Ecofriendly biosynthesis of copper nanoparticles from novel marine S. rhizophila species for enhanced antibiofilm, antimicrobial and antioxidant potential.

Marine microorganisms offer a promising avenue for the eco-friendly synthesis of nanoparticles due to their unique biochemical capabilities and adaptability to various environments. This study focuses on exploring the potential of a marine bacterial species, Stenotrophomonas rhizophila BGNAK1, for the synthesis of biocompatible copper nanoparticles and their application for hindering biofilms formed by monomicrobial species. The study begins with the isolation of the novel marine S. rhizophila species from marine soil samples collected from the West coast region of Kerala, India. The isolated strain is identified through 16S rRNA gene sequencing and confirmed to be S. rhizophila species. Biosynthesis of copper nanoparticles using S. rhizophila results in the formation of nanoparticles with size of range 10-50 nm. The nanoparticles exhibit a face-centered cubic crystal structure of copper, as confirmed by X-Ray Diffraction analysis. Furthermore, the synthesized nanoparticles display significant antimicrobial activity against various pathogenic bacteria and yeast. The highest inhibitory activity was against Staphylococcus aureus with a zone of 27 ± 1.00 mm and the least activity was against Pseudomonas aeruginosa with a zone of 22 ± 0.50 mm. The zone of inhibition against Candida albicans was 16 ± 0.60 mm. The antibiofilm activity against biofilm-forming clinical pathogens was evidenced by the antibiofilm assay and SEM images. Additionally, the copper nanoparticles exhibit antioxidant activity, as evidenced by their scavenging ability against DPPH, hydroxyl, nitric oxide, and superoxide radicals, as well as their reducing power in the FRAP assay. The study highlights the potential of the marine bacterium S. rhizophila BGNAK1 for the eco-friendly biosynthesis of copper nanoparticles with diverse applications. Synthesized nanoparticles exhibit promising antibiofilm, antimicrobial, and antioxidant properties, suggesting their potential utility in various fields such as medicine, wastewater treatment, and environmental remediation.

Biotransformation of diclofenac by Stenotrophomonas humi strain DIC_5 and toxicological examination of the resulting metabolites.

The widely used non-steroidal anti-inflammatory drug, diclofenac, detected in increasing concentrations in freshwater ecosystems, is among the most pressing environmental problems today. In this study, the bacterial isolate Stenotrophomonas humi strain DIC_5 was capable of degrading diclofenac. It eliminated 75.1% of diclofenac at an initial concentration of 1.5 mg/L after 8 days in the presence of glucose (3.0 g/L). During the process, nitro-diclofenac was identified as a resulting metabolite, whose concentration increased significantly in the bacterial medium from the 7th day of the experiment, while the concentration of diclofenac decreased correspondingly. The ecotoxicological tests on Aliivibrio fischeri and zebrafish embryos showed that the bacterial metabolites without diclofenac have a higher toxicity (up to 35.5% bacterial bioluminescence inhibition and 36.7% embryo mortality) than the diclofenac degradation residues (28% and 26.7%, respectively). Based on these results, neither diclofenac nor its degradation products exhibit toxic effects on the test organisms. Conversely, the toxic effect caused by the bacteria was reduced in the presence of diclofenac. Our work highlights the importance of using biotic controls in biotransformation trials, especially when the foreign material is applied in intermediate or environmentally relevant concentration ranges. KEY POINTS: • Biotransformation of diclofenac by bacteria isolated from a bacterial biofilm. • Biotransformation of diclofenac led to the formation of nitro-diclofenac. • Microorganisms are alternatives for reducing the concentration of diclofenac in water.

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.

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.

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.

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.

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.

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.

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.

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.

Genome analysis to decipher syntrophy in the bacterial consortium 'SCP' for azo dye degradation.

BACKGROUND: A bacterial consortium SCP comprising three bacterial members, viz. Stenotrophomonas acidaminiphila APG1, Pseudomonas stutzeri APG2 and Cellulomonas sp. APG4 was developed for degradation of the mono-azo dye, Reactive Blue 28. The genomic analysis of each member of the SCP consortium was done to elucidate the catabolic potential and role of the individual organism in dye degradation. RESULTS: The genes for glycerol utilization were detected in the genomes of APG2 and APG4, which corroborated with their ability to grow on a minimal medium containing glycerol as the sole co-substrate. The genes for azoreductase were identified in the genomes of APG2 and APG4, while no such trait could be determined in APG1. In addition to co-substrate oxidation and dye reduction, several other cellular functions like chemotaxis, signal transduction, stress-tolerance, repair mechanisms, aromatic degradation, and copper tolerance associated with dye degradation were also annotated. A model for azo dye degradation is postulated, representing the predominant role of APG4 and APG2 in dye metabolism while suggesting an accessory role of APG1. CONCLUSIONS: This exploratory study is the first-ever attempt to divulge the genetic basis of azo-dye co-metabolism by cross-genome comparisons and can be harnessed as an example for demonstrating microbial syntrophy.

Molecular mechanisms of heavy metals resistance of Stenotrophomonas rhizophila JC1 by whole genome sequencing.

In this study, a higher metal ions-resistant bacterium, Stenotrophomonas rhizophila JC1 was isolated from contaminated soil in Jinchang city, Gansu Province, China. The Pb2+ (120 mg/L) and Cu2+ (80 mg/L) removal rate of the strain reached at 76.9% and 83.4%, respectively. The genome comprises 4268161 bp in a circular chromosome with 67.52% G + C content and encodes 3719 proteins. The genome function analysis showed czc operon, mer operon, cop operon, arsenic detoxification system in strain JC1 were contributed to the removal of heavy metals. Three efflux systems (i.e., RND, CDF, and P-ATPase) on strain JC1 genome could trigger the removal of divalent cations from cells. cAMP pathway and ABC transporter pathway might be involved in the transport and metabolism of heavy metals. The homology analysis exhibited multi-gene families such as ABC transporters, heavy metal-associated domain, copper resistance protein, carbohydrate-binding domain were distributed across 410 orthologous groups. In addition, heavy metal-responsive transcription regulator, thioredoxin, heavy metal transport/detoxification protein, divalent-cation resistance protein CutA, arsenate reductase also played important roles in the heavy metals adsorption and detoxification process. The complete genome data provides insight into the exploration of the interaction mechanism between microorganisms and heavy metals.

Isolation and characterization of amoxicillin-resistant bacteria and amoxicillin-induced alteration in its protein profiling and RNA yield.

Amoxicillin-resistant bacteria were isolated using selective enrichment procedure. The morphological, biochemical and molecular characterization based on 16S rRNA gene sequencing and phylogenetic analysis of the bacterial strain WA5 confirmed that the strain belongs to the genus Stenotrophomonas. The bacteria were named as Stenotrophomonas sp. strain WA5 (MK110499). Substantial growth was seen in M9 minimal media supplemented with 5 mg L-1 of amoxicillin as a sole source of carbon and energy. RNA yield was also observed to be decreased in the presence of amoxicillin. Amoxicillin (5 mg L-1)-induced alteration is seen on bacterial protein profile and unique polypeptide bands were seen to be induced in the presence of amoxicillin, the bands were subjected to trypsin digestion, and LC-MS/MS analysis showed that the bands belong to the family of DNA-dependent RNA polymerase subunit ß (rpoC). Plasmid DNA isolation indicated the presence of antibiotic-resistant genes being harboured by the plasmid.

Bioaccumulation of lead, chromium, and nickel by bacteria from three different genera isolated from industrial effluent.

The potential of indigenous bacterial strains to accumulate three metals (Cr, Ni, Pb) was exploited here to remediate the polluted environment. In the present study, metal resistance profiles identified three most potential isolates which could tolerate 700-1000 µg/ml of Ni, 500-1000 µg/ml of Cr, and 1000-1600 µg/ml of Pb. These three bacterial strains were identified as Stenotrophomonas sp. MB339, Klebsiella pneumoniae MB361, and Staphylococcus sp. MB371. UV-Visible and atomic absorption spectrophotometric (AAS) analysis revealed gradual increase in percentage accumulation with increase in time due to increased biomass. Quantitative assessments exhibited maximum removal of Cr (83.51%) by Klebsiella pneumoniae MB361, Pb (85.30%), and Ni (48.78%) by Stenotrophomonas MB339, at neutral pH and 37 °C, whereas Staphylococcus sp. MB371 sorbed 88.33% of Pb at slightly acidic pH. The present study therefore supports the effective utilization of indigenous bacteria for comprehensive treatment of metal-rich industrial effluents.

Forest soil bacteria able to produce homo and copolymers of polyhydroxyalkanoates from several pure and waste carbon sources.

Two bacterial strains able to produce polyhydroxyalkanoates (PHAs) from a wide variety of pure carbon sources (dextrose, xylose, sucrose, lactose and glycerol) were isolated from forest soils and identified as Achromobacter mucicolens and Stenotrophomonas rhizophila. Achromobacter mucicolens also produced poly(3-hydroxybutyrate) (PHB) from different wastes (cheese whey, molasses, agave bagasse hydrolysate, nejayote and mango waste pulp). Stenotrophomonas rhizophila, produced the copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-co-HV) from glycerol (7·7 mol% of HV), and from sucrose with addition of propionic or valeric acid (4·5 and 25 mol% of HV, respectively). The copolymers presented a lower melting point (145, 156 and 127°C) and crystallinity (23, 26 and 16%) than PHB. The maximum biopolymer accumulation (PHB) for each strain growing in pure carbon source was as follows: 31·3 g per 100 g dry cell weight (DCW) for A. mucicolens from xylose; and 13·7 g per 100 g DCW for S. rhizophila from sucrose. Regarding the waste carbon sources, the highest PHB accumulation was obtained from agave bagasse hydrolysate (20·4 g per 100 g DCW) by A. mucicolens. The molecular weights of the biopolymers obtained ranged from 200 to 741 kDa. SIGNIFICANCE AND IMPACT OF THE STUDY: The economic cost of the carbon source for the culture of polyhydroxyalkanoates (PHAs)-producing microorganisms is one of the main process limitations. Therefore, it is vital to find versatile microorganisms able to grow and to accumulate homo and copolymers of PHAs from low-cost substrates. In this research, we report two bacterial strains that produce poly(3-hydroxybutyrate), poly(3-hydroxybutyrate-co-3-hydroxyvalerate) or both from at least five pure and five waste carbon sources. These results, by such bacterial strains have not been reported, especially the production of copolymer from glycerol without addition of precursors by Stenotrophomonas rhizophila and the production of PHB from xylose and agave bagasse hydrolysate by Achromobacter mucicolens.

Endophytic Bacteria Potentially Promote Plant Growth by Synthesizing Different Metabolites and their Phenotypic/Physiological Profiles in the Biolog GEN III MicroPlateTM Test.

Endophytic bacteria, as the most promising components of effective, biofertilizers biostimulating and biocontrol preparations, should be very intensively obtained from various plants and studied in terms of the conditions determining the potential ability to promote plant growth. For this reason, endophytic bacteria have been isolated from both stems and roots of up to six systematically distant species of vascular plants: one species belonging to the seedless vascular plants (Monilophyta), and five seed plants (Spermatophyta). The 23 isolated strains represented nine genera: Delftia, Stenotrophomonas, Rhizobium, Brevundimonas, Variovorax, Achromobacter, Novosphingobium, Comamonas and Collimonas, notably which were closely related-belonging to the phylum Proteobacteria. Stenotrophomonas sp. strains showed the greatest ability to synthesize indole-3-acetic acid (IAA)-like compounds, while Achromobacter sp. strains produced the highest levels of siderophores. The presence of the nifH gene and nitrogen binding activity was demonstrated for 95% of the strains tested. Stenotrophomonas maltophila (ES2 strain) showed the highest metabolic activity based on Biolog GEN III test. The ability to solubilize phosphate was determined only for three tested strains from genus: Delftia, Rhizobium and Novosphingobium. The presented work demonstrated that the metabolic and phenotypic properties of plant growth-promoting endophytes are correlated with the genus of bacteria and are not correlated with the host plant species or part of plant (stem, root).

The Bioreduction of Selenite under Anaerobic and Alkaline Conditions Analogous to Those Expected for a Deep Geological Repository System.

The environmental conditions for the planned geological disposal of radioactive waste -including hyper-alkaline pH, radiation or anoxia-are expected to be extremely harsh for microbial activity. However, it is thought that microbial communities will develop in these repositories, and this would have implications for geodisposal integrity and the control of radionuclide migration through the surrounding environment. Nuclear waste contains radioactive isotopes of selenium (Se) such as 79Se, which has been identified as one of the main radionuclides in a geodisposal system. Here, we use the bacterial species Stenotrophomonas bentonitica, isolated from bentonites serving as an artificial barrier reference material in repositories, to study the reduction of selenite (SeIV) under simulated geodisposal conditions. This bacterium is able to reduce toxic SeIV anaerobically from a neutral to alkaline initial pH (up to pH 10), thereby producing elemental selenium (Se0) nanospheres and nanowires. A transformation process from amorphous Se (a-Se) nanospheres to trigonal Se (t-Se) nanowires, through the formation of monoclinic Se (m-Se) aggregates as an intermediate step, is proposed. The lesser solubility of Se0 and t-Se makes S. bentonitica a potential candidate to positively influence the security of a geodisposal system, most probably with lower efficiency rates than those obtained aerobically.

Bioinformatics Analysis and Characterization of Highly Efficient Polyvinyl Alcohol (PVA)-Degrading Enzymes from the Novel PVA Degrader Stenotrophomonas rhizophila QL-P4.

Polyvinyl alcohol (PVA) is used widely in industry, and associated environmental pollution is a serious problem. Herein, we report a novel, efficient PVA degrader, Stenotrophomonas rhizophila QL-P4, isolated from fallen leaves from a virgin forest in the Qinling Mountains. The complete genome was obtained using single-molecule real-time (SMRT) technology and corrected using Illumina sequencing. Bioinformatics analysis revealed eight PVA/vinyl alcohol oligomer (OVA)-degrading genes. Of these, seven genes were predicted to be involved in the classic intracellular PVA/OVA degradation pathway, and one (BAY15_3292) was identified as a novel PVA oxidase. Five PVA/OVA-degrading enzymes were purified and characterized. One of these, BAY15_1712, a PVA dehydrogenase (PVADH), displayed high catalytic efficiency toward PVA and OVA substrate. All reported PVADHs only have PVA-degrading ability. Most importantly, we discovered a novel PVA oxidase (BAY15_3292) that exhibited higher PVA-degrading efficiency than the reported PVADHs. Further investigation indicated that BAY15_3292 plays a crucial role in PVA degradation in S. rhizophila QL-P4. Knocking out BAY15_3292 resulted in a significant decline in PVA-degrading activity in S. rhizophila QL-P4. Interestingly, we found that BAY15_3292 possesses exocrine activity, which distinguishes it from classic PVADHs. Transparent circle experiments further proved that BAY15_3292 greatly affects extracellular PVA degradation in S. rhizophila QL-P4. The exocrine characteristics of BAY15_3292 facilitate its potential application to PVA bioremediation. In addition, we report three new efficient secondary alcohol dehydrogenases (SADHs) with OVA-degrading ability in S. rhizophila QL-P4; in contrast, only one OVA-degrading SADH was reported previously.IMPORTANCE With the widespread application of PVA in industry, PVA-related environmental pollution is an increasingly serious issue. Because PVA is difficult to degrade, it accumulates in aquatic environments and causes chronic toxicity to aquatic organisms. Biodegradation of PVA, as an economical and environment-friendly method, has attracted much interest. To date, effective and applicable PVA-degrading bacteria/enzymes have not been reported. Herein, we report a new efficient PVA degrader (S. rhizophila QL-P4) that has five PVA/OVA-degrading enzymes with high catalytic efficiency, among which BAY15_1712 is the only reported PVADH with both PVA- and OVA-degrading abilities. Importantly, we discovered a novel PVA oxidase (BAY15_3292) that is not only more efficient than other reported PVA-degrading PVADHs but also has exocrine activity. Overall, our findings provide new insight into PVA-degrading pathways in microorganisms and suggest S. rhizophila QL-P4 and its enzymes have the potential for application to PVA bioremediation to reduce or eliminate PVA-related environmental pollution.

Essential Gene Clusters Identified in Stenotrophomonas MB339 for Multiple Metal/Antibiotic Resistance and Xenobiotic Degradation.

Stenotrophomonas MB339, a bacterium, which could potentially utilize aromatic compounds and tolerate different heavy metals was isolated from industrial wastewater. Subsequent experiments revealed strains ability to resist antibiotics ofloxacin, streptomycin, rifampicillin, erythromycin, ampicillin, clindamycin, and toxicants including As2+, Hg2+, Cu2+, Ni2+, Pb2+. The shotgun sequencing strategy, genome assembly and annotation uncovered specific features, which make this strain MB339 effectively promising to cope with highly contaminated conditions. This report presents isolate's assembled genome and its functional annotation identifying a set of protein coding genes (4711), tRNA (69 genes), and rRNA (9 genes). More than 2900 genes were assigned to various Clusters of Orthologous Groups (COGs) and 1114 genes attributed to 37 different Koyoto Encyclopedia of Genes and Genomes (KEGGs) pathways. Among these annotated genes, eighteen were for key enzymes taking part in xenobiotic degradation. Furthermore, 149 genes have been assigned to virulence, disease, and defense mechanisms responsible for multidrug and metal resistance including mercury, copper, and arsenic operons. These determinants comprised genes for membrane proteins, efflux pumps, and metal reductases, suggesting its potential applications in bioremediation.