Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments.

Environmental selection of antibiotic resistance genes (ARGs) is considered to be caused by antibiotic or metal residues, frequently used in livestock. In this study we examined three commercial poultry farms to correlate the co-occurrence patterns of antibiotic and metal residues to the presence of ARGs. We quantified 283 ARGs, 12 mobile genetic elements (MGEs), 49 targeted antibiotics, 7 heavy metals and sequenced 16S rRNA genes. The abundance and type of ARG were significantly enriched in manure while soil harbored the most diverse bacterial community. Procrustes analysis displayed significant correlations between ARGs/MGEs and the microbiome. Cadmium (Cd), arsenic (As), zinc (Zn), copper (Cu) and lead (Pb) were responsible for a majority of positive correlations to ARGs when compared to antibiotics. Integrons and transposons co-occurred with ARGs corresponding to 9 classes of antibiotics, especially Class1 integrase intI-1LC. Redundancy analysis (RDA) and Variance partitioning analysis (VPA) showed that antibiotics, metals, MGEs and bacteria explain solely 0.7%, 5.7%, 12.4%, and 21.9% of variances of ARGs in the microbial community, respectively. These results suggested that bacterial composition and horizontal gene transfer were the major factors shaping the composition of ARGs; Metals had a bigger effect on ARG profile than detected antibiotics in this study.

Efficiency and risks of selenite combined with different water conditions in reducing uptake of arsenic and cadmium in paddy rice.

The co-contamination of arsenic (As) and cadmium (Cd) in soils is a common problem. Selenium (Se) can reduce the uptake of As and Cd in plants, and in practice, the alternate wetting and drying is a common culture mode in rice production. However, it is unknown whether Se can efficiently reduce As and Cd concentrations in crops suffering from a high-level contamination of As and Cd under different soil water conditions. In this study, we assessed the efficiency and risks of selenite [Se(IV)], in a pot experiment, to reduce the uptake of As and Cd in a rice plant (YangDao No 6) growing in a heavily contaminated soil by As and Cd (pH 7.28) under different soil water conditions. The results showed that Se(IV) failed to control the grain total As and Cd concentrations within their individual limited standard (0.2 mg kg-1) despite that Se(IV) significantly reduced the grain total As and Cd concentrations. The soil drying treatment alone could reduce the accumulation of arsenite [As(III)] in the grains, but additional Se(IV) stimulated the accumulation of As(III) in the grains under soil drying conditions. In addition, the addition of Se(IV) enhanced the As and Cd concentrations in the shoots and/or roots of rice plants under certain conditions. The above results all suggested that the utilization of Se(IV) in a high contaminated soil by As and Cd cannot well control the total concentrations of As and Cd in plants. In this study, the available concentrations of As and Cd in the rhizosphere soil, the rhizosphere soil pH, the formation of root iron/manganese plaques and the concentrations of essential elements in the grains were monitored, and the related mechanisms on the changes of these parameters were also discussed. This study will give a guideline for the safe production of rice plants in a heavily co-contaminated soil by As and Cd.

Simultaneous analysis of multiclass antibiotic residues in complex environmental matrices by liquid chromatography with tandem quadrupole mass spectrometry.

A simultaneous extraction and cleanup method was optimized and validated for the determination of 40 antibiotics from cephalosporin, fluoroquinolone, lincosamide, macrolide, nitroimidazole, quinolone, sulfonamide and tetracycline groups in sediments by liquid chromatography with tandem quadrupole mass spectrometry (LC-MS/MS). The method involved hydration of freeze-dried sediment sample (2.0 g) with 2.5 ml of 0.1 M Na-EDTA McIlvaine buffer and extraction with 5 ml of MeOH and MeCN (1:3 v/v) followed by dispersive solid phase extraction by using 100 mg mix of C18 and PSA (1:2 w/w) and 50 mg MgSO4 prior to LC-MS/MS analysis. The method was validated for 10, 20, 50 and 100 µg/kg spiking levels by using blank sediment sample obtained from a drinking water reservoir according to the guidelines of European Commission Decision (2002) 2002/657/EC. The method produced clean extracts with generally low matrix effect during LC-MS/MS analysis. The mean recoveries ranged between 24-162%, 48-151%, 51-159%, and 50-149% for 10, 20, 50 and 100 µg/kg spiking levels, respectively, with acceptable precision. The analytical method was sensitive enough to achieve 0.01-34.3 µg/kg and 0.03-115 µg/kg limits of detection and quantitation, respectively. The scope of the method was demonstrated by analyzing complex solid environmental matrices (chicken manure, swine manure, poultry feed and soil) spiked at 10, 20, 50 and 100 µg/kg levels. The method was also applied for the antibiotic analysis in samples with incurred residues. Different matrices in the order of the magnitude as sediments < poultry feed < swine manure < soil < chicken manure were detected with the residues of fluoroquinolone, macrolide, sulfonamide and tetracycline antibiotics.

Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine.

The highly heavy metal resistant strain Cupriavidus metallidurans BS1 was isolated from the Zijin gold-copper mine in China. This was of particular interest since the extensively studied, closely related strain, C. metallidurans CH34 was shown to not be only highly heavy metal resistant but also able to reduce metal complexes and biomineralizing them into metallic nanoparticles including gold nanoparticles. After isolation, C. metallidurans BS1 was characterized and complete genome sequenced using PacBio and compared to CH34. Many heavy metal resistance determinants were identified and shown to have wide-ranging similarities to those of CH34. However, both BS1 and CH34 displayed extensive genome plasticity, probably responsible for significant differences between those strains. BS1 was shown to contain three prophages, not present in CH34, that appear intact and might be responsible for shifting major heavy metal resistance determinants from plasmid to chromid (CHR2) in C. metallidurans BS1. Surprisingly, the single plasmid - pBS1 (364.4 kbp) of BS1 contains only a single heavy metal resistance determinant, the czc determinant representing RND-type efflux system conferring resistance to cobalt, zinc and cadmium, shown here to be highly similar to that determinant located on pMOL30 in C. metallidurans CH34. However, in BS1 another homologous czc determinant was identified on the chromid, most similar to the czc determinant from pMOL30 in CH34. Other heavy metal resistance determinants such as cnr and chr determinants, located on megaplasmid pMOL28 in CH34, were shown to be adjacent to the czc determinant on chromid (CHR2) in BS1. Additionally, other heavy metal resistance determinants such as pbr, cop, sil, and ars were located on the chromid (CHR2) and not on pBS1 in BS1. A diverse range of genomic rearrangements occurred in this strain, isolated from a habitat of constant exposure to high concentrations of copper, gold and other heavy metals. In contrast, the megaplasmid in BS1 contains mostly genes encoding unknown functions, thus might be more of an evolutionary playground where useful genes could be acquired by horizontal gene transfer and possibly reshuffled to help C. metallidurans BS1 withstand the intense pressure of extreme concentrations of heavy metals in its environment.

Draft Genome Sequence of Pseudarthrobacter sp. Strain AG30, Isolated from a Gold and Copper Mine in China.

Here, we report the features and draft genome sequence of Pseudarthrobacter sp. strain AG30, isolated from the Zijin gold and copper mine in China. The genome size of Pseudarthrobacter sp. AG30 was 4,618,494 bp, with a G+C content of 66.2%. Interesting genes and operons putatively conferring resistance to copper and arsenic were identified.