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1.
Prediction of prokaryotic transposases from protein features with machine learning approaches.
Wang, Q, Ye, J, Xu, T, Zhou, N, Lu, Z, Ying, J
Microbial genomics. 2021;(7)
Abstract
Identification of prokaryotic transposases (Tnps) not only gives insight into the spread of antibiotic resistance and virulence but the process of DNA movement. This study aimed to develop a classifier for predicting Tnps in bacteria and archaea using machine learning (ML) approaches. We extracted a total of 2751 protein features from the training dataset including 14852 Tnps and 14852 controls, and selected 75 features as predictive signatures using the combined mutual information and least absolute shrinkage and selection operator algorithms. By aggregating these signatures, an ensemble classifier that integrated a collection of individual ML-based classifiers, was developed to identify Tnps. Further validation revealed that this classifier achieved good performance with an average AUC of 0.955, and met or exceeded other common methods. Based on this ensemble classifier, a stand-alone command-line tool designated TnpDiscovery was established to maximize the convenience for bioinformaticians and experimental researchers toward Tnp prediction. This study demonstrates the effectiveness of ML approaches in identifying Tnps, facilitating the discovery of novel Tnps in the future.
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2.
Modeling of Nitrous Oxide Production from Nitritation Reactors Treating Real Anaerobic Digestion Liquor.
Wang, Q, Ni, BJ, Lemaire, R, Hao, X, Yuan, Z
Scientific reports. 2016;:25336
Abstract
In this work, a mathematical model including both ammonium oxidizing bacteria (AOB) and heterotrophic bacteria (HB) is constructed to predict N2O production from the nitritation systems receiving the real anaerobic digestion liquor. This is for the first time that N2O production from such systems was modeled considering both AOB and HB. The model was calibrated and validated using experimental data from both lab- and pilot-scale nitritation reactors. The model predictions matched the dynamic N2O, ammonium, nitrite and chemical oxygen demand data well, supporting the capability of the model. Modeling results indicated that HB are the dominant contributor to N2O production in the above systems with the dissolved oxygen (DO) concentration of 0.5-1.0 mg O2/L, accounting for approximately 75% of N2O production. The modeling results also suggested that the contribution of HB to N2O production decreased with the increasing DO concentrations, from 75% at DO = 0.5 mg O2/L to 25% at DO = 7.0 mg O2/L, with a corresponding increase of the AOB contribution (from 25% to 75%). Similar to HB, the total N2O production rate also decreased dramatically from 0.65 to 0.25 mg N/L/h when DO concentration increased from 0.5 to 7.0 mg O2/L.
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3.
Side-stream sludge treatment using free nitrous acid selectively eliminates nitrite oxidizing bacteria and achieves the nitrite pathway.
Wang, Q, Ye, L, Jiang, G, Hu, S, Yuan, Z
Water research. 2014;:245-55
Abstract
Nitrogen removal via nitrite (i.e. the nitrite pathway) is beneficial for carbon-limited biological wastewater treatment plants. This study presents a novel strategy for achieving the nitrite pathway, which involves recirculating a portion of the activated sludge through a side-stream sludge treatment unit, where the sludge is subject to treatment with free nitrous acid (FNA i.e. HNO2). The strategy is proposed based on a novel discovery reported in this work that in the concentration range of 0.24-1.35 mg HNO2(-)-N/L, FNA is substantially more biocidal to nitrite oxidizing bacteria (NOB) than to ammonium oxidizing bacteria (AOB). Two sequencing batch reactors (SBR) treating synthetic domestic wastewater were used to demonstrate the concept, with one serving as an experimental reactor and the other as a control. In the experimental system, 22% of the sludge from the SBR was transferred to the side-stream treatment unit each day, and was subject to FNA treatment at 1.35 mg N/L for 24 h and then returned to the SBR. The nitrite pathway was rapidly (in 15 d) established in the experimental reactor with an average nitrite accumulation ratio (NO2(-)-N/(NO2(-)-N + NO3(-)-N) × 100%) of above 80%. Fluorescence in-situ hybridization demonstrated that the NOB population in the experimental reactor was 80% lower than that in the control reactor, indicating that the majority of NOB were eliminated from the experimental reactor. The FNA-based strategy for establishing the nitrite pathway substantially improved total nitrogen removal, and did not increase N2O emission or deteriorate sludge settleability. The strategy can be easily integrated with a previously demonstrated strategy, which enhances methane production through pre-treatment of secondary activated sludge, to enable maximum energy recovery while achieving improved nitrogen removal.
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4.
Experimental evaluation of decrease in bacterial activity due to cell death and activity decay in activated sludge.
Hao, X, Wang, Q, Zhang, X, Cao, Y, van Mark Loosdrecht, CM
Water research. 2009;(14):3604-12
Abstract
Decrease in bacterial activity (cell decay) in activated sludge can be attributed to cell death (reduction in the amount of active bacteria) and activity decay (reduction in the specific activity of active bacteria). The aim of this study was to experimentally differentiate between cell death and activity decay as a source of decrease in microbial activity. By means of measuring maximal oxygen uptake rates, verifying membrane integrity by live/dead staining and verifying presence of 16S rRNA with fluorescence in-situ hybridization, the decay rates and the death rates of ammonium oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and ordinary heterotrophic organisms (OHOs) were determined respectively in a nitrifying sequencing batch reactor (SBR) and a heterotrophic SBR. The experiments revealed that in the nitrifying system activity decay contributed 47% and 82% to the decreased activities of AOB and NOB and that cell death was responsible for 53% and 18% of decreases in their respective activities. In the heterotrophic system, activity decay took a share of 78% in the decreased activity of OHOs, and cell death was only responsible for 22% of decrease in their activity. The difference between the importance of cell death on the decreased activities of AOB and OHOs might be caused by the mechanisms of substrate storage and/or cryptic growth/death-regeneration of OHOs. The different nutrient sources for AOB and NOB might be the reason for a relatively smaller fraction of cell death in NOB.
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5.
Denitrification of nitrate contaminated groundwater with a fiber-based biofilm reactor.
Wang, Q, Feng, C, Zhao, Y, Hao, C
Bioresource technology. 2009;(7):2223-7
Abstract
A fiber-based biofilm reactor was developed using a laboratory-scale apparatus for treatment of nitrate-contaminated groundwater. Denitrification bacteria were inoculated by anaerobic sludge from a wastewater treatment plant. Nitrate removal efficiency, nitrite accumulation, COD and pH in the treated water were investigated under various conditions set by several parameters including hydraulic retention times (HRTs) (24, 20, 16, 12, 8, 4 and 2h), influent nitrate loading (around 50, 100 and 150 NO(3)(-)-N mg L(-1)), pH (5, 6, 7, 8, and 9) and ratios of carbon to nitrogen (C/N=3.00, 2.00, 1.50 1.25 and 1.00). The experimental results demonstrated that the optimum reaction parameters were pH 7-7.5,C/N=1.25 and HRT=8h, under which over 99% of NO(3)(-)-N was removed, almost no NO(2)(-)-N accumulated and COD was nearly zero in treated water when the concentration of NO(3)(-)-N was around 100.00 mg L(-1) in influent.