Transposon Mutagenesis Identifies Genes Critical for Growth of Pseudomonas nitroreducens TX1 on Octylphenol Polyethoxylates

Quantitative analysis of nonylphenol ethoxylates in textiles using ultrasonic/microwave-assisted extraction coupled with ultra-high-performance supercritical fluid chromatography-photodiode array-tandem mass spectrometry

A sensitive and robust analytical method was developed for the simultaneous determination of nonylphenol ethoxylates (NPEOs) in textiles. The method utilizes ultra-high-performance supercritical fluid chromatography with photodiode array detection (UHPSFC-PDA) to assess monomer proportions across varying polymerization degrees, followed by quantitation via tandem mass spectrometry (UHPSFC-MS/MS) in multiple reaction monitoring (MRM) mode. Under optimized conditions, NPEOs (n = 2-39) were separated within 7 min on a BEH C18 column using compressed CO₂ and methanol as the mobile phase. Additionally, response surface methodology and Box-Behnken design were employed to optimize ultrasonic/microwave-assisted extraction (UMAE) parameters. The method demonstrated excellent linearity (R² > 0.99) for 13 NPEO homologues (n = 2-14), with limits of detection (LODs) and quantitation (LOQs) values ranging from 0.26 to 45.09 μg/kg and 2.28-188.06 μg/kg, respectively. Intra- and inter-day precision values ranged from 0.8 % to 4.23 % and from 1.34 % to 9.59 %, respectively. Recoveries at low, medium, and high spiking levels were between 71.1 % and 102.5 % (RSD ≤ 12.98 %). The method was validated using quality control standards and successfully applied to commercial textile samples, revealing NPEO concentrations up to 2626.63 μg/kg. The combination of UMAE with UHPSFC-PDA-MS/MS offers a rapid, sensitive, and environmentally friendly solution for comprehensive NPEO analysis in textiles.

Analysis of the Genomes and Adaptive Traits of Skermanella cutis sp. nov., a Human Skin Isolate, and the Type Strains Skermanella rosea and Skermanella mucosa

The genus Skermanella comprises important soil bacteria that are often associated with the crop rhizospheres, but its physiological traits remain poorly understood. This study characterizes Skermanella sp. TT6T, isolated from human skin, with a focus on its metabolic and environmental adaptations. Genome sequencing and phylogenomic analyses revealed that the strain TT6T is most closely related to S. rosea M1T, with average nucleotide identity and digital DNA-DNA hybridization values of 94.14% (±0.5%) and 64.7%, respectively. Comparative genomic analysis showed that the strains TT6T, S. rosea M1T and S. mucosa 8-14-6T share the Calvin cycle, and possess photosynthetic genes associated with the purple bacteria-type photosystem II. The strains TT6T and S. rosea M1T exhibited growth in a nitrogen-free medium under microaerobic conditions, which were generated in test tubes containing 0.1% soft agar. Under these conditions, with nitrate as a nitrogen source, S. rosea M1T formed gases, indicating denitrification. Strain TT6T also contains gene clusters involved in trehalose and carotenoid biosynthesis, along with salt-dependent colony morphology changes, highlighting its adaptive versatility. Genomic analyses further identified pathways related to hydrogenase and sulfur oxidation. Phenotypic and chemotaxonomic traits of strain TT6T were also compared with closely related type strains, confirming its genotypic and phenotypic distinctiveness. The new species, Skermanella cutis sp. nov., is proposed, with TT6T (=KCTC 82306T = JCM 34945T) as the type strain. This study underscores the agricultural and ecological significance of the genus Skermanella.

Transcriptional and post-transcriptional mechanisms modulate cyclopropane fatty acid synthase through small RNAs in Escherichia coli

The small RNA (sRNA) RydC strongly activates cfa, which encodes the cyclopropane fatty acid synthase. Previous work demonstrated that RydC activation of cfa increases the conversion of unsaturated fatty acids to cyclopropanated fatty acids in membrane lipids and changes the biophysical properties of membranes, making cells more resistant to acid stress. The regulators that control RydC synthesis had not previously been identified. In this study, we identify a GntR-family transcription factor, YieP, that represses rydC transcription. YieP positively autoregulates its own transcription and indirectly regulates cfa through RydC. We further identify additional sRNA regulatory inputs that contribute to the control of RydC and cfa. The translation of yieP is repressed by the Fnr-dependent sRNA, FnrS, making FnrS an indirect activator of rydC and cfa. Conversely, RydC activity on cfa is antagonized by the OmpR-dependent sRNA OmrB. Altogether, this work illuminates a complex regulatory network involving transcriptional and post-transcriptional inputs that link the control of membrane biophysical properties to multiple environmental signals.

IMPORTANCE

Bacteria experience many environmental stresses that challenge their membrane integrity. To withstand these challenges, bacteria sense what stress is occurring and mount a response that protects membranes. Previous work documented the important roles of small RNA (sRNA) regulators in membrane stress responses. One sRNA, RydC, helps cells cope with membrane-disrupting stresses by promoting changes in the types of lipids incorporated into membranes. In this study, we identified a regulator, YieP, that controls when RydC is produced and additional sRNA regulators that modulate YieP levels and RydC activity. These findings illuminate a complex regulatory network that helps bacteria sense and respond to membrane stress.

Fitness-Conditional Genes for Soil Adaptation in the Bioaugmentation Agent Pseudomonas veronii 1YdBTEX2

Strain inoculation (bioaugmentation) is a potentially useful technology to provide microbiomes with new functionalities. However, there is limited understanding of the genetic factors contributing to successful establishment of inoculants. This work aimed to characterize the genes implicated in proliferation of the monoaromatic compound-degrading Pseudomonas veronii 1YdBTEX2 in nonsterile polluted soils. We generated two independent mutant libraries by random minitransposon-delivered marker insertion followed by deep sequencing (Tn-seq) with a total of 5.0 × 10⁵ unique insertions. Libraries were grown in multiple successive cycles for up to 50 generations either in batch liquid medium or in two types of soil microcosms with different resident microbial content (sand or silt) in the presence of toluene. Analysis of gene insertion abundances at different time points (passed generations of metapopulation growth), in comparison to proportions at start and to in silico generated randomized insertion distributions, allowed to define ~800 essential genes common to both libraries and ~2,700 genes with conditional fitness effects in either liquid or soil (195 of which resulted in fitness gain). Conditional fitness genes largely overlapped among all growth conditions but affected approximately twice as many functions in liquid than in soil. This indicates soil to be a more promiscuous environment for mutant growth, probably because of additional nutrient availability. Commonly depleted genes covered a wide range of biological functions and metabolic pathways, such as inorganic ion transport, fatty acid metabolism, amino acid biosynthesis, or nucleotide and cofactor metabolism. Only sparse gene sets were uncovered whose insertion caused fitness decrease exclusive for soils, which were different between silt and sand. Despite detectable higher resident bacteria and potential protist predatory counts in silt, we were, therefore, unable to detect any immediately obvious candidate genes affecting P. veronii biological competitiveness. In contrast to liquid growth conditions, mutants inactivating flagella biosynthesis and motility consistently gained strong fitness advantage in soils and displayed higher growth rates than wild type. In conclusion, although many gene functions were found to be important for growth in soils, most of these are not specific as they affect growth in liquid minimal medium more in general. This indicates that P. veronii does not need major metabolic reprogramming for proliferation in soil with accessible carbon and generally favorable growth conditions. IMPORTANCE Restoring damaged microbiomes is still a formidable challenge. Classical widely adopted approaches consist of augmenting communities with pure or mixed cultures in the hope that these display their intended selected properties under in situ conditions. Ecological theory, however, dictates that introduction of a nonresident microbe is unlikely to lead to its successful proliferation in a foreign system such as a soil microbiome. In an effort to study this systematically, we used random transposon insertion scanning to identify genes and possibly, metabolic subsystems, that are crucial for growth and survival of a bacterial inoculant (Pseudomonas veronii) for targeted degradation of monoaromatic compounds in contaminated nonsterile soils. Our results indicate that although many gene functions are important for proliferation in soil, they are general factors for growth and not exclusive for soil. In other words, P. veronii is a generalist that is not a priori hindered by the soil for its proliferation and would make a good bioaugmentation candidate.

Complete Genome Sequence of Micrococcus yunnanensis TT9, Isolated from a Healthy Volunteer

Micrococcus yunnanensis TT9 was isolated from the forehead of human skin. This strain can grow on Triton X-100. We report the complete whole-genome sequence of this strain, which has one chromosome of 2,470,932 bp (73.0% G+C content) with 2,151 coding sequences.

Identification and Biodegradation Potential of a Novel Strain of Kosakonia oryzae Isolated from a Polyoxyethylene Tallow Amine Paddy Soil

Polyoxyethylene tallow amine (POEA) is a nonionic surfactant added to insecticide and herbicide formulations. Experimental data have been shown the toxic effects of POEA on aquatic organisms and remain to be a serious concern. In this study, total of thirty-two potential bacteria that were isolated from herbicide-contaminated soil samples showed the ability to use POEA as the sole carbon and energy source. In which, a bacterial strain LA was further investigated based on the efficiency utilization of POEA and classified as Kosakonia oryzae by the 16S rRNA gene. Response surface methodology was successfully applied to understand the interaction of distinct factors on POEA degradation by LA strain. Degradation of POEA was confirmed with UV-Visible spectrophotometric analysis and HPLC analysis. The POEA utilization mechanism was explored by target gene detection and carbon source utilization. The results indicate that strain LA has the potential to serve as an in situ candidate for bioremediation polluted by POEA.

Complete Genome Sequence of Aureimonas sp. Strain OT7, Isolated from Human Skin

Aureimonas sp. strain OT7 was isolated from human skin. This strain can grow on Triton X-100. Here, we present the complete whole-genome sequence of this species, which has one chromosome of 4,181,223 bp (G+C content, 65.05%). Analysis of the Aureimonas sp. strain OT7 genome sequence indicated potential for autotrophic growth.

Isolation and characterization of Aeromonas sp. TXBc10 capable of high-efficiency degradation of octylphenol polyethoxylate from tannery wastewater

Octylphenol polyethoxylate (OP _n EO) is a potential endocrine-disrupting chemical. Biodegradation of OP _n EO was investigated using the bacterium Aeromonas sp. TXBc10 isolated from the influent of tannery waste treatment plant in Hunan Province, China. The bacterium was capable of utilizing OP _n EO as the sole source of carbon and energy while OP _n EO was degraded under aerobic batch culture conditions. Microbial degradation of OP _n EO was studied in batch experiments for optimization of environmental factors. The effect of initial OP _n EO concentrations on the degradation was investigated between 100 and 1000 mg·L^-1 and the results showed that the biodegradation process conformed to the first-order kinetic model. The optimum pH, temperature, salinity and size of inoculum for OP _n EO degradation by Aeromonas sp. TXBc10 was found to be 8.0°C, 30°C, 2.5% and 2.0%, respectively. The major metabolites of OP _n EO degradation were identified as short-chain octylphenol polyethoxylate without octylphenol by high-performance liquid chromatography - mass spectrometer, which indicated that sequential cleavage of single ethoxylate units to form OP _{n- 1}EC might be the transformation mechanism of strain TXBc10. Considering that strain TXBc10 exhibits prominent advantage for biodegradation of OP _n EO, it might serve as a promising candidate for in situ remediation of OP _n EO and compounds with similar structure in tannery wastewater.

Bio-Fenton reaction involved in the cleavage of the ethoxylate chain of nonionic surfactants by dihydrolipoamide dehydrogenase from Pseudomonas nitroreducens TX1

Bacteria in the environment play a major role in the degradation of widely used man-made recalcitrant organic compounds. Pseudomonas nitroreducens TX1 is of special interest because of its high efficiency to remove nonionic ethoxylated surfactants. In this study, a novel approach was demonstrated by a bacterial enzyme involved in the formation of radicals to attack ethoxylated surfactants. The dihydrolipoamide dehydrogenase was purified from the crude extract of strain TX1 by using octylphenol polyethoxylate (OPEO_n) as substrate. The extent of removal of OPEOs during the degradation process was conducted by purified recombinant enzyme from E. coli BL21 (DE3) in the presence of the excess of metal mixtures (Mn²⁺, Mg²⁺, Zn²⁺, and Cu²⁺). The metabolites and the degradation rates were analyzed and determined by liquid chromatography-mass spectrometry. The enzyme was demonstrated to form Fenton reagent in the presence of an excess of metals. Under this in vitro condition, it was shown to be able to shorten the ethoxylate chains of OPEO_n. After 2 hours of reaction, the products obtained from the degradation experiment revealed a prominent ion peak at m/z = 493.3, namely the ethoxylate chain unit is 6 (OPEO₆) compared to OPEO₉ (m/z = 625.3), the main undegraded surfactant in the no enzyme control. It revealed that the concentration of OPEO₁₅ and OPEO₉ decreased by 90% and 40% after 4 hours, respectively. The disappearance rates for the OPEO_n homologs correlated to the length of the exothylate chains, suggesting it is not a specific enzymatic reaction which cleaves one unit by unit from the end of the ethoxylate chain. The results indicate the diverse and novel strategy by bacteria to catabolize organic compounds by using existing housekeeping enzyme(s).

Evaluation of the plant growth-promoting activity of Pseudomonas nitroreducens in Arabidopsis thaliana and Lactuca sativa

KEY MESSAGE

Pseudomonas nitroreducens: strain IHB B 13561 (PnIHB) enhances the growth of Arabidopsis thaliana and Lactuca sativa via the stimulation of cell development and nitrate absorption. Plant growth-promoting rhizobacteria (PGPR) enhance plant development through various mechanisms; they improve the uptake of soil resources by plants to greatly promote plant growth. Here, we used Arabidopsis thaliana seedlings and Lactuca sativa to screen the growth enhancement activities of a purified PGPR, Pseudomonas nitroreducens strain IHB B 13561 (PnIHB). When cocultivated with PnIHB, both species of plants exhibited notably improved growth, particularly in regard to biomass. Quantitative reverse transcription polymerase chain reaction analysis indicated high expression levels of the nitrate transporter genes, especially NRT2.1, which plays a major role in the high-affinity nitrate transport system in roots. Moreover, enhanced activity of the cyclin-B1 promoter was observed when wild-type 'Columbia-0' Arabidopsis seedlings were exposed to PnIHB, whereas upregulation of cyclin-B also occurred in the inoculated lettuce seedlings. Overall, these results suggest that PnIHB improves A. thaliana and L. sativa growth via specific pathways involved in the promotion of cell development and enhancement of nitrate uptake.

Cloning and expression of the carbaryl hydrolase gene mcbA and the identification of a key amino acid necessary for carbaryl hydrolysis

Carbamate hydrolase is the initial and key enzyme for degradation of carbamate pesticides. In the present study, we report the isolation of a carbaryl-degrading strain Pseudomonas sp. XWY-1, the cloning of its carbaryl hydrolase gene (mcbA) and the characterization of McbA. Strain XWY-1 was able to utilize carbaryl as a sole carbon source and degrade it using 1-naphthol as an intermediate. Transposon mutagenesis identified a mutant of XWY-1M that was unable to hydrolyze carbaryl. The transposon-disrupted gene mcbA was cloned by self-formed adaptor PCR, then expressed in Escherichia coli BL21(DE3) and purified. McbA was able to hydrolyze carbamate pesticides including carbaryl, isoprocarb, fenobucarb, carbofuran efficiently, while it hydrolyzed aldicarb, and propoxur poorly. The optimal pH of McbA was 7.0 and the optimal temperature was 40°C. The apparent K_m and k_cat values of McbA for carbaryl were 77.67±12.31μM and 2.12±0.10s^-1, respectively. Three amino acid residues (His467, His477 and His504) in the predicted polymerase/histidinol phosphatase-like domain were shown to be closely related to the activity of McbA, with His504 being the most important, as a replacement of His504 led to the complete loss of activity. This is the first study to identify key amino acids in McbA.

Complete Genome Sequences of Three Moraxella osloensis Strains Isolated from Human Skin

Here, we present the complete whole-genome sequences of three Moraxella osloensis strains with octylphenol polyethoxylate-degrading abilities. These strains were isolated from human skin.