Unveiling Agricultural Biotechnological Prospects: The Draft Genome Sequence of Stenotrophomonas geniculata LGMB417.

Stenotrophomonas species are recognized as rhizobacteria that play a pivotal role in promoting plant growth by making substantial contributions to enhanced soil fertility, nutrient recycling, and phytopathogen control. Employing them as bioinputs constitutes an environmentally sound strategy, particularly within the rhizospheric community. This study revealed the draft genome sequence of Stenotrophomonas geniculata LGMB417, which was originally isolated from root samples of maize (Zea mays L.). This research assessed the potential of a bacterial strain at the molecular level through genome mining, aiming to identify genes with biotechnological significance for promoting plant growth and protection. The assembly findings indicate that strain LGMB417 possesses a genome size of 4,654,011 bp, with a G + C content of 66.50%. The draft genome sequence revealed the presence of gene clusters responsible for the synthesis of secondary metabolites and carbohydrate active enzymes (CAZymes), glycoside hydrolases (23), glycosyltransferases (18), carbohydrate esterases (5), polysaccharide lyases (2), carbohydrate-binding modules (2), and auxiliary activities (1). Several genes related to growth promotion were found in the genome, including those associated with phosphate transport and solubilization, nitrogen metabolism, siderophore production and iron transport, hormonal modulation, stress responses (such as to drought, temperature fluctuations, osmotic challenges, and oxidative conditions), and volatile organic compounds (VOCs). Subsequent phases will encompass investigations utilizing gene expression methodologies, with future explorations concentrating on facets pertinent to agricultural production, including comprehensive field studies.

Antifungal Activity and Mechanisms of 2-Ethylhexanol, a Volatile Organic Compound Produced by Stenotrophomonas sp. NAU1697, against Fusarium oxysporum f. sp. cucumerinum.

Researchers often consider microorganisms from Stenotrophomonas sp. to be beneficial for plants. In this study, the biocidal effects and action mechanisms of volatile organic compounds (VOCs) produced by Stenotrophomonas sp. NAU1697 were investigated. The mycelial growth and spore germination of Fusarium oxysporum f. sp. cucumerinum (FOC), which is a pathogen responsible for cucumber wilt disease, were significantly inhibited by VOCs emitted from NAU1697. Among the VOCs, 33 were identified, 11 of which were investigated for their antifungal properties. Among the tested compounds, 2-ethylhexanol exhibited the highest antifungal activity toward FOC, with a minimum inhibitory volume (MIV) of 3.0 µL/plate (equal to 35.7 mg/L). Damage to the hyphal cell wall and cell membrane integrity caused a decrease in the ergosterol content and a burst of reactive oxygen species (ROS) after 2-ethylhexanol treatment. DNA damage, which is indicative of apoptosis-like cell death, was monitored in 2-ethylhexanol-treated FOC cells by using micro-FTIR analysis. Furthermore, the activities of mitochondrial dehydrogenases and mitochondrial respiratory chain complex III in 2-ethylhexanol-treated FOC cells were significantly decreased. The transcription levels of genes associated with redox reactions and the cell wall integrity (CWI) pathway were significantly upregulated, thus indicating that stress was caused by 2-ethylhexanol. The findings of this research provide a new avenue for the sustainable management of soil-borne plant fungal diseases.

Comparative transcriptomics revealed the mechanism of Stenotrophomonas rhizophila JC1 response and biosorption to Pb2.

Nowadays, there is limited research focusing on the biosorption of Pb2+ through microbial process, particularly at the level of gene expression. To overcome this knowledge gap, we studied the adsorption capacity of Stenotrophomonas rhizophila JC1 to Pb2+, and investigated the physiological mechanism by means of SEM, EDS, FTIR, membrane permeability detection, and investigated the molecular mechanism through comparative transcriptomics. The results showed that after 16 h of cultivation, the biosorption capacity of JC1 for 100 mg/L of Pb2+ reached at 79.8%. The main mechanism of JC1 adsorb Pb2+ is via intracellular accumulation, accounting for more than 90% of the total adsorption. At the physiological level, Pb2+ can precipitate with anion functional groups (e.g., -OH, -NH) on the bacterial cell wall or undergo replacement reaction with cell component elements (e.g., Si, Ca) to adsorb Pb2+ outside of the cell wall, thus accomplishing extracellular adsorption of Pb2+ by strains. Furthermore, the cell membrane acts as a "switch" that inhibits the entry of metal ions into the cell from the plasma membrane. At the molecular level, the gene pbt specificity is responsible for the adsorption of Pb2+ by JC1. In addition, phosphate permease is a major member of the ABC transporter family involved in Pb2+, and czcA/cusA or Co2+/Mg2+ efflux protein plays an important role in the efflux of Pb2+ in JC1. Further, cellular macromolecule biosynthesis, inorganic cation transmembrane transport, citrate cycle (TCA) and carbon metabolism pathways all play crucial roles in the response of strain JC1 to Pb2+ stress.

Mechanistic insights into tris(2-chloroisopropyl) phosphate biomineralization coupled with lead (II) biostabilization driven by denitrifying bacteria.

The ubiquity and persistence of organophosphate esters (OPEs) and heavy metal (HMs) pose global environmental risks. This study explored tris(2-chloroisopropyl)phosphate (TCPP) biomineralization coupled to lead (Pb2+) biostabilization driven by denitrifying bacteria (DNB). The domesticated DNB achieved synergistic bioremoval of TCPP and Pb2+ in the batch bioreactor (efficiency: 98 %).TCPP mineralized into PO43- and Cl-, and Pb2+ precipitated with PO43-. The TCPP-degrading/Pb2+-resistant DNB: Achromobacter, Pseudomonas, Citrobacter, and Stenotrophomonas, dominated the bacterial community, and synergized TCPP biomineralization and Pb2+ biostabilization. Metagenomics and metaproteomics revealed TCPP underwent dechlorination, hydrolysis, the TCA cycle-based dissimilation, and assimilation; Pb2+ was detoxified via bioprecipitation, bacterial membrane biosorption, EPS biocomplexation, and efflux out of cells. TCPP, as an initial donor, along with NO3-, as the terminal acceptor, formed a respiratory redox as the primary energy metabolism. Both TCPP and Pb2+ can stimulate phosphatase expression, which established the mutual enhancements between their bioconversions by catalyzing TCPP dephosphorylation and facilitating Pb2+ bioprecipitation. TCPP may alleviate the Pb2+-induced oxidative stress by aiding protein phosphorylation. 80 % of Pb2+ converted into crystalized pyromorphite. These results provide the mechanistic foundations and help develop greener strategies for synergistic bioremediation of OPEs and HMs.

In vitro and in vivo screening of bacterial species from contaminated soil for heavy metal biotransformation activity.

Heavy metals (HMs) are widely used in various industries. High concentrations of HMs can be severely toxic to plants, animals and humans. Microorganism-based bioremediation has shown significant potential in degrading and detoxifying specific HM contaminants. In this study, we cultivated a range of bacterial strains in liquid and solid nutrient medium containing different concentrations of different HMs to select and analyze bacteria capable of transforming HMs. The bacterial strains most resistant to selected HMs and exhibiting the ability to remove HMs from contaminated soils were identified. Then, the bacterial species capable of utilizing HMs in soil model experiments were selected, and their ability to transform HMs was evaluated. This study has also generated preliminary findings on the use of plants for further removal of HMs from soil after microbial bioremediation. Alcaligenes faecalis, Delftia tsuruhatensis and Stenotrophomonas sp. were selected for their ability to grow in and utilize HM ions at the maximum permissible concentration (MPC) and two times the MPC. Lysinibacillus fusiformis (local microflora) can be used as a universal biotransformation tool for many HM ions. Brevibacillus parabrevis has potential for the removal of lead ions, and Brevibacillus reuszeri and Bacillus safensis have potential for the removal of arsenic ions from the environment. The bacterial species have been selected for bioremediation to remove heavy metal ions from the environment.

Characterization of the extended substrate spectrum of the class A ß-lactamase CESS-1 from Stenotrophomonas sp. and structure-based investigation into its substrate preference.

OBJECTIVES: Stenotrophomonas spp. intrinsically resistant to many ß-lactam antibiotics are found throughout the environment. CESS-1 identified in Stenotrophomonas sp. KCTC 12332 is an uncharacterized class A ß-lactamase. The goal of this study was to reveal biochemical and structural characteristics of CESS-1. METHODS: The hydrolytic activities of CESS-1 towards penicillins (penicillin G and ampicillin), cephalosporins (cephalexin, cefaclor, and cefotaxime), and carbapenems (imipenem and meropenem) was spectrophotometrically monitored. Structural information on E166Q mutants of CESS-1 acylated by cefaclor, cephalexin, or ampicillin were determined by X-ray crystallography. RESULTS: CESS-1 displayed hydrolytic activities toward penicillins and cephalosporins, with negligible activity toward carbapenems. Although cefaclor, cephalexin, and ampicillin have similar structures with identical R1 side chains, the catalytic parameters of CESS-1 toward them were distinct. The kcat values for cefaclor, cephalexin, and ampicillin were 1249.6 s-1, 204.3 s-1, and 69.8 s-1, respectively, with the accompanying KM values of 287.6 µM, 236.7 µM, and 28.8 µM, respectively. CONCLUSIONS: CESS-1 was able to discriminate between cefaclor and cephalexin with a single structural difference at C3 position: -Cl (cefaclor) and -CH3 (cephalexin). Structural comparisons among three E166Q mutants of CESS-1 acylated by cefaclor, cephalexin, or ampicillin, revealed that cooperative positional changes in the R1 side chain of substrates and their interaction with the ß5-ß6 loop affect the distance between Asn170 and the deacylating water at the acyl-enzyme intermediate state. This is directly associated with the differential hydrolytic activities of CESS-1 toward the three structurally similar ß-lactam antibiotics.

Degradation of tetracycline, oxytetracycline & ampicillin by purified multiple copper oxidase like laccase from Stentrophomonas sp. YBX1.

Multiple copper oxidase (MCO) like laccase is widely distributed in higher plant, fungi and bacteria. This study identified MCO like laccase producing bacterium isolated from a wastewater treatment plant based on 16S rRNA sequence analysis, and they were further confirmed by phylogenetic reconstruction. Biochemical and gene characterization of MCO like laccase from Stenotrophomonas sp. YBX1 is presented. Purification of MCO like laccase was carried out by ion exchange HQ Trap column and followed by gel filtration spheracryl S-100 column. The purified MCO like laccase from Stenotrophomonas sp. YBX1 shows a total activity of 1252 units and specific activity 391.2 U/mg and protein concentration 0.32 mg/mL. In SDS PAGE, the approximate molecular mass was found at 66 kDa and further confirmed from an MS spectrum of MALDI-TOF. The purified MCO like laccase is capable of degradation of antibiotics such as tetracycline completely, whereas oxytetracycline (78%) and ampicillin (62%) degraded within 96 min without any redox mediators at pH 5 and 30 ºC. Its degradation pathway was based on identification of metabolites by LC-MS spectrum. The enzymatic degradation may be used in advanced treatment of antibiotics containing wastewater.

Identification and characterization of a versatile keratinase, KerZJ, from Stenotrophomonas sp. LMY.

Keratinases have drawn increasing attention in recent decades owing to their catalytic versatility and broad applications from agriculture to medicine. In the present study, we isolated a highly keratinolytic and fibrinolytic bacterium from the campus soil and named it Stenotrophomonas sp. LMY based on genetic information. To identify the potential keratinase genes, the genome sequence of the strain was obtained and analyzed. Sequence alignment and comparison revealed that the protein 1_737 (KerZJ) had the highest sequence homology to a reported keratinase KerBL. We recombinantly expressed KerZJ in Escherichia coli Origami™ (DE) pLysS and purified it to homogeneity. KerZJ showed the highest activity at 40 °C and pH 9.0, and metal ions exhibited no significant effects on its activity. Although reducing agents would break the disulfide bonds in KerZJ and reduce its activity, KerZJ still exhibited the ability to hydrolyze feather keratin in the presence of ß-ME. KerZJ could efficiently digest human prion proteins. In addition, KerZJ showed fibrinolytic activity on fibrin plates and effectively eliminated blood clots in a thrombosis mouse model without side effects. Our results suggest that KerZJ is a versatile keratinase with significant potential for keratin treatment, decontamination of prions, and fibrinolytic therapy.

Biodegradation and Detoxification of Low-Density Polyethylene (LDPE) by Stenotrophomonas sp. and Alcaligenaceae bacterium.

Every year, human activities introduce large amounts of synthetic plastics into the environment. Decomposition of the plastic derivatives is very difficult and time consuming, so it is essential to eliminate these pollutants using different methods. Bioremediation, is suitable option, because of the low cost and environmentally safe. In this research, degradation of low-density polyethylene (LDPE) was investigated by two strains, isolated from Hamadan province (Iran) landfill soil. After identification by 16sr DNA primers, their abilities of polyethylene biodegradation were examined by Fourier transform infrared (FTIR), SEM and Gas Chromatography-Mass Spectrometry (GC-MS). Using media contain polyethylene) after and before addition of bacteria), toxicity test was conducted by measuring the germination index, root and hypocotyl length of Lactuca sativa seed. After three months, 10.15% ± 1.04 weight loss of LDPE achieved through strain Stenotrophomonas sp. degradation. Both strains had high biofilm formation capacity, confirmed by Electron microscope images and FTIR analysis. GC-MS confirmed the presence of the end-product of LDPE degradation (Pentacosane, Hexacosane, and Octadecane). Both, Stenotrophomonas sp. and Alcaligenaceae bacterium had significant detoxification ability. In media contain LDPE (without bacteria), decrease in the germination of lettuce seeds was observed.

The mechanism of Se(IV) multisystem resistance in Stenotrophomonas sp. EGS12 and its prospect in selenium-contaminated environment remediation.

Human activities have led to elevated levels of selenium (Se) in the environment, which poses a threat to ecosystems and human health. Stenotrophomonas sp. EGS12 (EGS12) has been identified as a potential candidate for the bioremediation of repair selenium-contaminated environment because of its ability to efficiently reduce Se(IV) to form selenium nanospheres (SeNPs). To better understand the molecular mechanism of EGS12 in response to Se(IV) stress, a combination of transmission electron microscopy (TEM), genome sequencing techniques, metabolomics and transcriptomics were employed. The results indicated that under 2 mM Se(IV) stress, 132 differential metabolites (DEMs) were identified, and they were significantly enriched in metabolic pathways such as glutathione metabolism and amino acid metabolism. Under the Se(IV) stress of 2 mM, 662 differential genes (DEGs) involved in heavy metal transport, stress response, and toxin synthesis were identified in EGS12. These findings suggest that EGS12 may respond to Se(IV) stress by engaging various mechanisms such as forming biofilms, repairing damaged cell walls/cell membranes, reducing Se(IV) translocation into cells, increasing Se(IV) efflux, multiplying Se(IV) reduction pathways and expelling SeNPs through cell lysis and vesicular transport. The study also discusses the potential of EGS12 to repair Se contamination alone and co-repair with Se-tolerant plants (e.g. Cardamine enshiensis). Our work provides new insights into microbial tolerance to heavy metals and offers valuable information for bio-remediation techniques on Se(IV) contamination.

Combined bioreduction and volatilization of SeVI by Stenotrophomonas bentonitica: Formation of trigonal selenium nanorods and methylated species.

Nowadays, metal pollution due to the huge release of toxic elements to the environment has become one of the world's biggest problems. Bioremediation is a promising tool for reducing the mobility and toxicity of these contaminants (e.g. selenium), being an efficient, environmentally friendly, and inexpensive strategy. The present study describes the capacity of Stenotrophomonas bentonitica to biotransform SeVI through enzymatic reduction and volatilization processes. HAADF-STEM analysis showed the bacterium to effectively reduce SeVI (200 mM) into intra- and extracellular crystalline Se0 nanorods, made mainly of two different Se allotropes: monoclinic (m-Se) and trigonal (t-Se). XAS analysis appears to indicate a Se crystallization process based on the biotransformation of amorphous Se0 into stable t-Se nanorods. In addition, results from headspace analysis by gas chromatography-mass spectometry (GC-MS) revealed the formation of methylated volatile Se species such as DMSe (dimethyl selenide), DMDSe (dimethyl diselenide), and DMSeS (dimethyl selenenyl sulphide). The biotransformation pathways and tolerance are remarkably different from those reported with this bacterium in the presence of SeIV. The formation of crystalline Se0 nanorods could have positive environmental implications (e.g. bioremediation) through the production of Se of lower toxicity and higher settleability with potential industrial applications.

Synergy of surface adsorption and intracellular accumulation for removal of uranium with Stenotrophomonas sp: Performance and mechanisms.

Uranium is well-known to have serious adverse effects on the ecological environment and human health. Bioremediation stands out among many remediation methods owing to its being economically feasible and environmentally friendly. This study reported a great promising strategy for eliminating uranium by Stenotrophomonas sp. CICC 23833 in the aquatic environment. The bacterium demonstrated excellent uranium adsorption capacity (qmax = 392.9 mg/g) because of the synergistic effect of surface adsorption and intracellular accumulation. Further analysis revealed that hydroxyl, carboxyl, phosphate groups and proteins of microorganisms were essential in uranium adsorption. Intracellular accumulation was closely related to cellular activity, and the efficiency of uranium processing by the permeabilized bacterial cells was significantly improved. In response to uranium stress, the bacterium was found to release multiple ions in conjunction with uranium adsorption, which facilitates the maintenance of bacterial life activities and the conversion of uranyl to precipitates. These above results indicated that Stenotrophomonas sp. Had great potential application value for the remediation of uranium.

Comparative transcriptomic analysis of Stenotrophomonas sp. MNB17 revealed mechanisms of manganese tolerance at different concentrations and the role of histidine biosynthesis in manganese removal.

Bacteria possess protective mechanisms against excess Mn(Ⅱ) to reduce its toxicity. Stenotrophomonas sp. MNB17 showed high Mn(Ⅱ) removal capacity (92.24-99.16 %) by forming Mn-precipitates (MnCO3 and Mn-oxides), whose Mn-oxides content increased with increasing Mn(Ⅱ) concentrations (10-50 mM). Compared with 0 mM Mn(Ⅱ)-stressed cells, transcriptomic analysis identified genes with the same transcriptional trends in 10 mM and 50 mM Mn(Ⅱ)-stressed cells, including genes involved in metal transport, cell envelope homeostasis, and histidine biosynthesis, as well as genes with different transcriptional trends, such as those involved in oxidative stress response, glyoxylate cycle, electron transport, and protein metabolism. The upregulation of histidine biosynthesis and oxidative stress responses were the most prominent features of these metabolisms under Mn(Ⅱ) stress. We confirmed that the increased level of reactive oxygen species was one of the reasons for the increased Mn-oxides formation at high Mn(Ⅱ) concentrations. Metabolite analysis indicated that the enhanced histidine biosynthesis rather than the tricarboxylic acid cycle resulted in an elevated level of α-ketoglutarate, which helped eliminate reactive oxygen species. Consistent with these results, the exogenous addition of histidine significantly reduced the production of reactive oxygen species and Mn-oxides and enhanced the removal of Mn(Ⅱ) as MnCO3. This study is the first to correlate histidine biosynthesis, reactive oxygen species, and Mn-oxides formation at high Mn(Ⅱ) concentrations, providing novel insights into the molecular regulatory mechanisms associated with Mn(Ⅱ) removal in bacteria.

Isoenzyme N-Acyl-l-Amino Acid Amidohydrolase NA Increases Ochratoxin A Degradation Efficacy of Stenotrophomonas sp. CW117 by Enhancing Amidohydrolase ADH3 Stability.

Ochratoxin A (OTA) is a potent mycotoxin mainly produced by toxicogenic strains of Aspergillus spp. and seriously contaminates foods and feedstuffs. OTA detoxification strategies are significant to food safety. A superefficient enzyme ADH3 to OTA hydrolysis was isolated from the difunctional strain Stenotrophomonas sp. CW117 in our previous study. Here, we identified a gene N-acyl-l-amino acid amidohydrolase NA, which is an isoenzyme of ADH3. However, it is not as efficient a hydrolase as ADH3. The kinetic constant showed that the catalytic efficiency of ADH3 (Kcat/Km = 30,3938 s-1 · mM-1) against OTA was 29,113 times higher than that of NA (Kcat/Km = 10.4 s-1 · mM-1), indicating that ADH3 was the overwhelming superior detoxifying gene in CW117. Intriguingly, when gene na was knocked out from the CW117 genome, degradation activity of the Δna mutant was significantly reduced at the first 6 h, suggesting that the two enzymes might have an interactive effect on OTA transformation. Gene expressions and Western blotting assay showed that the Δna mutant and wild-type CW117 showed similar adh3 expression levels, but na deficiency decreased ADH3 protein level in CW117. Collectively, isoenzyme NA was identified as a factor that improved the stability of ADH3 in CW117 but not as a dominant hydrolase for OTA transformation. IMPORTANCE Ochratoxin A (OTA) is a potent mycotoxin mainly produced by toxicogenic strains of Aspergillus spp. and seriously contaminates foods and feedstuffs. Previous OTA detoxification studies mainly focused on characterizations of degradation strains and detoxifying enzymes. Here, we identified a gene N-acyl-l-amino acid amidohydrolase NA from strain CW117, which is an isoenzyme of the efficient detoxifying enzyme ADH3. Isoenzyme NA was identified as a factor that improved the stability of ADH3 in CW117 and, thus, enhanced the degradation activity of the strain. This is the first study on an isoenzyme improving the stability of another efficient detoxifying enzyme in vivo.

Transcriptome Profiling of Stenotrophomonas sp. Strain WZN-1 Reveals Mechanisms of 2,2',4,4'-Tetrabromodiphenyl Ether (BDE-47) Biotransformation.

The brominated flame retardant 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) is extensively used, stable, and difficult to degrade in the environment. The existence of BDE-47 could pose a certain risk to the environment and human health. However, the biotransformation mechanisms of BDE-47 by microorganisms remain unclear. In this study, aerobic degradation of BDE-47 by Stenotrophomonas sp. strain WZN-1 and transcriptome analysis were carried out. BDE-47 degradation by Stenotrophomonas sp. strain WZN-1 was mainly through the biological action of intracellular enzymes via the route of debromination and hydroxylation. The results of the transcriptome sequencing indicated the differentially expressed genes were related to transport, metabolism, and stress response. The key processes involved the microbial transmembrane transportation of BDE-47, energy anabolism, synthesis, and metabolism of functional enzymes, stress response, and other biological processes of gene regulation. In particular, bacterial chemotaxis played a potential role in biodegradation of BDE-47 by Stenotrophomonas sp. strain WZN-1. This study provides the first insights into the biotransformation of Stenotrophomonas sp. strain WZN-1 to BED-47 stress and shows potential for application in remediation of polluted environments.

Diffusible signal factor enhances the saline-alkaline resistance and rhizosphere colonization of Stenotrophomonas rhizophila by coordinating optimal metabolism.

Quorum sensing (QS) regulates various physiological processes in a cell density-dependent mode via cell-cell communication. Stenotrophomonas rhizophila DSM14405T having the diffusible signal factor (DSF)-QS system, is a plant growth-promoting rhizobacteria (PGPR) that enables host plants to tolerate saline-alkaline stress. However, the regulatory mechanism of DSF-QS in S. rhizophila is not fully understood. In this study, we used S. rhizophila DSM14405T wild-type (WT) and an incompetent DSF production rpfF-knockout mutant to explore the regulatory role of QS in S. rhizophila growth, stress responses, biofilm formation, and colonization under saline-alkaline stress. We found that a lack of DSF-QS reduces the tolerance of S. rhizosphere ΔrpfF to saline-alkaline stress, with a nearly 25-fold reduction in the ΔrpfF population compared with WT at 24 h under stress. Transcriptome analysis revealed that QS helps S. rhizophila WT respond to saline-alkaline stress by enhancing metabolism associated with the cell wall and membrane, oxidative stress response, cell adhesion, secretion systems, efflux pumps, and TonB systems. These metabolic systems enhance penetration defense, Na+ efflux, iron uptake, and reactive oxygen species scavenging. Additionally, the absence of DSF-QS causes overexpression of biofilm-associated genes under the regulation of sigma 54 and other transcriptional regulators. However, greater biofilm formation capacity confers no advantage on S. rhizosphere ΔrpfF in rhizosphere colonization. Altogether, our results show the importance of QS in PGPR growth and colonization; QS gives PGPR a collective adaptive advantage in harsh natural environments.

The role of nitrogen metabolism on polyethylene biodegradation.

Polyethylene (PE) is the most widely used plastic and its accumulation on natural environments has reached alarming levels causing severe damage to wildlife and human health. Despite the significance of this global issue, little is known about specific metabolic mechanisms behind PE biodegradation-a promising and sustainable remediation method. Herein, we describe a novel role of nitrogen metabolism in the fragmentation and oxidation of PE mediated by biological production of NOx in three PE-degrading strains of Comamonas, Delftia, and Stenotrophomonas. Resultant nitrated PE fragments are assimilated and then metabolized by these bacteria in a process assisted by nitronate monooxygenases and nitroreductases to support microbial growth. Due to the conservation of nitrogen metabolism genes, we anticipate that this oxidative mechanism is potentially shared by other nitrifier and denitrifier microbes.

Development and Application of a New Arabinose-Inducible Vector in High-Attachment Strain Stenotrophomonas AGS-1 from Aerobic Granular Sludge.

To explore the molecular structure of attachment genes, we constructed and characterized a new arabinose-inducible vector for the high-attachment strain Stenotrophomonas AGS-1 isolated from aerobic granular sludge (AGS). mCherry was used as a simple observation biomarker, and the araC-PBAD-inducible promoter was chosen to artificially regulate the expression of target genes. The system achieved little leaky basal expression and high maximal induced expression. The araC-PBAD-based inducible expression was modulated over a wide range of 0.0005 to 0.2% l-arabinose. Notably, a "lag expression" phenomenon was observed in which mCherry was expressed after bacterial growth in LB medium. Using the system and the strategy of fusion expression of target genes (rmlA and AsCas12a) plus mCherry, the recombinant AGS-1 strain achieved the effective induction of rmlA and AsCas12a-mCherry gene expression in the range of 0.0005 to 0.1% l-arabinose. These results demonstrate that the new arabinose-inducible vector could be used as an important molecular tool in the gene function and genome-editing research of strain AGS-1.

Kinetics and molecular mechanism of enhanced fluoranthene biodegradation by co-substrate phenol in co-culture of Stenotrophomonas sp. N5 and Advenella sp. B9.

Polycyclic aromatic hydrocarbons (PAHs) and phenol are persistent pollutants that coexist in coking wastewater (CWW). Fluoranthene (Flu) is the predominant PAH species in the CWW treatment system. Our work emphasized on distinguishing the effects of phenol on Flu biodegradation by co-culture of Stenotrophomonas sp. N5 and Advenella sp. B9 and illustrated the molecular mechanisms. Results showed Flu biodegradation by co-culture was enhanced by phenol. According to the first-order degradation kinetic analysis of Flu, phenol significantly increased the biodegradation rate constant and shortened the half-life of Flu. Transcriptome analysis pointed out the up-regulation of DNA repair activity and 3717 significantly differentially expressed genes (DEGs), were triggered by 800 mg/L phenol. GO enrichment analysis suggested these DEGs are mainly concentrated in biochemical processes such as metal ion binding and alpha-amino acid biosynthesis, which are closely associated with Flu biodegradation, indicating that phenol promotes DNA repair activity and reduces Flu genotoxicity. qRT-PCR was performed to detect the gene expression of aromatic ring-opening dioxygenase. Combined with transcriptome analysis, the qRT-PCR results suggested phenol did not induce the expression of related PAHs-degrading enzymes. RNA extraction and microbial growth curves of COC and COC + Ph provided further evidence that phenol serves as co-substrate which increases biomass and the concentration of degrading enzymes, therefore promoting the Flu degradation.

The decolorization and degradation of azo dyes by two Stenotrophomonas strains isolated from textile effluent (Tepetitla, Mexico).

Stenotrophomonas' metabolic versatility plays important roles in the remediation of contaminated environment and plant growth promotion. We investigated two Stenotrophomonas strains isolated from textile polluted sewage for their ability to decolorize and degrade azo dyes. Two Stenotrophomonas strains (TepeL and TepeS) were isolated from textile effluents (Tepetitla, Mexico) using the selective agar Stenotrophomonas vancomycin, imipenem, amphotericin B agar (SVIA). Isolates' identity was determined by the sequencing of their partial 16S rRNA fragments. Their abilities to decolorize dyes were tested in a Luria broth supplemented with varying concentrations (50 mg/L-1 g/L) of textile dyes (acidic red, methyl orange, reactive green, acidic yellow, and reactive black). Fourier-transform infrared (FTIR) spectroscopy and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) metabolite analyses were used to determine the effect of the isolates' growth on the dyes (acidic red, methyl orange). We also identified the enzymes that may be involved in the degradation process. Phylogenetic analysis based on the 16S rDNA sequences showed that the isolates belong to the genus Stenotrophomonas. Stenotrophomonas sp. TepeL and TepeS respectively decolorize all the azo dyes at the tested concentration except at 1 g/L and degraded the azo dyes. The degradation resulted in the formation of N, N-dimethyl p-phenylenediamine, and sodium 4-amino-1-naphthalenesulfonate from methyl orange and acid red. TepeL and TepeS rapidly decolorized and degraded the azo dyes tested. This result showed that the two isolates have a good potential for the decontamination of textile effluents.