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.

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.

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.

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.

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.

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.

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.

[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.

Comparison of rhizosphere bacterial communities of reed and Suaeda in Shuangtaizi River Estuary, Northeast China.

Microbial communities in wetland soils play vital roles in biogeochemical cycling of nutrients. In this study, the soil samples were collected from Suaeda, reed and Suaeda-reed hybrid zones in Shuangtaizi River Estuary, Northeast China, and the rhizosphere bacterial communities were compared using Illumina MiSeq sequencing. The microbial richness, diversity and structure of bacterial communities varied greatly in reed and Suaeda. Canonical correspondence analysis and Mantel test indicated that pH was the most significant factor (P < 0.05) in bacterial community assembly. Proteobacteria was the most dominant phylum, accounting for 45.7-58.0% of the total sequences. Thioprofundum, Thiohalomonas and Exiguobacterium were the predominant genera in Suaeda, while Exiguobacterium, Gillisia, Desulfomonile, Citrobacter, Thioprofundum and Acinetobacter were the core species in reed. PICRUSt analysis revealed similar functional profiles of rhizosphere microbiota in reed and Suaeda. Nitrate reduction related genes were abundant for nitrogen metabolism, whereas assimilatory sulfate reduction was the major process for sulfur metabolism.

Performance and Microbial Community Analysis of Bioaugmented Activated Sludge System for Indigo Production from Indole.

Indole is a typical nitrogen-containing aromatic pollutant in coking wastewater, and it can be used for the microbial production of indigo, one of the oldest dyestuffs. In this study, the activated sludge system bioaugmented with two indigo-producing bacterial strains, wild strain Comamonas sp. MQ and recombinant Escherichia coli (ND_IND), was constructed to investigate indigo bioproduction from indole. During the operation, the bioaugmentation could promote the production of indigo, especially in early stages, and the indigo yields gradually increased from 17.5 ± 0.4 to 44.3 ± 0.5 mg/L with the increase of influent indole (80 to 282 mg/L). Illumina MiSeq sequencing revealed that the microbial community could have a noticeable shift driven by the bioaugmentation and high indole pressure. The indigenous bacteria could be more responsible for indigo production, and the dominant genera Comamonas, Diaphorobacter, Paracoccus, Aquamicrobium, Pseudomonas, and Truepera could be the key functional taxa. Based on FAPROTAX (Functional Annotation of Prokaryotic Taxa) analysis, the nitrogen metabolism-related functional groups could play important roles in indole biotransformation and indigo biosynthesis. This study should provide insights into microbial production of indigo by microbial communities.

Biodegradation and Biotransformation of Indole: Advances and Perspectives.

Indole is long regarded as a typical N-heterocyclic aromatic pollutant in industrial and agricultural wastewater, and recently it has been identified as a versatile signaling molecule with wide environmental distributions. An exponentially growing number of researches have been reported on indole due to its significant roles in bacterial physiology, pathogenesis, animal behavior and human diseases. From the viewpoint of both environmental bioremediation and biological studies, the researches on metabolism and fates of indole are important to realize environmental treatment and illuminate its biological function. Indole can be produced from tryptophan by tryptophanase in many bacterial species. Meanwhile, various bacterial strains have obtained the ability to transform and degrade indole. The characteristics and pathways for indole degradation have been investigated for a century, and the functional genes for indole aerobic degradation have also been uncovered recently. Interestingly, many oxygenases have proven to be able to oxidize indole to indigo, and this historic and motivating case for biological applications has attracted intensive attention for decades. Herein, the bacteria, enzymes and pathways for indole production, biodegradation and biotransformation are systematically summarized, and the future researches on indole-microbe interactions are also prospected.

Phenol removal performance and microbial community shift during pH shock in a moving bed biofilm reactor (MBBR).

A moving bed biofilm reactor (MBBR) effectively removes pollutants and even runs under extreme conditions. However, the pH shock resistance of a biofilm in MBBRs has been rarely reported. In this study, simulated phenol wastewater with acidic shock (pH 7.5-3.0) was used. In the pH shock phase, the phenol and COD removal efficiencies initially decreased and gradually increased to more than 90%. Microscopic studies showed that the superficial biofilm was mainly composed of fungi (yeasts) in the acidic pH shock phase. The microbial community composition in the acidic pH shock phase was significantly different from those in other phases. Firmicutes and Ascomycota were the dominant bacterial and fungal phyla in this stage, respectively. 16S rRNA gene-based functional annotation indicated that functional profiles related to aromatic compound degradation existed in all of the stages. Therefore, MBBRs show potential for the treatment of phenolic wastewater exposed to pH shock.

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 using fungus Mariannaea sp. HJ and their catalysis in reduction of 4-nitrophenol.

In the present study, biosynthesis of gold nanoparticles (AuNPs) by the cells (cells-AuNPs) and cell-free extracts (extracts-AuNPs) of a new fungus Mariannaea sp. HJ was reported. The as-synthesized particles were characterized by UV-vis spectroscopy, transmission electron microscopy (TEM), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). The effects of different parameters on AuNP biosynthesis were investigated, and initial gold ion concentration of 2 mM, pH 7, was demonstrated to be suitable for both cells-AuNP and extracts-AuNP syntheses. The cells-AuNPs were of various shapes, including sphere, hexagon, and irregular shapes, with an average size of 37.4 nm, while the extracts-AuNPs were almost spherical and pseudo-spherical with an average size of 11.7 nm. XRD pattern suggested that the crystal structure of both AuNPs was face-centered cubic. FTIR spectra implied that some biomolecules from the fungal cell walls or cell-free extracts were involved in the formation of AuNPs. The as-synthesized AuNPs were demonstrated to have excellent catalytic activities for the reduction of 4-nitrophenol with the catalytic rate constants of 5.7 × 10-3/s for cells-AuNPs and 24.7 × 10-3/s for extracts-AuNPs. To the best of our knowledge, this is the first report on AuNP biosynthesis by Mariannaea sp.

Interface modulation of bacteriogenic Ag/AgCl nanoparticles by boosting the catalytic activity for reduction reactions using Co2+ ions.

Boosting the low catalytic activity of bacteriogenic Ag/AgCl nanoparticles (NPs) by adding Co2+ in a model reaction, i.e. p-nitrophenol (PNP) reduction, was observed. Under optimal conditions, Co-Ag/AgCl NPs show an apparent rate constant (kapp) of 0.0837 s-1 upon PNP reduction. Considering the trace amount of Co-Ag/AgCl NPs used in catalysis (about 1.2 µg), the activity parameter κ (which is the ratio of kapp and catalyst mass) can reach more than 6.97 × 104 s-1 g-1, which is 214-fold higher than that of pristine Ag/AgCl NPs. Meanwhile, this κ value is also the highest value reported to date. In addition, the biogenic Co-Ag/AgCl NPs exhibit superior catalytic activities over other substrates, such as m-nitrophenol, o-nitrophenol, methyl orange and rhodamine B. The activity enhancement mechanism is supposed to be that Co2+ acts as a Lewis acid, and coordinates with the surface peptides to affect the electric field distribution at the Ag/AgCl NP interface.

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.