Maeda et al. 2015;Ushiba et al. 2003;Young et al. 2007). ...
Background
Spingobium sp. PAMC 28499 is isolated from the glaciers of Uganda. Uganda is a unique region where hot areas and glaciers coexist, with a variety of living creatures surviving, but the survey on them is very poor. The genetic character and complete genome information of Sphingobium strains help with environmental studies and the development of better to enzyme industry.Objective
In this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region.Methods
Genome sequencing
was performed using PacBio sequel single-molecule real-time (SMRT) sequencing technology. The predicted gene sequences were functionally annotated and gene prediction was carried out using the program NCBI non-redundant database. And using dbCAN2 and KEGG data base were degradation pathway predicted and protein prediction about carbohydrate active enzymes (CAZymes).ResultsThe genome sequence
has 64.5% GC content, 4432 coding protein coding genes, 61 tRNAs, and 12 rRNA operons. Its genome encodes a simple set of metabolic pathways relevant to pectin and its predicted degradation protein an unusual distribution of CAZymes with extracellular esterases and pectate lyases. CAZyme annotation analyses revealed 165 genes related to carbohydrate active, and especially we have found GH1, GH2, GH3, GH38, GH35, GH51, GH51, GH53, GH106, GH146, CE12, PL1 and PL11 such as known pectin degradation genes from Sphingobium yanoikuiae. These results confirmed that this Sphingobium sp. strain PAMC 28499 have similar patterns to RG I pectin-degrading pathway.Conclusion
In this study, isolated and sequenced the complete genome of Spingobium sp. PAMC 28499. Also, this strain has comparative genome analysis. Through the complete genome we can predict how this strain can store and produce energy in extreme environment. It can also provide bioengineered data by finding new genes that degradation the pectin.
