Negative effects of oxytetracycline and copper on nitrogen metabolism in an aerobic fermentation system: Characteristics and mechanisms.

Aerobic fermentation is a sustainable option for livestock waste treatment, but little is known about the microbial mechanism that allows oxytetracycline (OTC) and copper (Cu) to affect nitrogen metabolism during aerobic fermentation. In this study, contamination with OTC and Cu alone or in combination reduced the total nitrogen (TN) content of the fermentation products. Metagenomic analysis demonstrated that the contribution of microorganisms to nitrogen metabolism changed significantly in different stages of fermentation. OTC and Cu affected the formation and utilization pattern of NO2--N by microorganisms, which were mainly responsible for the reduced N2O emissions. In the presence of OTC and/or Cu, Myxococcus_stipitatus, Myxococcus_xanthus, and Gimesia_maris were evidently enriched at the end of fermentation, and their increased roles in the dissimilatory reduction of nitrite to ammonium were confirmed by network analysis. Ardenticatena_maritima was the main contributor to denitrification (NO3--N to NO). Furthermore, organic matter (OM) was the most important factor responsible for driving the variation in nitrogen-transforming microorganisms and controlling denitrification. OTC affected the formation of OM, which can directly affect TN (λ = -0.37, p < 0.001), and the adverse impact of Cu on nirK- and nifH-dominant microorganisms was validated (p < 0.05).

Elucidating the microbiological characteristics of cyromazine affecting the nitrogen cycle during aerobic composting of pig manure.

Cyromazine as insect growth inhibitor have been frequently detected in the environment, which show a potential threat to environment and soil health. Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet. In this study, quantitative polymerase chain reaction (qPCR) and sequencing of nitrifying and denitrifying bacteria were conducted to investigate the dynamic effects of cyromazine on nitrogen conversion during laboratory-based composting. Results showed that the presence of cyromazine significantly reduced the abundance of amoA gene during the thermophilic phase of composting (p < 0.01), resulting in lower oxidation of NH4+-N. The archaea amoA gene was more resistant to cyromazine. The nirK gene was more abundant than the nirS gene during composting and was significantly reduced only under high concentrations of cyromazine (p < 0.01). The high dose of cyromazine (15 mg/kg) severely damaged the nitrogen fixation capacity of compost products. Cyromazine exhibited an inhibition effect on richness (ACE, Chao) of nitrifying and denitrifying microorganisms during the thermophilic period, while increased the diversity (shannon) at all stages of composting. Pseudomonas_formosensis was the core denitrifiers that harbored nosZ gene, Nitrosomonas_eutropha and Nitrosospira_sp_Nl5 were the dominant nitrifier that harbored amoA gene, and these species have a negative response to cyromazine. Network analysis indicated that the dominant bacteria harboring amoA and nosZ genes were hubs of nitrogen oxidation and reduction processes. Structural equation modeling revealed that NO2--N conversion played a crucial role in driving denitrification, and increase of NH4+-N content was attributed to the inhibition of nitrification and denitrification during composting caused by cyromazine.

Impacts of cadmium addition on the alteration of microbial community and transport of antibiotic resistance genes in oxytetracycline contaminated soil.

The large-scale development in livestock feed industry has increased the chances of antibiotics and heavy metals contamination in the soil. The fate of antibiotic resistance genes (ARGs) and microbial community in heavy metals and antibiotic contaminated soil is still unclear. In this study, we investigated the effect of cadmium (Cd) addition on the transport of ARGs, microbial community and human pathogenic bacteria in oxytetracycline (OTC) contaminated soil. Results showed that the addition of OTC significantly increased the abundance of ARGs and intI1 in the soil and lettuce tissues. The addition of Cd to OTC treated soil further increased the abundance and translocation of ARGs and intI1. Moreover, Cd promoted the transfer of potential human pathogenic bacteria (HPB) into lettuce tissues. Compared with O10 treatment, the addition of Cd decreased the concentration of OTC in soil and lettuce tissue, but slightly increased the fresh weight of lettuce tissues. Redundancy analysis indicated that bacterial community succession is a major factor in ARGs variation. Network analysis indicated that the main host bacteria of ARGs were mainly derived from Proteobacteria. Correlation analysis showed that intI1 was significantly correlated with tetG, tetC, sul1, sul2, ermX, and ermQ. Meanwhile, potential HPB (Clostridium, and Burkholderia) was significantly correlated with intI1 and eight ARGs (tetG, tetC, tetW, tetX, sul1, sul2, ermX, and ermQ.). The findings of this study suggest that the addition of heavy metals to agricultural fields must be considered in order to reduce the transfer of ARGs in the soil and crops.

Elucidating the effect of microbial inoculum and ferric chloride as additives on the removal of antibiotic resistance genes from chicken manure during aerobic composting.

This experiment investigated the effect of adding a microbial inoculum (M) and ferric chloride (F) on the fate of antibiotic resistance genes (ARGs) during chicken manure composting. Adding M and F improved the microbial activity in the compost and facilitated the removal of ARGs, whereas the combined treatment achieved the best results, especially in reducing the enrichment of sul resistance genes. Tn916/1545 and intI1 were important genetic elements that affected the transfer of ARGs, and Tn916/1545 was closely related to the transfer of tetM, tetW, and ermQ in Firmicutes. Kyoto Encyclopedia of Genes and Genomes functional predictions indicated that M and F could reduce the abundance of membrane transport and signal transduction molecules in the compost products. Thus, these findings suggest that the combined application of M and F is a promising strategy that could potentially inhibit the transfer of ARGs during composting.

Some Physiological and Biochemical Mechanisms during Seed-to-Seedling Transition in Tomato as Influenced by Garlic Allelochemicals.

The effects of aqueous garlic extracts (AGEs), diallyl disulfide (DADS), and allicin (AAS) were investigated during seed-to-seedling transition of tomato. Independent bioassays were performed including seed priming with AGE (0, 100, and 200 µg∙mL-1), germination under the allelochemical influence of AGE, DADS, and AAS, and germination under volatile application of AGE. Noticeable differences in germination indices and seedling growth (particularly root growth and fresh weights) were observed in a dose-dependent manner. When germinated under 50 mM NaCl, seeds primed with AGE exhibited induced defense via antioxidant enzyme activities (superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)), lipid peroxidation (malondialdehyde content (MDA)), and H2O2 scavenging. Enzyme-linked immunosorbent analysis (ELISA) of the endogenous phytohormones auxin (IAA), abscisic acid (ABA), cytokinin (ZR), and gibberellic acid (GA3) in the roots and shoots of the obtained seedlings and the relative expression levels of auxin-responsive protein (IAA2), like-auxin (LAX5), mitogen-activated protein kinase (MAPK7 and MPK2), respiratory burst oxidase homolog (RBOH1), CHI3 and SODCC1 suggested allelopathic functions in stimulating growth responses. Our findings suggest that garlic allelochemicals act as plant biostimulants to enhance auxin biosynthesis and transportation, resulting in root growth promotion. Additionally, the relative expressions of defense-related genes, antioxidant enzymes activities and phytohormonal regulations indicate activation of the defense responses in tomato seedlings resulting in better growth and development. These results, thus, provide a basis to understand the biological functions of garlic allelochemicals from the induced resistance perspective in plants.

Microbial driven reduction of N2O and NH3 emissions during composting: Effects of bamboo charcoal and bamboo vinegar.

In this study, we systematically analyzed the microbial-driven effects of bamboo charcoal (BC) and bamboo vinegar (BV) on reducing NH3 and N2O emissions during aerobic composting. The results showed that BC and BV improved the nitrogen conversion and compost quality, but the combined BC + BV treatment obtained the best improvements. The BC, BV, and BC + BV treatments reduced the NH3 emissions by 14.35%, 17.90%, and 29.83%, respectively, and the N2O emissions by 44.83%, 55.96%, and 74.53%. BC and BV reduced the NH3 and N2O emissions during composting by controlling ammonia oxidation, where napA, nirK, and nosZ served as useful indicators of the N2O emissions from compost, especially the nirK gene. The dominant nitrifying and denitrifying bacteria belonged to Proteobacteria, and the changes in environmental factors during composting significantly affected the succession of the nitrifying and denitrifying bacterial communities. Nitrosomonas was a key nitrifying bacterial genus in the mesophilic composting period, and BC and BV may have reduced the NH3 emissions by enhancing its conversion to NH4+-N by Nitrosomonas. In addition, norank_p__environmental_samples, unclassified_k__norank_d__Bacteria, and unclassified_p__Proteobacteria were jointly responsible for driving the production of N2O during the compost maturity stage.

Beneficial effects of bacterial agent/bentonite on nitrogen transformation and microbial community dynamics during aerobic composting of pig manure.

This study investigated the effects of adding a bacterial agent (B) and bentonite (BT) on nitrogen transformation, nitrogen functional genes, and the microbial community dynamics during the aerobic composting of pig manure, as well as their contributions to NH3 and N2O emissions. Treatments B, BT, and BT + B reduced the NH3 emissions by 31.34%, 18.82%, and 23.67%, respectively, and the N2O emissions by 53.16%, 72.56%, and 63.41%. N2O and NH3 emissions were strongly related to the functional genes. Adding bacterial agent promoted the ammonia oxidation process to reduce NH3 emissions, whereas the influence of bentonite on nitrogen conversion was mostly related to nirS and nirK in denitrification processes. Nitrification and denitrification were dominated by different functional microorganisms in various stages of composting, where Proteobacteria comprised the most important denitrifying microorganisms. Thus, the additives reduced NH3 and N2O emissions by regulating nitrification and denitrification processes, and adding both was highly advantageous.

Responses of antibiotic and heavy metal resistance genes to bamboo charcoal and bamboo vinegar during aerobic composting.

The application of compost in agriculture has led to the accumulation of antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) in the soil environment. In this study, the response of ARGs and MRGs to bamboo charcoal (BC) and bamboo vinegar (BV) during aerobic composting was investigated. Results showed that BC + BV treatment reduced the abundances of ARGs and mobile genetic elements (MGEs) during the thermophilic period, as well as achieved the lowest rebound during the cooling period. BC + BV promoted the growth of Firmicutes, thereby facilitating the thermophilic period of composting. The rebound of ARGs and MGEs can be explained by increasing the abundance of Actinobacteria and Proteobacteria at the end of composting. Composting reduced the abundances of MRGs comprising pcoA, tcrB, and cueO, whereas cusA and copA indicated the selective pressure imposed by heavy metals on bacteria. The fate of ARGs was mainly driven by MGEs, and heavy metals explained most of the variation in MRGs. Interestingly, nitrogen conversion also had an important effect on ARG and MRG profiles. Our current findings suggest that the addition of BC + BV during compost preparation is an effective method in controlling the mobility of ARGs and MRGs, thereby reducing the environmental problems.

Reliable model established depending on soil properties to assess arsenic uptake by Brassica chinensis.

Generally, prediction of arsenic (As) bioavailability, mobility and its transfer from soil to plant is very important with respect to management of environment and food safety. In this study, pakchoi (Brassica chinensis) was sown in a greenhouse to evaluate the As transfer characteristics from different soils to plant system, and to investigate the possible prediction equations and key factors involved in As bioavailability. The results showed that As uptake of plant and soil As concentration was significantly and positively correlated (R2 = 0.778; P < 0.01). A log-transformed data provided a better correlation (R2 = 0.901; P < 0.01). Results obtained from stepwise multiple linear regression (SMLR) showed that soil pH and total As were important variables involved in the contribution of As transfer to plant. The As accumulation in plant exhibited a positive correlation with soil As content and pH. Various prediction equations were obtained from different As sources, whereas the most favourable equation was screened by root mean square error (RMSE) between the measured and predicted Log [plant As] content. The prediction model (Log [plant As] =1.34 Log [soil As] +0.18pH-1.25) showed the greatest accuracy of R2 = 0.978 and RMSE = 0.11, by combining the data of three As treatments (45 observed data points). These current findings are quite useful and could be used for predicting the As transfer from soil to plant system.

Role of Bentonite on the Mobility of Antibiotic Resistance Genes, and Microbial Community in Oxytetracycline and Cadmium Contaminated Soil.

The effects of bentonite (BT), a commonly used heavy metal deactivator, on the ARGs and microbial communities in soils and lettuce systems contaminated by heavy metals and antibiotics are unclear. A study was conducted to investigate the effect of BT on the mobility of antibiotic resistance genes in oxytetracycline and cadmium contaminated soil. Results showed that the addition of BT reduced the accumulation of OTC and ARGs in the soil and lettuce roots, but increased the abundance of ARGs in lettuce leaves, and increase the risk of human pathogenic bacteria (HPB) transferring to lettuce leaves. Redundancy analysis showed that environmental factors (OTC, H2O, SOM, and pH) were the dominant factors that influence the distribution of ARGs and intI1. Network analysis showed that Proteobacteria and Bacteroidetes were the major host bacteria which caused changes in ARGs and intI1. There were significant positive correlations between ermX and ermQ, and a large number of HPB. The co-occurrence of intl1 with some ARGs (tetC, tetG, ermQ, sul1, and sul2), may threaten human health due to the dispersion of ARGs via horizontal gene transfer.

Omics Approaches for Engineering Wheat Production under Abiotic Stresses.

Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence and heavy metals. The effective management at the molecular level is mandatory for a thorough understanding of plant response to abiotic stress. Understanding the molecular mechanism of stress tolerance is complex and requires information at the omic level. In the areas of genomics, transcriptomics and proteomics enormous progress has been made in the omics field. The rising field of ionomics is also being utilized for examining abiotic stress resilience in wheat. Omic approaches produce a huge amount of data and sufficient developments in computational tools have been accomplished for efficient analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. Though, the incorporation of omic-scale data to address complex genetic qualities and physiological inquiries is as yet a challenge. In this review, we have reported advances in omic tools in the perspective of conventional and present day approaches being utilized to dismember abiotic stress tolerance in wheat. Attention was given to methodologies, for example, quantitative trait loci (QTL), genome-wide association studies (GWAS) and genomic selection (GS). Comparative genomics and candidate genes methodologies are additionally talked about considering the identification of potential genomic loci, genes and biochemical pathways engaged with stress resilience in wheat. This review additionally gives an extensive list of accessible online omic assets for wheat and its effective use. We have additionally addressed the significance of genomics in the integrated approach and perceived high-throughput multi-dimensional phenotyping as a significant restricting component for the enhancement of abiotic stress resistance in wheat.

Impacts of wheat straw addition on dissolved organic matter characteristics in cadmium-contaminated soils: Insights from fluorescence spectroscopy and environmental implications.

Incorporating straw in soil can change the dissolved organic matter (DOM) content and also affect the mobility and solubility of soil pollutants. However, few studies have focused on the spectral features of DOM released by soil after amendment with crop residues. In this study, excitation-emission matrix (EEM) fluorescence and UV-visible absorbance spectroscopy were used to monitor the quality and quantity of the DOM derived from wheat straw incorporation in the soil. We found remarkable changes in the dissolved organic carbon (DOC) concentration (0.10-0.34 g kg-1). But the mean DOC concentrations were lower in the cadmium (Cd2+) added treatments compared with the control treatment due to additional Cd2+. The specific UV-visible absorbance at 254 nm was positively correlated with Cd2+ content, thereby suggesting a strong relationship between aromatic materials and heavy metals. Three fluorescent components were identified by EEM fluorescence combined with parallel factor analysis (PARAFAC) modeling, i.e., UVC humic-like, fulvic acid-like, and tryptophan-like. The relative abundances of these three components and dynamic variations in fluorescent indices predicted the changes in DOM composition during the wheat straws decomposition process. Therefore, the findings obtained in this study can be utilized to evaluate the variations in DOM for soil incorporated with straws in order to support agricultural production and overcome the heavy metal pollution.

Comparison of DGT with traditional extraction methods for assessing arsenic bioavailability to Brassica chinensis in different soils.

Several predictive models and methods have been used for heavy metals bioavailability, but there is no universally accepted approach in evaluating the bioavailability of arsenic (As) in soil. The technique of diffusive gradients in thin-films (DGT) is a promising tool, but there is a considerable debate with respect to its suitability. The DGT method was compared with other traditional chemical extractions techniques (soil solution, NaHCO3, NH4Cl, HCl, and total As method) for estimating As bioavailability in soil based on a greenhouse experiment using Brassica chinensis grown in various soils from 15 provinces in China. In addition, we assessed whether these methods are independent of soil properties. The correlations between plant and soil As concentration measured with traditional extraction techniques were pH and iron oxide (Feox) dependent, indicating that these methods are influenced by soil properties. In contrast, DGT measurements were independent of soil properties and also showed a better correlation coefficient than other traditional techniques. Thus, DGT technique is superior to traditional techniques and should be preferable for evaluating As bioavailability in different type of soils.

Comparison of DGT with traditional methods for assessing cadmium bioavailability to Brassica chinensis in different soils.

There is no universally accepted method for evaluating cadmium (Cd) bioavailability in soil. The diffusive gradient in thin films (DGT) technique is a promising tool, but there is considerable debate about its suitability. The ability of this technique to estimate Cd bioavailability in soils was compared with the abilities of other traditional chemical extraction techniques (soil solution, ethylene diamine tetraacetic acid (EDTA), acetic acid (HAc), calcium chloride (CaCl2), and pseudo-total Cd methods) based on a greenhouse experiment using pakchoi (Brassica chinensis) grown in 15 soils from different provinces of China. In addition, we assessed whether these methods were independent of the soil properties. Correlations between the plant and soil Cd concentrations measured with the traditional extraction techniques were dependent on the pH and organic carbon (OC) content, indicating that these methods are influenced by the soil properties. In contrast, the DGT measurements were independent of the soil properties and showed a higher correlation coefficient compared to that of the traditional techniques. Hence, the DGT technique is better and should be preferable for assessing Cd biological effectiveness in different soil types.

Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing.

To improve the understanding of bacterial community in heavy metals contaminated soils, we studied the effects of environmental factors on the bacterial community structure in contaminated fields located in Shaanxi Province of China. Our results showed that microbial community structure varied among sites, and it was significantly affected by soil environmental factors such as pH, soil organic matter (SOM), Cd, Pb and Zn. In addition, Spearman's rank-order correlation indicated heavy metal sensitive (Ralstonia, Gemmatimona, Rhodanobacter and Mizugakiibacter) and tolerant (unidentified-Nitrospiraceae, Blastocatella and unidentified-Acidobacteria) microbial groups. Our findings are crucial to understanding microbial diversity in heavy metal polluted soils of China and can be used to evaluate microbial communities for scientific applications such as bioremediation projects.