Microplastics affect soil bacterial community assembly more by their shapes rather than the concentrations.

Polyethylene film mulching is a key technology for soil water retention in dryland agriculture, but the aging of the films can generate a large number of microplastics with different shapes. There exists a widespread misunderstanding that the concentrations of microplastics might be the determinant affecting the diversity and assembly of soil bacterial communities, rather than their shapes. Here, we examined the variations of soil bacteria community composition and functioning under two-year field incubation by four shapes (ball, fiber, fragment and powder) of microplastics along the concentration gradients (0.01%, 0.1% and 1%). Data showed that specific surface area of microplastics was significantly positively correlated with the variations of bacterial community abundance and diversity (r=0.505, p<0.05). The fragment- and fiber-shape microplastics displayed more pronounced interfacial continuity with soil particles and induced greater soil bacterial α-diversity, relative to the powder- and ball-shape ones. Strikingly, microplastic concentrations were not significantly correlated with bacterial community indices (r=0.079, p>0.05). Based on the variations of the ßNTI, bacterial community assembly actually followed both stochastic and deterministic processes, and microplastic shapes significantly modified soil biogeochemical cycle and ecological functions. Therefore, the shapes of microplastics, rather than the concentration, significantly affected soil bacterial community assembly, in association with microplastic-soil-water interfaces.

The driving effects of nitrogen deposition on nitrous oxide and associated gene abundances at two water table levels in an alpine peatland.

Alpine peatlands are recognized as a weak or negligible source of nitrous oxide (N2O). Anthropogenic activities and climate change resulted in the altered water table (WT) levels and increased nitrogen (N) deposition, which could potentially transition this habitat into a N2O emission hotspot. However, the underlying mechanism related with the effects is still uncertain. Hence, we conducted a mesocosm experiment to address the response of growing-season N2O emissions and the gene abundances of nitrification (bacterial amoA) and denitrification (narG, nirS, norB and nosZ) to the increased N deposition (20 kg N ha-1 yr-1) at two WT levels (WT-30, 30 cm below soil surface; WT10, 10 cm above soil surface) in the Zoige alpine peatland, Qinghai-Tibetan Plateau. The results showed that the WT did not affect N2O emissions, and this was attributed with the limitation of soil NO3-. The higher WT level increased denitrification (narG and nirS gene abundance) resulting in the depletion of soil NO3-, but the consequent NO3- deficiency further limited denitrification, while the WT did not affect nitrification (bacterial amoA gene abundance). Meanwhile, the N deposition increased N2O emissions, regardless of WT levels. This was associated with the N-deposition induced increase in denitrification-related gene abundances of narG, nirS, norB and nosZ at WT-30 and narG at WT10. Additionally, the N2O emission factor assigned to N deposition was 1.3 % at WT-30 and 0.9 % at WT10, respectively. Our study provided comprehensive understanding of the mechanisms referring N2O emissions in response to the interactions between climate change and human disturbance from this high-altitude peatland.

Evaluation of the effect of the indoor environment on the physiological responses of early-gestation sows in a commercial house in China.

Objective: The environment influences the sow's health and physiology during gestation. This study was conducted to evaluate indoor environmental parameters and physiological responses of early-gestation sows and investigate the possible methods for assessing the thermal environment in commercial houses. Methods: A total of 20 early-gestation sows (commercial purebred Yorkshire) with an average body weight of 193.20 ± 3.62 kg were used for this study in winter, spring, summer, and autumn. The indoor environment parameters comprising dry-bulb temperature (Tdb), relative humidity (RH), and carbon dioxide (CO2) were recorded in 30-min intervals. Physiological parameters including heart rate (HR) and respiration rate (RR) of sows were also measured every 30 min. Wet-bulb temperature (Twb) was calculated using Tdb, RH and atmospheric pressure was recorded at a nearby weather station. Results: The average indoor Tdb and RH were 12.98 ± 2.03°C and 80.4 ± 6.4% in winter, 18.98 ± 2.68°C and 74.4 ± 9.0% in spring, 27.49 ± 2.05°C and 90.6 ± 6.4% in summer, and 17.10 ± 2.72°C and 64.5 ± 10.9% in autumn. A higher average concentration of CO2 was observed in winter (1,493 ± 578 mg/m3) than in spring (1,299 ± 489 mg/m3), autumn (1,269 ± 229 mg/m3), and summer (702 ± 128 mg/m3). Compared with the HR and RR in the optimum environment, high RH in the house led to a significant decrease in both HR and RR (P < 0.05). In addition, a significant decline in HR was also obtained at high temperatures (P < 0.05). A temperature humidity index (THI), THI = 0.82 × Tdb + 0.18 × Twb, was determined for early-gestation sows, and the THI thresholds were 25.6 for HR. The variation in THI in summer showed that heat stress still occurred under the pad-fan cooling system. Conclusion: This study demonstrated the critical significance of considering physiological responses of early-gestation sows in commercial houses and THI thresholds. We recommend that much more cooling measures should be taken for early-gestation sows in summer.

Thickness-dependent release of microplastics and phthalic acid esters from polythene and biodegradable residual films in agricultural soils and its related productivity effects.

It is crucial to elucidate the release rate of microplastics (MPs) and phthalic acid esters (PAEs) in agricultural soil and their effects on crop productivity regarding film types and thicknesses. To address this issue, two-year landfill test was performed using 0.016 mm-thick polyethylene (PEt1) & biodegradable (BIOt1), and 0.01 mm-thin polyethylene (PEt2) & biodegradable (BIOt2) residual films as materials with no landfill as CK. Scanning electron microscopy (SEM) and infrared analyses revealed that two-year landfill caused considerable changes in physical forms and spectral peaks in BIO film, which was more pronounced in thin BIO (36.90 % weight loss). Yet, less changes were presented in the above analyzes in polyethylene (PE) films, and thick films damaged relatively less. MPs number was 86,829.11 n/kg in BIOt1 and 134,912.27 n/kg in BIOt2, equivalent to 2.55 and 3.72 times higher than in PEt1 and PEt2, respectively. This was closely associated with PAEs release, as soil PAEs concentration was substantially lower in PEt1 (17.60 g/kg) and PEt2 (21.43 g/kg) than in BIOt1 and BIOt2 (37.12 g/kg and 49.20 g/kg), respectively. Furthermore, maize productivity parameters were negatively correlated with the amount of MPs and PAEs. BIOt2 and PEt1 had the lowest and highest grain yield, respectively. BIO exhibited greater environmental risk and adverse effects on soil and crop productivity than PE film due to physical degradation and release of PAEs. Thickness-wise comparison exhibited that thin film residues had more adverse effect relative to thick film ones.

Greenhouse Gas Emissions From Biofilters for Composting Exhaust Ammonia Removal.

Emissions of odorous compounds, such as ammonia (NH3), from composting have negative agronomic and environmental impacts. A biofilter is widely used for NH3 removal, with one of its potential detrimental by-products being nitrous oxide (N2O), which is a higher warming potential greenhouse gas (GHG). The aim of the study was to evaluate the effect of empty bed retention time (EBRT) on GHG emissions from biofilters for removing NH3 from composting. Composting experimental trials lasted 6 weeks, and composting materials were mixtures of dead pigs and manure. Three groups of biofilters with 1.2 m-height, 0.3 m-inner diameter, and 1.0 m media depth were conducted with EBRT of 30, 60, and 100s, respectively. Each treatment was performed in triplicate, and the gas was monitored using the dynamic emission vessel method. The Spearman's correlation analysis showed a significantly positive correlation between inlet concentrations (ICs) of NH3 and increased N2O concentrations: ρ = 0.707, 0.762, and 0.607 with p ≤ 0.0001 for biofilters with EBRT of 30, 60, and 100s, respectively. The fraction of NH3-N denitrified into N2O-N in biofilters with EBRT of 60 and 100s was higher than that with EBRT of 30s. The total global warming potential (GWP) increased by 126%, 162%, and 144% for biofilters with EBRT of 30, 60, and 100s, respectively. These results indicated that biofilters with longer EBRT will lead to higher GWP production. Future research on odorous mitigation for composting with biofilters should focus more on greenhouse gas emissions.

Multiscale Simulation of Protein Corona Formation on Silver Nanoparticles: Study of Ovispirin-1 Peptide Adsorption.

The exposure of nanoparticles (NPs) to biofluids leads to the rapid coverage of proteins, named protein corona, which alters the NPs' chemicophysical and biological properties. Fundamental studies of the protein corona are thus critical to the increasing applications of NPs in nanotechnology and nanomedicines. The present work utilizes multiscale simulations of a model biological system, small ovispirin-1 peptides, and bare silver nanoparticles (AgNPs) to examine the NPs' size and surface hydrophilicity effects on formation dynamics and the structure of the peptide corona. Our simulations revealed the different adsorption dynamics of ovispirin-1 peptides on the NPs, including the direct adsorption of a single peptide and peptide aggregates and multistep adsorption, as well as an intermediate cycle of desorption and readsorption. Notably, the whole process of peptide adsorption on hydrophilic AgNP surfaces can be generalized as three stages: diffusion to the surface, initial landing via hydrophilic residues, and the final attachment. The decrease in AgNP's size leads to faster adsorption with more heterogeneous peptide interfacial dynamics, a denser and inhomogeneous peptide packing structure, and a wider distribution of adsorption orientations. Subsequent atomistic molecular dynamics simulations demonstrated that on the hydrophilic AgNP surfaces, adsorbed peptides display moderate changes in their secondary structure, resulting in further changes of corona composition, i.e., amino acid residue distribution on the surface.

Simultaneous removal of ammonia and volatile organic compounds from composting of dead pigs and manure using pilot-scale biofilter.

Odor emission is one of the most common problems associated with dead animals composting. Biofiltration treatment for eliminating exhaust odors formed during dead pigs and manure composting has been studied. The composting and biofiltration process consisted of two series of tests. Composting experimental trials lasted 6 weeks, and composting was performed using six pilot-scale reactor vessels. A total of 37 kinds of volatile organic compounds (VOCs) present in the air were identified, and temporal variations were determined during the 42 days of composting. Dimethyl sulfide (DMS), dimethyl disulfide (DMDS), dimethyl trisulfide (DMTS), and trimethylamine (TMA) were identified as the main odors VOCs component according to odor active values (OAVs). Nine biofilter vessels containing mature compost were used in studying the effect of different (30, 60, and 100 s) empty bed retention times (EBRT) on the simultaneous removal efficiencies (REs) of NH3, DMS, DMDS, DMTS, and TMA. Results indicated that the inlet concentration of NH3 applied was 12-447 mg m-3, and the average removal efficiencies were 85.4%, 88.7%, and 89.0% for EBRTs of 30, 60, and 100 s, respectively. The average REs of DMS, DMDS, DMTS, and TMA were 79.2%-95.4%, 81.9%-94.0%, 76.7%-99.1%, and 92.9%-100%, respectively, and their maximum elimination capacity (ECs) were 220, 1301, 296, and 603 mg m-3 h-1, respectively. The optimal EBRT for the stimulation removal of NH3, DMS, DMDS, DMTS, and TMA was 60 s.Implications: Dimethyl sulfide (DMS), dimethyl disulfide (DMDS), dimethyl trisulfide (DMTS), and trimethylamine (TMA) were identified as the main odors VOCs component during dead pigs and manure composting. Biofilter with mature as media can be used to stimulation remove NH3, DMS, DMDS, DMTS, and TMA, the optimal empty bed retention times EBRT was 60 s.

Protein Corona on Gold Nanoparticles Studied with Coarse-Grained Simulations.

Understanding protein corona formation in an aqueous environment at the molecular and atomistic levels is critical to applications such as biomolecule-detection and drug delivery. In this work, we employed mesoscopic coarse-grained simulations to study ovispirin-1 and lysozyme protein coronas on bare gold nanoparticles. Our study showed that protein corona formation is governed by protein-surface and protein-protein interactions, as well as the surface hydrophobic effect. The corona structure was found to be dependent on protein types and the size of nanoparticles. Ovispirin proteins form homogeneous single-layered adsorption in comparison with the lysozyme's inhomogeneous multilayered aggregates on gold NP surfaces. The decrease in nanoparticle size leads to more angular degrees of freedom for protein adsorption orientation. Subsequent atomistic molecular dynamics simulations further demonstrate the loss of secondary structure of ovispirin upon adsorption and the heterogeneity of its local structure.

Effects of anaerobic digestion on chlortetracycline and oxytetracycline degradation efficiency for swine manure.

Manure containing antibiotics is considered a hazardous substance that poses a serious health risk to the environment and to human health. Anaerobic digestion (AD) could not only treatment animal waste but also generate valuable biogas. However, the interaction between antibiotics in manure and the AD process has not been clearly understood. In this study, experiments on biochemical methane potential (BMP) were conducted to determine the inhibition of the AD process from antibiotics and the threshold of complete antibiotic removal. The thresholds of the complete antibiotic removal were 60 and 40mg/kg·TS for CTC and OTC, respectively. CTC and OTC with concentrations below thresholds could increase the BMP of manure. When the CTC and OTC concentrations exceeded the thresholds, they inhibited manure fermentation, and the CTC removal rate declined exponentially with concentration (60-500mg/kg·TS). The relationship between OTC antibiotic concentration and its removal rate in AD treatment was described with exponential (40-100mg/kg·TS) and linear equations (100-500mg/kg·TS).

Decision tree and ensemble learning algorithms with their applications in bioinformatics.

Machine learning approaches have wide applications in bioinformatics, and decision tree is one of the successful approaches applied in this field. In this chapter, we briefly review decision tree and related ensemble algorithms and show the successful applications of such approaches on solving biological problems. We hope that by learning the algorithms of decision trees and ensemble classifiers, biologists can get the basic ideas of how machine learning algorithms work. On the other hand, by being exposed to the applications of decision trees and ensemble algorithms in bioinformatics, computer scientists can get better ideas of which bioinformatics topics they may work on in their future research directions. We aim to provide a platform to bridge the gap between biologists and computer scientists.

Extensive exploration of conformational space improves Rosetta results for short protein domains.

With some simplifications, computational protein folding can be understood as an optimization problem of a potential energy function on a variable space consisting of all conformation for a given protein molecule. It is well known that realistic energy potentials are very "rough" functions, when expressed in the standard variables, and the folding trajectories can be easily trapped in multiple local minima. We have integrated our variation of Parallel Tempering optimization into the protein folding program Rosetta in order to improve its capability to overcome energy barriers and estimate how such improvement will influence the quality of the folded protein domains. Here we report that (1) Parallel Tempering Rosetta (PTR) is significantly better in the exploration of protein structures than previous implementations of the program; (2) systematic improvements are observed across a large benchmark set in the parameters that are normally followed to estimate robustness of the folding; (3) these improvements are most dramatic in the subset of the shortest domains, where high-quality structures have been obtained for >75% of all tested sequences. Further analysis of the results will improve our understanding of protein conformational space and lead to new improvements in the protein folding methodology, while the current PTR implementation should be very efficient for short (up to approximately 80 a.a.) protein domains and therefore may find practical application in system biology studies.

Spin waves in paramagnetic bcc iron: spin dynamics simulations.

Large scale computer simulations are used to elucidate a long-standing controversy regarding the existence, or otherwise, of spin waves in paramagnetic bcc iron. Spin dynamics simulations of the dynamic structure factor of a Heisenberg model of Fe with first principles interactions reveal that well defined peaks persist far above Curie temperature Tc. At large wave vectors these peaks can be ascribed to propagating spin waves; at small wave vectors the peaks correspond to overdamped spin waves. Paradoxically, spin wave excitations exist despite only limited magnetic short-range order at and above Tc.