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Polycyclic aromatic hydrocarbons (PAHs) pose a global environmental risk, impacting human health. Enhancing phytoremediation with microbial-plant interactions could help mitigate these pollutants. However, tree responses to PAHs are unclear, necessitating controlled studies before field experiments. This study examined how PAH-degrading microbes affect black alder (Alnus glutinosa L.) seedlings grown hydroponically, hypothesizing that specific microbes improve growth and stress tolerance. Two half-sib families (41-65-7 K, 13-99-1 K) were inoculated with Rhodotorula sphaerocarpa (R.s.), Pseudomonas putida (P.p.), and Sphingobium yanoikuyae (S.y.). Results showed family-dependent and microbe-specific effects, with family 41-65-7 K showing enhanced shoot growth (threefold increase by R.s.) and higher carotenoid levels. Antioxidant enzyme activities varied: R.s. elevated superoxide dismutase activity by 4.8-fold in 13-99-1 K, while catalase activity increased but decreased in 41-65-7 K. Principal component analysis revealed distinct phytochemical clustering based on microbial treatment, highlighting genotype-specific modulations. Each microorganism had unique plant growth-promoting traits, with P.p. producing the most phytohormone and S.y. fixing nitrogen. These findings support targeted microbial inoculation for effective remediation of PAH-contaminated environments., (© 2024 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd.)

Recent research has reported the strong herbicidal activity of Artemisia argyi leaf powder (AALP), indicating its high potential for use as an environmentally friendly weed management solution for ecological agriculture. However, AALP's impacts on soil physicochemical properties and microbial communities have remained uninvestigated. This study explores these effects through pot experiments assessing the AALP's efficacy in weed suppression and its ability to promote the growth of Pinellia ternata, a plant utilized in traditional Chinese medicine. The results demonstrate that a 10% concentration of AALP suppressed nearly 100% of all weeds. Additionally, AALP treatments at 2.5%, 5%, 7.5%, and 10% concentrations increased P. ternata yields by 29.79%, 24.76%, 35.67%, and 31.00%, respectively. A soil analysis revealed that AALP enhanced soil fertility by increasing the contents of nutrients such as SOM, AN, AP, AK, Ca, Fe, Mn, and Zn, as well as the enzyme activity of CAT, ACP, UE, and SC, creating an optimal growth environment for P. ternata. In addition, AALP significantly increased the PA (phenolic acid) content in soil, which is a key factor in inhibiting weed germination and growth. Furthermore, a microbial community structure analysis indicated an enrichment of Actinobacteriota and Bacteroidota after AALP treatment, with notable increases in the growth-promoting bacteria Sphingobium and Flavobacterium. A permutational multivariate analysis of variance (PERMANOVA) based on the Bray-Curtis distance reaveled that all of the tested soil properties were significantly correlated with changes in bacterial community composition except for pH. Further two-factor correlation network analysis identified AN, Zn, SC, and PA as key environmental factors. Finally, the Sphingobium sp. strain AFR15, isolated from AALP-treated soil, exhibited significant growth-promoting effects on P. ternata. After inoculation with Sphingobium sp. strain AFR15 for one month, the heights of P. ternata were increased significantly. The leaf length and leaf width of P. ternata were also positively correlated with the treatment concentration of AFR15, and the chlorophyll contents of the leaves also increased. This results highlighted Sphingobium sp. strain AFR15's potential as a specialized microbial fertilizer in crop yield increased. In conclusion, AALP applications not only control weeds but also promote P. ternata growth by improving soil physiochemical properties and fostering beneficial bacterial allies. These findings lay the groundwork for future research and promote the use of AALP in ecological agriculture., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The widely used phenylurea herbicide isoproturon (IPU) and its residues can inhibit the growth of subsequently planted crops. However, reports on bioremediation of IPU-contaminated soil are scarce. In this study, Sphingobium sp. strain YBL2-gfp (a derivative of the IPU-degrading Sphingobium sp. strain YBL2 isolated by our lab) was constructed to bioremediate IPU-contaminated soil. In pot experiments, strain YBL2-gfp colonized the roots of wheat and eliminated IPU residues in the soil within 21 d, effectively alleviating its toxicity and restoring wheat growth. IPU treatment reduced the richness and diversity of soil bacteria, while inoculation YBL2-gfp mainly affected richness with less impact on diversity. The high concentrations of IPU and inoculation of YBL2-gfp alone reduced the soil microbial community connections, while bioaugmentation treatment enhanced the soil microbial community connections. Additionally, strain YBL2-gfp stimulated the metabolic capacity of the indigenous microbes, promoting the degradation of IPU and reducing the negative impact of high concentrations of IPU on microbial community. Taken together, this study offers relatively comprehensive insights into the practical application of bioaugmentation, demonstrating that strain YBL2 has the potential to remediate IPU-contaminated soils., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Sphingobium japonicum strain UT26, whose γ-hexachlorocyclohexane-degrading ability has been studied in detail, is a typical aerobic and heterotrophic bacterium that needs organic carbon sources for its growth, and cannot grow on a minimal salt agar medium prepared without adding any organic carbon sources. Here, we isolated a mutant of UT26 with the ability to grow to visible state on such an oligotrophic medium from a transposon-induced mutant library. This high-yield growth under oligotrophic conditions (HYGO) phenotype was CO 2 -dependent and accompanied with CO 2 incorporation. In the HYGO mutant, a transposon was inserted just upstream of the putative Zn-dependent alcohol dehydrogenase (ADH) gene ( adhX ) so that the adhX gene was constitutively expressed, probably by the transposon-derived promoter. The adhX -deletion mutant (UT26DAX) harbouring a plasmid carrying the adhX gene under the control of a constitutive promoter exhibited the HYGO phenotype. Moreover, the HYGO mutants spontaneously emerged among the UT26-derived hypermutator strain cells, and adhX was highly expressed in these HYGO mutants, while no HYGO mutant appeared among UT26DAX-derived hypermutator strain cells, indicating the necessity of adhX for the HYGO phenotype. His-tagged AdhX that was expressed in Escherichia coli and purified to homogeneity showed ADH activity towards methanol and other alcohols. Mutagenesis analysis of the adhX gene indicated a correlation between the ADH activity and the HYGO phenotype. These results demonstrated that the constitutive expression of an adhX -encoding protein with ADH activity in UT26 leads to the CO 2 -dependent HYGO phenotype. Identical or nearly identical adhX orthologues were found in other sphingomonad strains, and most of them were located on plasmids, suggesting that the adhX -mediated HYGO phenotype may be an important adaptation strategy to oligotrophic environments among sphingomonads.

Grasses are advantageous in the removal of polycyclic aromatic hydrocarbons (PAHs) in soil because of their fibrous root, high tolerance to environmental stress, and low nutritional requirements. In this study, a pot experiment was conducted to test the ability of four grasses to remove PAHs in the soil, and to investigate the corresponding bacterial community shift in the rhizosphere of each. Sudangrass achieved the maximum removal of PAHs at 98% dissipation rate after 20 days. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing revealed that sudangrass specially enriched the growth of a known PAHs degrader, Sphingomonadales, regardless of the presence or absence of PAHs in the soil. Moreover, the gene copy numbers of PAHs catabolic genes, PAH-RHDα and nidA, as measured by real time-PCR (RT-PCR) were highest in the soil planted with sudangrass. Overall, this study suggested that sudangrass further enhanced the dissipation of PAHs by enriching Sphingomonadales in its rhizosphere., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Tetralin (1,2,3,4-tetrahydonaphthalene) is a recalcitrant compound that consists of an aromatic and an alicyclic ring. It is found in crude oils, produced industrially from naphthalene or anthracene, and widely used as an organic solvent. Its toxicity is due to the alteration of biological membranes by its hydrophobic character and to the formation of toxic hydroperoxides. Two unrelated bacteria, Sphingopyxis granuli strain TFA and Rhodococcus sp. strain TFB were isolated from the same niche as able to grow on tetralin as the sole source of carbon and energy. In this review, we provide an overview of current knowledge on tetralin catabolism at biochemical, genetic and regulatory levels in both strains. Although they share the same biodegradation strategy and enzymatic activities, no evidences of horizontal gene transfer between both bacteria have been found. Moreover, the regulatory elements that control the expression of the gene clusters are completely different in each strain. A special consideration is given to the complex regulation discovered in TFA since three regulatory systems, one of them involving an unprecedented communication between the catabolic pathway and the regulatory elements, act together at transcriptional and posttranscriptional levels to optimize tetralin biodegradation gene expression to the environmental conditions.

Membrane filtration systems are widely applied for the production of clean drinking water. However, the accumulation of particles on synthetic membranes leads to fouling. Biological fouling (i.e., biofouling) of reverse osmosis and nanofiltration membranes is difficult to control by existing cleaning procedures. Improved strategies are therefore needed. The bacterial diversity on fouled membranes has been studied, especially to identify bacteria with specialized functions and to develop targeted approaches against these microbes. Previous studies have shown that Sphingomonadaceae are initial membrane colonizers that remain dominant while the biofilm develops. Here, we characterized 21 Sphingomonadaceae isolates, obtained from six different fouled membranes, to determine which physiological traits could contribute to colonization of membrane surfaces. Their growth conditions ranged from temperatures between 8 and 42  o C, salinity between 0.0 and 5.0% w/v NaCl, pH from 4 and 10, and all isolates were able to metabolize a wide range of substrates. The results presented here show that Sphingomonadaceae membrane isolates share many features that are uncommon for other members of the Sphingomonadaceae family: all membrane isolates are motile and their tolerance for different temperatures, salt concentrations, and pH is high. Although relative abundance is an indicator of fitness for a whole group, for the Sphingomonadaceae it does not reveal the specific physiological traits that are required for membrane colonization. This study, therefore, adds to more fundamental insights in membrane biofouling., Competing Interests: The authors declare no competing interests.

Autoimmunity is a consequence of both genetic and environmental factors, occurring in genetically susceptible hosts with environmental triggers. While genome-wide association studies have revealed a number of susceptible genes contributing to etiology, the environmental triggers remain poorly understood. Primary biliary cholangitis, formally known as primary biliary cirrhosis, is considered a model autoimmune disease for which our group has extensively evaluated environmental factors involved in its etiology. Bacterial infection and xenobiotics have been proposed as candidate environmental factors that may explain tolerance breakdown and production of primary biliary cholangitis-specific antimitochondrial autoantibodies. Large-scale case-control studies have consistently detected an association of primary biliary cholangitis with urinary tract infections caused by Escherichia coli, as E. coli PDC-E2 is molecularly similar to human PDC-E2, the immunodominant target of AMAs. Another bacterium of interest is Novosphingobium aromaticivorans, a ubiquitous xenobiotic-metabolizing bacterium that produces lipoylated proteins, which are highly reactive with sera from primary biliary cholangitis patients. Regarding xenobiotics, case-control studies have suggested that frequent use of nail polish is associated with an increased susceptibility to primary biliary cholangitis. We found that 2-octynamide, the conjugate derived from 2-octynoic acid present in cosmetics, lipsticks, and some chewing gums, was unique in both its quantitative structure-activity relationship analysis and reactivity with primary biliary cholangitis sera. 2-nonyamide is another xenobiotic that also has the optimal chemical structure for xenobiotic modification of the PDC-E2 epitope, as demonstrated by the enhanced epitope recognition with AMA-positive PBC sera. Moreover, we found that C57BL/6 mice immunized with 2-octynoic acid-BSA possess many of the features characteristic to primary biliary cholangitis. Impact statement Autoimmunity is believed to develop in genetically susceptible hosts with triggers from the environment. Researchers have recently demonstrated that bacteria and xenobiotics commonly present in our environment are potential triggers of tolerance breakdown against autoantigens and autoimmunity, particularly in primary biliary cholangitis (PBC). The link between xenobiotics and PBC has been further confirmed with the establishment of PBC model mice by immunizing mice with xenobiotics.

Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp). The study determined the precise location of lin genes (genes associated with the degradation of HCH isomers), for example, linA2, linB, linDER, linF, linGHIJ, and linKLMN on the chromosome; linA1, linC, and linF on pSRL1 and linDEbR on pSRL3. Strain B90A contained 26 copies of IS6100 element and most of them (15 copies) was found to be associated with lin genes. Duplication of several lin genes including linA, linDER, linGHIJ, and linF along with two variants of linE, that is, linEa (hydroquinone 1,2-dioxygenase) and linEb (chlorohydroquinone/hydroquinone 1,2-dioxygenase) were identified. This suggests that strain B90A not only possess efficient machinery for upper and lower HCH degradation pathways but it can also act on both hydroquinone and chlorohydroquinone metabolites produced during γ-HCH degradation. Synteny analysis revealed the duplication and transposition of linA gene (HCH dehydrochlorinase) between the chromosome and pSRL1, possibly through homologous recombination between adjacent IS6100 elements. Further, in silico analysis and laboratory experiments revealed that incomplete tyrosine metabolism was responsible for the production of extracellular brown pigment which distinguished strain B90A from other HCH degrading sphingomonads. The precise localization of lin genes, and transposable elements (IS6100) on different replicons now opens up several experimental avenues to elucidate the functions and regulatory mechanism of lin genes acquisition and transfer that were not completely known among the bacterial population inhabiting the HCH contaminated environment., (© The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Nickel acts as cofactor for a number of enzymes of many bacteria species. Its homeostasis is ensured by proteins working as ion efflux or accumulation systems. These mechanisms are also generally adopted to counteract life-threatening high extra-cellular Ni 2+ concentrations. Little is known regarding nickel tolerance in the genus Sphingobium. We studied the response of the novel Sphingobium sp. ba1 strain, able to adapt to high Ni 2+ concentrations. Differential gene expression in cells cultured in 10 mM Ni 2+ , investigated by RNA-seq analysis, identified 118 differentially expressed genes. Among the 90 up-regulated genes, a cluster including genes coding for nickel and other metal ion efflux systems (similar to either cnrCBA, nccCBA or cznABC) and for a NreB-like permease was found. Comparative analyses among thirty genomes of Sphingobium species show that this cluster is conserved only in two cases, while in the other genomes it is partially present or even absent. The differential expression of genes encoding proteins which could also work as Ni 2+ -accumulators (HupE/UreJ-like protein, NreA and components of TonB-associated transport and copper-homeostasis systems) was also detected. The identification of Sphingobium sp. ba1 strain adaptive mechanisms to nickel ions, can foster its possible use for biodegradation of poly-aromatic compounds in metal-rich environments.

With the aim of searching for potent diazotrophic bacteria that are free of public health concerns and optimize rice cultivation, the endophytic colonization and plant growth-promoting activities of some endophytic diazotrophic bacteria isolated from rice were evaluated. Among these bacteria, the emerging diazotrophic strains of the genus Novosphingobium effectively associated with rice plant interiors and consequently promoted the growth of rice, even with the lack of a nitrogen source. These results suggest that diazotrophic Novosphingobium is an alternative microbial resource for further development as a safe biological enhancer in the optimization of organic rice cultivation.

The present study described biosynthesis of silver nanoparticles (AgNPs) using a bacterial strain Novosphingobium sp. THG-C3, isolated from soil, and their application in antibacterial activity. The maximum absorbance values of the synthesized AgNPs was measured at 406 nm in ultraviolet-visible spectrophotometry and were mostly spherical in shape with particle size in range of 8-25 nm by field emission transmission electron microscopy analysis. X-ray diffraction pattern corresponding to planes (111), (200), (220), and (311) demonstrated the crystalline nature of the AgNPs. The synthesized AgNPs exhibited antimicrobial activity against various pathogens inculding Staphylococcus aureus, Candida tropicalis, Pseudomonas aeruginosa, Escherichia coli, Vibrio parahaemolyticus, Candida albicans, Salmonella enterica, Bacillus subtilis, and Bacillus cereus. In addition, the AgNPs in combination with commercial antibiotics enhanced antimicrobial activity against P. aeruginosa, S. enterica, E. coli, and V. parahaemolyticus. The AgNPs synthesized by strain Novosphingobium sp. THG-C3 are comparatively simple, green, cost-effective, and may serve as a potential antimicrobial agent.

The effect of bioaugmentation with Sphingobium sp. AM strain on different soils microbiomes, pristine soil (PS), chronically contaminated soil (IPK) and recently contaminated soil (Phe) and their implications in bioremediation efficiency was studied by focusing on the ecology that drives bacterial communities in response to inoculation. AM strain draft genome codifies genes for metabolism of aromatic and aliphatic hydrocarbons. In Phe, the inoculation improved the elimination of phenanthrene during the whole treatment, whereas in IPK no improvement of degradation of any PAH was observed. Through the pyrosequencing analysis, we observed that inoculation managed to increase the richness and diversity in both contaminated microbiomes, therefore, independently of PAH degradation improvement, we observed clues of inoculant establishment, suggesting it may use other resources to survive. On the other hand, the inoculation did not influence the bacterial community of PS. On both contaminated microbiomes, incubation conditions produced a sharp increase on Actinomycetales and Sphingomonadales orders, while inoculation caused a relative decline of Actinomycetales. Inoculation of most diverse microbiomes, PS and Phe, produced a coupled increase of Sphingomonadales, Burkholderiales and Rhizobiales orders, although it may exist a synergy between those genera; our results suggest that this would not be directly related to PAH degradation., (© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Many ecosystems are currently co-contaminated with heavy metals such as cadmium (Cd(2+) ) and pesticides such as chlorpyrifos (CP) and γ-hexachlorocyclohexane (γ-HCH). A feasible approach to remediate the combined pollution of heavy metals and pesticides is the use of γ-HCH degrading bacteria endowed with CP hydrolysis and heavy metal biosorption capabilities. In this work, a recombinant microorganism capable of simultaneously detoxifying Cd(2+) , CP, and γ-HCH was constructed by display of synthetic phytochelatins (EC20) and methyl parathion hydrolase (MPH) fusion protein on the cell surface of the γ-HCH degrading Sphingobium japonicum UT26 using the truncated ice nucleation protein (INPNC) as an anchoring motif. The surface localization of INPNC-EC20-MPH was verified by cell fractionation, Western blot analysis, immunofluorescence microscopy, and proteinase accessibility experiment. Expression of EC20 on the cell surface not only improved Cd(2+) binding but also alleviated the cellular toxicity of Cd(2+) . As expected, the rates of CP and γ-HCH degradation were reduced in the presence of Cd(2+) for cells without EC20 expression. However, expression of EC20 (higher Cd(2+) accumulation) significantly restored the levels of CP and γ-HCH degradation. These results demonstrated that surface display of EC20 enhanced not only Cd(2+) accumulation but also protected the recombinant strain against the toxic effects of Cd(2+) on CP and γ-HCH degradation., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A mercury resistant bacterial strain, SA2, was isolated from soil contaminated with mercury. The 16S rRNA gene sequence of this isolate showed 99% sequence similarity to the genera Sphingobium and Sphingomonas of α-proteobacteria group. However, the isolate formed a distinct phyletic line with the genus Sphingobium suggesting the strain belongs to Sphingobium sp. Toxicity studies indicated resistance to high levels of mercury with estimated EC50 values 4.5 mg L(-1) and 44.15 mg L(-1) and MIC values 5.1 mg L(-1) and 48.48 mg L(-1) in minimal and rich media, respectively. The strain SA2 was able to volatilize mercury by producing mercuric reductase enzyme which makes it potential candidate for remediating mercury. ICP-QQQ-MS analysis of Hg supplemented culture solutions confirmed that almost 79% mercury in the culture suspension was volatilized in 6 h. A very small amount of mercury was observed to accumulate in cell pellets which was also evident according to ESEM-EDX analysis. The mercuric reductase gene merA was amplified and sequenced. The deduced amino acid sequence demonstrated sequence homology with α-proteobacteria and Ascomycota group., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

In the present study, spheroplasts from the aerobic anoxygenic photosynthetic marine bacterium Erythrobacter litoralis were generated and cultivated. In the presence of penicillin, the spheroplasts grew and enlarged in marine broth without undergoing cell division. However, continuous light inhibited their enlargement, and they were therefore cultivated in the dark. Cellular DNA was quantified at various time points (0, 24, and 48 h) and temperatures (20°C, 25°C, and 30°C) using real-time quantitative PCR. The DNA content was highest at 30°C in the absence of penicillin, whereas there was no observable change with exposure to penicillin at all evaluated temperatures. During growth, larger spheroplasts were more frequently observed at 25°C in the presence of penicillin. These results demonstrate that the optimal culture conditions for the enlargement of spheroplasts in E. litoralis differ from those required for cell division.

A tri- and dibutyl phosphate (TBP/DBP) non-degrading spontaneous mutant, Sphingobium SS22, was derived from the Sphingobium sp. strain RSMS (wild type). Unlike the wild type strain, Sphingobium SS22 could not grow in a minimal medium supplemented with TBP or DBP as the sole source of carbon or phosphorous. Sphingobium SS22 also did not form any of the intermediates or end products of TBP or DBP degradation, namely DBP, butanol or inorganic phosphate. Proteomic analysis revealed the absence of three prominent proteins in Sphingobium SS22 as compared to wild type. These proteins were identified by MALDI mass spectrometry, and they showed similarities to phosphohydrolase- and exopolyphosphatase-like proteins from other bacteria, which belong to the class of phosphoesterases. Cellular proteins of Sphingobium SS22 showed none or negligible phosphodiesterase (PDE) and phosphomonoesterase (PME) activities at pH 7 and displayed approximately five- and approximately twofold less DBP and monobutyl phosphate (MBP) degradation activity, respectively, in comparison to the wild type strain. In-gel zymographic analysis revealed two PDE and PME activity bands in the wild type strain, one of which was absent in the Sphingobium SS22 mutant. The corresponding proteins from the wild type strain could degrade DBP and MBP. The results demonstrate the involvement of phosphoesterase enzymes in the TBP degradation pathway elucidated earlier.