DMF mineralization and substrate specificity mechanism of Aminobacter ciceronei DMFA1.

N,N-dimethylformamide (DMF) is widely used in various industries, but its direct release into water poses high risks to human beings. Although a lot of DMF-degrading bacteria has been isolated, limited studies focus on the degradation preference among DMF and its analogues. In this study, an efficient DMF mineralization bacterium designated Aminobacter ciceronei DMFA1 was isolated from marine sediment. When exposed to a 0.2% DMF (∼1900 mg/L), strain DMFA1 exhibited a degradation efficiency of 100% within 4 days. The observed growth using formamide as the sole carbon source implied the possible DMF degradation pathway of strain DMFA1. Meanwhile,the strain DMFA1 possesses a broad-spectrum substrate degradation, which could effectively degraded 0.2% N,N-dimethylacetamide (DMAC) and N-methylformamide (NMF). Genomic analysis further confirmed the supposed pathway through annotating the genes encoding N, N-dimethylformamidase (DMFase), formamidase, and formate dehydrogenase. The existence of sole DMFase indicating its substrate specificity controlled the preference of DMAc of strain DMFA1. By integrating multiple sequence alignment, homology modeling and molecular docking, the preference of the DMFase in strain DMFA1 towards DMAc are related to: 1) Mutations in key active site residues; 2) the absence of small subunit; and 3) no energy barrier for substrates entering the active site.

Aerobic degradation of bisphenol A by Pseudomonas sp. LM-1: characteristic and pathway.

Bisphenol A (BPA) has been widely used in the manufacture of polymeric materials. BPA is regarded as an endocrine disrupting chemical, posing a great threat to the public health. In this study, a bacterial strain LM-1, capable of utilizing BPA as the sole carbon and energy source under aerobic conditions, was originally isolated from an activated sludge sample. The isolate was identified as Pseudomonas sp. based on 16S rRNA gene sequence analysis. Strain LM-1 was able to completely degrade 25-100 mg/L BPA within 14-24 h, and it also exhibited high capacity for BPA degradation at a range of pH (6.0-8.0). (NH4)2SO4 and NH4NO3 were the suitable nitrogen sources for its growth and BPA biodegradation, and the BPA degradation could be accelerated when exogenous carbon sources were introduced as the co-substrates. Metal ions such as Zn2+, Cu2+, and Ni2+ could considerably suppress the growth of strain LM-1 and BPA degradation. According to the analysis of liquid chromatography coupled to Q-Exactive high resolution mass spectrometry, hydroquinone, p-hydroxybenzaldehyde, and p-hydroxybenzoate were the predominate metabolites in the BPA biodegradation and the degradation pathways were proposed. This study is important for assessment of the fate of BPA in engineered and natural systems and possibly for designing bioremediation strategies.

Performance and microbial community analysis of bioaugmented activated sludge for nitrogen-containing organic pollutants removal.

Nitrogen-containing organic pollutants (quinoline, pyridine and indole) are widely distributed in coking wastewater, and bioaugmentation with specific microorganisms may enhance the removal of these recalcitrant pollutants. The bioaugmented system (group B) was constructed through inoculation of two aromatics-degrading bacteria, Comamonas sp. Z1 (quinoline degrader) and Acinetobacter sp. JW (indole degrader), into the activated sludge for treatment of quinoline, indole and pyridine, and the non-bioaugmented activated sludge was used as the control (group C). Both groups maintained high efficiencies (> 94%) for removal of nitrogen-containing organic pollutants and chemical oxygen demand (COD) during the long-term operation, and group B was highly effective at the starting period and the operation stage fed with raw wastewater. High-throughput sequencing analysis indicated that nitrogen-containing organic pollutants could shape the microbial community structure, and communities of bioaugmented group B were clearly separated from those of non-bioaugmented group C as observed in non-metric multidimensional scaling (NMDS) plot. Although the inoculants did not remain their dominance in group B, bioaugmentation could induce the formation of effective microbial community, and the indigenous microbes might play the key role in removal of nitrogen-containing organic pollutants, including Dokdonella, Comamonas and Pseudoxanthomonas. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis suggested that bioaugmentation could facilitate the enrichment of functional genes related to xenobiotics biodegradation and metabolism, probably leading to the improved performance in group B. This study indicated that bioaugmentation could promote the removal of nitrogen-containing organic pollutants, which should be an effective strategy for wastewater treatment.

Seasonal variations of soil bacterial communities in Suaeda wetland of Shuangtaizi River estuary, Northeast China.

Estuarine wetland is the transitional interface linking terrestrial with marine ecosystems, and wetland microbes are crucial to the biogeochemical cycles of nutrients. The soil samples were collected in four seasons (spring, S1; summer, S2; autumn, S3; and winter, S4) from Suaeda wetland of Shuangtaizi River estuary, Northeast China, and the variations of bacterial community were evaluated by high-throughput sequencing. Soil properties presented a significant seasonal change, including pH, carbon (C) and total nitrogen (TN), and the microbial diversity, richness and structure also differed with seasons. Canonical correspondence analysis (CCA) and Mantel tests implied that soil pH, C and TN were the key factors structuring the microbial community. Gillisia (belonging to Bacteroidetes) and Woeseia (affiliating with Gammaproteobacteria) were the two primary components in the rhizosphere soils, displaying opposite variations with seasons. Based on PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) prediction, the xenobiotics biodegradation related genes exhibited a seasonal decline, while the majority of biomarker genes involved in nitrogen cycle showed an ascending trend. These findings could advance the understanding of rhizosphere microbiota of Suaeda in estuarine wetland.

Biosynthesis of gold nanoparticles using cell-free extracts of Magnusiomyces ingens LH-F1 for nitrophenols reduction.

A green and eco-friendly method for the synthesis of gold nanoparticles (AuNPs) was developed using the cell-free extracts of a yeast strain Magnusiomyces ingens LH-F1. UV-vis spectra showed a distinct absorption band at ~ 540 nm, corresponding to the surface plasmon resonance of AuNPs. Transmission electron microscopy images revealed that the shapes of AuNPs were almost spherical and pseudo-spherical. Fourier transform infrared spectroscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses suggested that some proteins containing amino- and carboxyl-groups in the cell-free extracts were absorbed on the surface of nanoparticles, which could act as reducing and capping agents for AuNPs synthesis. Furthermore, with the concentration of cell-free extracts increasing from 25 to 200 mg L-1, the average size of AuNPs decreased from 28.3 to 20.3 nm. Meanwhile, the morphology became more uniform with less irregular shapes. In addition, the as-synthesized AuNPs showed an excellent catalytic activity for nitrophenols reduction (i.e., 4-nitrophenol, 3-nitrophenol and 2-nitrophenol) in the presence of excess NaBH4. The catalytic rate constant of nitrophenols reduction was also dependent on cell-free extract concentration. The larger AuNPs synthesized by less cell-free extracts were covered with a thinner corona and showed better capacity for reducing nitrophenols. This study suggested that the as-synthesized AuNPs could be employed as efficient catalysts in reduction of organic contaminants.

Green synthesis of gold nanoparticles by a newly isolated strain Trichosporon montevideense for catalytic hydrogenation of nitroaromatics.

OBJECTIVE: To investigate green synthesis of gold nanoparticles (AuNPs) by Trichosporon montevideense, and to study their reduction of nitroaromatics. RESULTS: AuNPs had a characteristic absorption maximum at 535 nm. Scanning electron microscopy images revealed that the biosynthesized nanoparticles were attached on the cell surface. X-ray diffraction analysis indicated that the particles formed as face-centered cubic (111)-oriented crystals. The average size of AuNPs decreased from 53 to 12 nm with increasing biomass concentration. The catalytic reduction of 2-nitrophenol, 3-nitrophenol, 4-nitrophenol, o-nitrophenylamine and m-nitrophenylamine (0.1 mM) by NaBH4 had reaction rate constants of 0.32, 0.44, 0.09, 0.24 and 0.39 min(-1) with addition of 1.45 × 10(-2) mM AuNPs. CONCLUSIONS: An eco-friendly approach for synthesis of AuNPs by T. montevideense is reported for the first time. The biogenic AuNPs could serve as efficient catalysts for hydrogenation of various nitroaromatics.

Responses of microbial communities to single-walled carbon nanotubes in phenol wastewater treatment systems.

The expanding use of single-walled carbon nanotubes (SWCNTs) raises environmental concerns. Wastewater treatment systems are potential recipients of SWCNTs containing influent, yet the impacts of SWCNTs on these systems are poorly documented. In this study, the microbial responses to SWCNTs in simulated phenol wastewater treatment systems were investigated. The phenol removal rates were improved in all SWCNTs-treated sequencing batch reactors during the first 20 days, but when facing higher phenol concentration (1000 mg/L) after 60 days, reactors with the highest concentration (3.5 g/L) of SWCNTs exhibited a notably decreased phenol removal capacity. Cell viability tests, scanning electron microscopy analysis and DNA leakage data suggested that SWCNTs protected microbes from inactivation, possibly by producing more bound extracellular polymeric substances (EPS), which could create a protective barrier for the microbes. Illumina sequencing of 16S rRNA gene amplicons revealed that the bacterial diversity did not change significantly except for a minor reduction after the immediate addition of SWCNTs. Bacterial community structure significantly shifted after SWCNTs addition and did not recover afterward. Zoogloea increased significantly upon SWCNTs shocking. At the final stage, Rudaea and Mobilicoccus increased, while Burkholderia, Singulisphaera, Labrys and Mucilaginibacter decreased notably. The shifts of these dominant genera may be associated with altered sludge settling, aromatic degradation and EPS production. This study suggested that SWCNTs exerted protective rather than cytotoxic effects on sludge microbes of phenol wastewater treatment systems and they affected the bacterial community structure and diversity at test concentrations. These findings provide new insights into our understanding of the potential effects of SWCNTs on wastewater treatment processes.

Activated sludge microbial community responses to single-walled carbon nanotubes: community structure does matter.

The ecological effects of carbon nanotubes (CNTs) have been a worldwide research focus due to their extensive release and accumulation in environment. Activated sludge acting as an important gathering place will inevitably encounter and interact with CNTs, while the microbial responses have been rarely investigated. Herein, the activated sludges from six wastewater treatment plants were acclimated and treated with single-walled carbon nanotubes (SWCNTs) under identical conditions. Illumina high-throughput sequencing was applied to in-depth analyze microbial changes and results showed SWCNTs differently perturbed the alpha diversity of the six groups (one increase, two decrease, three no change). Furthermore, the microbial community structures were shifted, and specific bacterial performance in each group was different. Since the environmental and operational factors were identical in each group, it could be concluded that microbial responses to SWCNTs were highly depended on the original community structures.

Deciphering the spatial distribution and function profiles of soil bacterial community in Liao River estuarine wetland, Northeast China.

Soil microbes play vital roles in estuarine wetlands. Understanding the soil bacterial community structure and function profiles is essential to reveal the ecological functions of microbes in estuarine wetlands. Herein, soil samples were collected from Liao River estuarine wetland, Northeast China, along the river to the estuarine mouth, and soil bacterial communities were explored. Results showed that soil physiochemical properties, bacterial community structure and functions exhibited distinct variations influenced by geographical location. Bacterial phyla in soils were dominated by Proteobacteria and Bacteroidetes, while Gillisia and Woeseia were the predominant genera. Soil pH, electrical conductivity and nitrogen-related nutrients were the important factors affecting bacterial community structure. Based on PICRUSt prediction, the genes related to metabolism of nitrogen, sulfur and methane showed spatial distribution patterns, and the abundances of most biomarker genes increased as the distance from estuarine mouth extended. These findings could enrich the understanding of soil microbiome in estuarine wetlands.

Tuning the substrate selectivity of meta-cleavage product hydrolase by domain swapping.

meta-Cleavage product (MCP) hydrolases can catalyze relatively low reactive carbon-carbon bond hydrolysis of products, which are derived from the meta-cleavage of catechols. The strict substrate selectivity of MCP hydrolases attracts an interest to understand the determinants of substrate specificity. Compared with conventional site-directed mutagenesis, domain swapping is an effective strategy to explore substrate specificity due to the large-scale reorganization of three-dimensional structure. In the present study, the hybrid MCP hydrolases BphDLidA and MfphALidD were constructed by exchanging the lid domain of two parental enzymes MfphA and BphD. The residues Gly130/Ala196 (MfphA) and Gly136/Ala211 (BphD) were selected as crossover points according to structural disruption score analysis and molecular dynamics simulations. It was shown that the hybrid enzymes exhibited similar substrate selectivity with the parent enzyme providing the lid domain. Docking studies suggested that the lid domain may play a key role in determining substrate specificity by reshaping the active pocket and modulating the orientation of the substrate.

The key role of a non-active-site residue Met148 on the catalytic efficiency of meta-cleavage product hydrolase BphD.

meta-Cleavage product (MCP) hydrolases (EC 3.7.1.9) can catalyze a specific C-C bond fission during the microbial aerobic degradation of aromatics. The previous studies on structure-function relationship of MCP hydrolases mainly focus on the active site residues by site-directed mutagenesis. However, the information about the role of the non-active-site residues is still unclear. In this study, a non-active-site residue Met148 of MCP hydrolase BphD was selected as the mutagenesis site according to the sequence alignments, structure superimpose and the tunnel analysis, which underwent the saturation mutagenesis resulting 19 mutants. The catalytic efficiencies of the mutants on 6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) were all decreased compared with the wild-type one except for the M148D mutant. Especially, the M148P mutant exhibited 290-fold lower k cat/K m than that of the wild-type BphD. Transient kinetic analyses of M148P showed the reciprocal relaxation time corresponded to C-C bond cleavage and product release steps (9.6 s(-1)) was 4.08-fold lower than BphD WT (39.2 s(-1)). Tunnel cluster analysis of BphD WT, M148P and M148W demonstrated that only the bulky Trp148 could block tunnel T2 in the BphD WT, but it exhibited slight effects on the catalytic efficiency (0.94-fold of BphD WT). Therefore, product release was not the main reason for the efficiency decrease of M148P. On the other hand, molecular dynamics simulations on the BphD WT and BphD M148P in complex with HOPDA indicated that the dramatic decrease of the catalytic efficiencies of BphD M148P should be due to the unproductive binding of HOPDA. The study demonstrated the catalytic efficiency of MCP hydrolase can be engineered by modification of non-active site residue.

Genome sequence of a novel indigo-producing strain, Pseudomonas monteilii QM.

Pseudomonas monteilii is a versatile bacterium found in various niches. A newly isolated strain, P. monteilii QM, can effectively produce indigoids from indoles. Here we present a 5.76-Mb assembly of the P. monteilii genome for the first time. It may provide abundant molecular information for the transformation of aromatics.

Indigo biosynthesis by Comamonas sp. MQ.

An indigo-producing strain was isolated from activated sludge and identified as Comamonas sp. based on 16S rRNA analysis. It produced indigo at 26.5 mg/l with a conversion of indole to indigo of 47%. Indole at 50 mg/l plus 200 mg naphthalene/l gave 32.2 mg indigo/l with a 58% conversion. A pathway for indigo formation is proposed. This is the first study of indigo biosynthesis by Comamonas sp.

Optimization of indigo production by a newly isolated Pseudomonas sp. QM.

Optimization of indigo production process from indole using a newly isolated phenol-degrading bacterial strain was performed by Plackett-Burman design and response surface methodology. The strain designated as QM was identified as Pseudomonas sp. according to 16S rDNA analysis. Spectrum analysis of indole biotransformation products revealed the presence of indigo and a by-product indirubin. To improve indigo yield, Plackett-Burman design was used to select significant factors from 8 viriables. Then response surface methodology based on a 2(3) central composite design was used to further optimize the transformation process. Under the optimal conditons, strain QM can produce 27.20 mg/l indigo after 24 h cultivation at 30 °C, which was 151.3% higher than that from the initial conversion condition. The results indicated that Pseudomonas sp. QM should be a potential candidate for indigo industial production.

Performance and bacterial community profiles of sequencing batch reactors during long-term exposure to polyethylene terephthalate and polyethylene microplastics.

Microplastics (MPs) are ubiquitous in wastewater treatment plants (WWTPs), but much remains to be learned about their roles in WWTPs. Herein, polyethylene terephthalate (PET) and polyethylene (PE) particles were added into sequencing batch reactors (SBRs), and the sole impacts and co-impacts of MPs with other pollutants (phenol and Cu2+) on wastewater treatment processes were evaluated. Results indicated that MPs did not significantly affect SBR performance, either alone or co-occurrence with phenol, but the co-exposure to MPs and Cu2+ severely suppressed COD removal efficiency by 37.02%-64.70%. The functional groups of activated sludge had no changes after receiving MPs, but the MPs-Cu2+ co-exposure could greatly promote the secretion of extracellular polymeric substances. Furthermore, MPs had no negative impacts on diversity, richness and structure of bacterial communities, and PET and PE showed different preferences for enrichment of bacterial populations. Moreover, the MPs-Cu2+ co-exposure obviously reduced the overall abundances of Cu-related genes in SBRs.

Characteristics of sludge-based pyrolysis biochar and its application of enhancing denitrification.

A modified biochar for enhanced denitrification was developed through a facile pyrolysis method using sewage sludge as raw material and melamine as nitrogen source. Through electrochemical analysis, sludge-based pyrolysis biochar (SPBC) has superior electrical conductivity and poor redox activity. SPBC can increase the electron transfer through the geoconductor mechanism. The effect and the mechanism of SPBC on denitrification were studied. The nitrate treatment efficiency increased with the increase of SPBC dosage. From the perspective of molecular biology, the activities of NAR and NIR enzymes, the degradation efficiency of glucose and the ETSA of bacteria were all promoted with the increase of SPBC, thereby promoting the removal of NO3-. In addition, SPBC had a certain screening effect on microbial communities, and biodiversity decreased with the increase of SPBC dosage. Although the biodiversity decreased, the relative abundance of microorganisms conducive to denitrification increased with the increase of SPBC dosage. The transformation strategy of SPBC proposed in this paper provides a technical solution for sludge recycling and application for strengthening denitrification.

Diversity and structure of soil bacterial community in intertidal zone of Daliao River estuary, Northeast China.

Soil samples from the intertidal zone of Daliao River, Northeast China, were collected in three seasons (autumn, L1; winter, L2; and spring, L3) to evaluate the diversity and structure of bacterial community using high-throughput sequencing. Soil physicochemical characteristics varied greatly with seasons, and the potential nitrification rates were detected in the range of 1.04-2.71 µg NO3--N·g-1 dry soil·h-1 with the highest rate in spring (L3). Soil bacterial communities also differed seasonally, and nitrogen nutrients were the important variables affecting the bacterial communities as demonstrated by distance-based redundancy analysis and Mantel tests. Proteobacteria was the predominant phylum in soils showing a descending trend from L1 to L3. Woeseia and Ignatzschineria, both affiliating with Gammaproteobacteria, were the two most dominant genera, but they exerted different seasonal variations. The predicted functional profiles revealed 6 major nitrogen cycling processes, and the functional genes in relation to denitrification process were dominant in intertidal soils.

Determination of phenolic compounds in estuary water and sediment by solid-phase isotope dansylation coupled with liquid chromatography-high resolution mass spectrometry.

A method consisting of solid-phase isotope dansylation (derivatization with dansyl chloride) and liquid chromatography-high resolution mass spectrometry (LC-HRMS) was developed for the quantitative analysis of phenolic compounds (phenols) in environmental samples. A magnetic-HLB (hydrophilic lipophilic balanced) material was synthesized and applied as an adsorbent in magnetic solid-phase extraction (MSPE) for the enrichment of the analytical targets. Furthermore, with the solid-phase isotope labeling, the desalting and removal of labeling residuals could be simplified over conventional in-solution labeling. In addition to overcoming the matrix effect by isotope dansylation, the sensitivity for the analysis of phenols by LC-HRMS was remarkably improved by over 100-fold. The method was systematically verified, and good accuracy (86.5-104.9%) and precision (<8.6% and <11.4% for intra- and inter-day, respectively) were achieved for the tested 15 phenols. The limits of detection (LODs) of this method were estimated to be 0.2-5 ng L-1 and 5-100 ng kg-1 in estuary water and sediment samples, respectively. With this method, samples collected from the Daliao River estuary (Panjin, China) were analyzed. It was found that all of the targeted phenols were detected at concentrations ranging from unquantifiable to 485 ng L-1 (the total concentration of analytes found in each sample were in the range 822-957 ng L-1) and unquantifiable to 1368 ng kg-1 (the total concentration of analytes found in each sample were in the range 2251-2992 ng kg-1) in water and sediment, respectively.

[A new interspecies and interkingdom signaling molecule-Indole].

Indole, as a typical N-heterocyclic aromatic compound, is widespread in natural environment. A growing number of researches have proved that indole is a new interspecies and interkingdom signal molecule with certain biological activities. Indole could regulate virulence, biofilm formation, antibiotic tolerance and quorum sensing of bacteria. Indole not only modulates plant growth and defense system, but also affects intestinal inflammation, oxidative stress and hormone secretion in animals. Hence indole plays important roles in diverse aspects such as microbial metabolism, human health and plant growth, holding important significance both in biology and ecology. This review presents the history of indole from biological metabolism to signal transmission, the current knowledge on indole as an intercellular and interspecies signal of microorganisms, and interkingdom signal between bacteria and plants or animals. This review will help to explore the biological significant and ecological mechanism of indole metabolic and signal regulation in complex environment.