assisted-selection-biomarkers-linear-discriminant-analysis-effect

Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size (LEfSe) in Microbiome Data

There is growing attention toward closed biological genomes in the environment and in health. To explore and reveal the intergroup differences among ...

Huazhong University of Science and Technology

The microwave electrodeless lamp UV photocatalysis (MWUV) integrated with iron carbon micro-electrolysis (ME) was applied to degrade reactive brilliant red X-3B. In the present study, the removal rate of X-3B by MWUV/ME was 95%, which was significantly higher than 56% of MWUV and 62% of ME system. The experiment results demonstrated a synergistic effect in MWUV/ME system, wherein the ME system played an important role in color removal and the formation of ·OH in photocatalysis contributed most for the mineralization of X-3B and its intermediates. The removal efficiency of TOC was 32%, 7.5%, and 59.5% under MWUV, ME, and MWUV/ME processes at the end of the reaction, respectively. The Fe existed in the system was an enhancer of producing ·OH via self-generation of ·OH by UV irradiation or improving the separation of electron-hole in photocatalysis by capturing the electrons. Therefore, the combined treatment of MWUV and ME system has the potential of synergistic effect compared to the separate process. Lowering the initial solution pH and increasing the iron filing dosage and dissolved oxygen were beneficial for the enhancement of degradation efficiency. The inorganic anions showed a diversity influencing the degradation of X-3B. NO, CO, and SO (at higher concentration) promoted the degradation reaction, while Cl had non-significant effect.

Enhanced degradation of reactive brilliant red X-3B by photocatalysis integrated with micro-electrolysis.

This study investigated the environmental effects of two familiar emerging contaminants, sulfamethoxazole (SMX) and erythromycin (ERY), and their mixture (10:1 /) using a green microalga, . The cell density, pigment content, and the activities of superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) glutathione peroxidase (GSH-Px), and glutathione S-transferase (GST) were analyzed. The calculated EC values of SMX, ERY, and their mixture after 96 h were 0.49, 0.044, and 0.06 mg/L, respectively. High concentrations of antibiotics lead to a decrease in chlorophyll a and total carotenoid content, affecting the ability to photosynthesize ROS scavenging capacity. This may be a factor leading to the inhibition of algal growth. When  was exposed to SMX and the mixture, SOD and CAT increased to resist oxidative damage, while the activities of GSH and GST decreased, suggesting that this algae's antioxidant system was unbalanced due to oxidative stress.  reduced the ERY-induced ROS by increasing the activities of SOD, GSH, and GST. The difference in the contents of nonenzymatic antioxidants and enzyme antioxidants in  indicated the antioxidant mechanisms to SMX and ERY were not identical. This study provides insights into the oxidative stress process in  under different antibiotics.

Combined Effects of Sulfamethoxazole and Erythromycin on a Freshwater Microalga, : Toxicity and Oxidative Stress.

The effect of pyrene on the formation of naturally Au nanoparticles (AuNPs) in the presence of humic acid (HA) under UV irradiation is described. TEM, EDS, FTIR and XPS were carried out to prove the formation of AuNPs and display their morphologies and formation mechanism. There are little differences between size, morphology and function groups of surface coated materials of AuNPs formed with and without pyrene. With the presence of HA, pyrene showed an inhibiting effect on the reduction of Au ion via competition for O, thereby decreasing the production of AuNPs. However, AuNPs formed by HA-pyrene showed higher stability than AuNPs formed by HA with the sedimentation rates of 4.13% and 13.68% respectively after 30-d standing. As for the antibacterial activities against Staphylococcus aureus and Escherichia coli, AuNPs formed by HA-pyrene were more toxic than AuNPs formed by HA. Meanwhile, changes of environmental factors such as temperature, pH and ionic strength exhibited similar influence trend on the formation of AuNPs in the presence and absence of pyrene. The results suggest that the typical petroleum hydrocarbon pyrene contained in spilled oil could influence the formation, fate and ecotoxicity of AuNPs.

Influences of petroleum hydrocarbon pyrene on the formation, stability and antibacterial activity of natural Au nanoparticles.

Effects of antibiotics on microbial nitrogen transformation processes in natural aquatic ecosystems are largely unknown. In this study, we utilized the N stable isotope tracers and metagenomic sequencing to identify how antibiotics drive nitrogen transformation processes in Danjiangkou Reservoir, which is the largest artificial drinking water reservoir in China. We retrieved 51 nitrogen functional genes, and found that the highest abundances of nitrate reduction and denitrification-related genes occurred in dissimilatory nitrogen transformation pathways. N-labelling analysis substantiated that denitrification was the main pathway for nitrogen removal, accounting for 57.1% of nitrogen loss. Nitrogen functional genes and antibiotic resistance genes co-occurred in Danjiangkou Reservoir, and they were mainly carried by the denitrifying bacteria such as Rhodoferax, Polaromonas, Limnohabitans, Pararheinheimera, Desulfobulbus, and Pseudopelobacter. Genome annotation revealed that antibiotic deactivation, Resistance-Nodulation-Division and facilitator superfamily efflux pumps were responsible for the multiple-resistance to antibiotics in these bacteria. Moreover, antibiotics showed non-significant effects on nitrogen transformation processes. It is speculated that denitrifying bacteria harboring ARGs played crucial roles in protecting nitrogen transformation from low-level antibiotics stress in the reservoir. Our results highlight that denitrifying bacteria are important hosts of ARGs, which provides a novel perspective for evaluating the effects of antibiotics on nitrogen cycle in natural aquatic ecosystems.

Response of microbial nitrogen transformation processes to antibiotic stress in a drinking water reservoir.

This study utilized sulfamethoxazole (SMX) acclimatization to enhance the tolerance and biodegradation capacity of Chlorella vulgaris. Compared to wild C. vulgaris, the growth inhibition and oxidative damage induced by SMX evidently decreased in acclimated C. vulgaris, and meanwhile photosynthetic and antioxidant activities were significantly promoted. The physiological analyses with the aid of principal component analysis revealed the increase of catalase and glutathione reductase activities was the critical tolerant mechanism of acclimated C. vulgaris. As the consequence, the acclimated C. vulgaris exhibited enhanced efficiency and (pseudo-first-order) kinetic rate for removal of SMX. The distribution analysis of residual SMX demonstrated the biodegradation was the major removal mechanism of SMX by C. vulgaris, while bioadsorption and bioaccumulation made pimping contributions. During the degradation process of SMX, nine transformation products (TPs) were identified. Based on the identified TPs, a possible transformation pathway was proposed.

Enhanced removal efficiency of sulfamethoxazole by acclimated microalgae: Tolerant mechanism, and transformation products and pathways.

Roller experiments were conducted to explore the effect of nano-silver on the formation of marine snow and the underlying microbial mechanism. With the increasing concentration of nano-Ag from 1 ng/L to 1 mg/L, the formation and aggregation of marine snow particles were solidly suppressed in a dose-dependent pattern. Moreover, the formed marine snows tended to be thinner fibrous particles with smaller size and increased edge smoothness and compactness in the presence of nano-Ag. The microbial analyses indicated that nano-Ag not only inhibited the development of biomass but also changed the species composition and functional profile of the microbial community. Nano-Ag obviously inhibited most of the abundant species, except for some myxobacteria, which is unfavorable for the microbial community stability. For the microbial functions, some major biological processes including the growth, metabolic, and cellular processes were also inhibited by the high dosage of nano-Ag. The strong microbial inhibition of nano-Ag would contribute to the suppression on the formation of marine snow. Specifically, the function genes of extracellular polymeric substance synthesis and secretion were significantly reduced by nano-Ag, which might be the key and straight microbial factor in suppressing the formation of marine snow.

Effect of Nano-Silver on Formation of Marine Snow and the Underlying Microbial Mechanism.

The bacteria in the water column and surface sediments are inherently intertwined and inseparable in aquatic ecosystems, yet little is known about the integrated spatiotemporal dynamics and driving mechanisms of both planktonic and sedimentary bacterial communities in reservoirs. By investigating the planktonic and sedimentary bacteria during four seasons from 88 samples of 11 representative sites across the Danjiangkou reservoir, we depicted an integrated biogeographic pattern of bacterial communities in the water source of the world's largest water diversion project. Our study revealed both planktonic (mantel r = 0.502, P = 0.001) and sedimentary (mantel r = 0.131, P = 0.009) bacterial communities were significantly correlated with environmental heterogeneity, but a weak disparity along spatial heterogeneity, and the significant seasonal dynamics of planktonic (mantel r = 0.499, P = 0.001) rather than sedimentary bacteria. Particularly, rare biosphere played a main role in determining the community succession in the reservoir. It not only exhibited a more striking environmental separation than abundant taxa but also was an essential part in mediating spatiotemporal shifts of planktonic bacteria and maintaining the stability of bacterial community. These rare bacteria were respectively mediated by stochastic (62.68%) and selective (79.60%) processes in water and sediments despite abundant taxa being largely determined by stochastic processes (86.88-93.96%). Overall, our study not only fills a gap in understanding the bacterial community dynamics and underlying drivers in source water reservoirs, but also highlights the particular importance of rare bacteria in mediating biogeochemical cycles in world's large reservoir ecosystems.

Chenyuan Dang

School of Environmental Science and Engineering

Huazhong University of Science and Technology

Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size (LEfSe) in Microbiome Data

Chenyuan Dang

.css-o250i3{font-size:18px;font-family:Open Sans,sans-serif;line-height:21.6px;}School of Environmental Science and Engineering

Huazhong University of Science and Technology

Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size (LEfSe) in Microbiome Data

School of Environmental Science and Engineering