Publications

The over-use of antibiotics in animal husbandry in China and the concomitant enhanced selection of antibiotic resistance genes (ARGs) in animal manures are of serious concern. Thermophilic composting is an effective way of reducing hazards in organic wastes. However, its effectiveness in antibiotic degradation and ARG reduction in commercial operations remains unclear. In the present study, we determined the concentrations of 15 common veterinary antibiotics and the abundances of 213 ARGs and 10 marker genes for mobile genetic elements (MGEs) in commercial composts made from cattle, poultry and swine manures in Eastern China. High concentrations of fluoroquinolones were found in the poultry and swine composts, suggesting insufficient removal of these antibiotics by commercial thermophilic composting. Total ARGs in the cattle and poultry manures were as high as 1.9 and 5.5 copies per bacterial cell, respectively. After thermophilic composting, the ARG abundance in the mature compost decreased to 9.6% and 31.7% of that in the cattle and poultry manure, respectively. However, some ARGs (e.g. aadA, aadA2, qacEΔ1, tetL) and MGE marker genes (e.g. cintI-1, intI-1 and tnpA-04) were persistent with high abundance in the composts. The antibiotics that were detected at high levels in the composts (e.g. norfloxacin and ofloxacin) might have posed a selection pressure on ARGs. MGE marker genes were found to correlate closely with ARGs at the levels of individual gene, resistance class and total abundance, suggesting that MGEs and ARGs are closely associated in their persistence in the composts under antibiotic selection. Our research shows potential disseminations of antibiotics and ARGs via compost utilization.

Toxic metal pollution is ubiquitous in soils, yet its worldwide distribution is unknown. We analyzed a global database of soil pollution by arsenic, cadmium, cobalt, chromium, copper, nickel, and lead at 796,084 sampling points from 1493 regional studies and used machine learning techniques to map areas with exceedance of agricultural and human health thresholds. We reveal a previously unrecognized high-risk, metal-enriched zone in low-latitude Eurasia, which is attributed to influential climatic, topographic, and anthropogenic conditions. This feature can be regarded as a signpost for the Anthropocene era. We show that 14 to 17% of cropland is affected by toxic metal pollution globally and estimate that between 0.9 and 1.4 billion people live in regions of heightened public health and ecological risks.

Summary Single and double low varieties of oilseed rape were grown in the 1987/88 and 1988/89 seasons to study changes in the concentrations of total and individual glucosinolates within pods during development. Total glucosinolate concentration in seeds of all varieties increased during development when expressed on a fresh weight basis. The levels of the major alkenyl glucosinolates present in the seed; 2–hydroxy‐3–butenyl, 3–butenyl and 4–pentenyl had been reduced in the transition from single to double low varieties. The major indole glucosinolates in the seed, 4–hydroxy‐3–indolylmethyl and 3–indolylmethyl were present in the same amounts in single and double low varieties but in the latter represented a greater proportion of the total seed glucosinolate content. A decline in the total glucosinolate concentration in the pod walls with time together with the analogous profile of individual glucosinolates in the seeds and pod walls suggests that the pod wall is a major site of seed glucosinolate synthesis. Other plant parts may also have an important role to play in provision of intact glucosinolates or precursors to the pod walls for glucosinolate biosynthesis.

A novel bacterium with strong arsenic (As) methylation and volatilization abilities, designated strain SM-1T, was isolated from an As-contaminated paddy soil. SM-1T is strictly aerobic, rod-shaped, non-motile, Gram-negative and orange-coloured. Phylogenetic analysis revealed that strain SM-1T showed low 16S rRNA gene sequence similarities (≤88 %) to members of established genera in the family Cytophagaceae. Growth of this strain was observed at 15-45 °C (optimum, 37 °C), pH 6.0-8.0 (optimum, 7.0) and 0-0.5 % (w/v) NaCl. The major cellular fatty acids were C16 : 1ω5c and iso-C15 : 0. The respiratory quinone was MK-7, and the predominant polar lipids were phosphatidylethanolamine, an unidentified lipid (L), and an unidentified aminolipid (AL2). The DNA G+C content was 51.5 mol%. On the basis of phenotypic, phylogenetic and chemotaxonomic properties, strain SM-1T represents a novel species in a new genus within the family Cytophagaceae, for which the name Arsenicibacter rosenii gen. nov., sp. nov. is proposed. The type strain of Arsenicibacter rosenii is SM-1T (=CCTCC AB 2017086T=KCTC 52624T).

This chapter focuses on the role played by beneficial elements such as sodium (Na), silicon (Si), cobalt (Co), selenium (Se), and aluminum (Al). Sodium can stimulate growth of plants, particularly some C4 plants by aiding the movement of substrates between the mesophyll and the bundle sheath. It can also replace K to some extent in its role as osmoticum, and the application of Na fertilizers to sugar beet results in an increase in the leaf area index early in the growing season, thus increasing light interception and improving water use efficiency of leaves under conditions of moderate drought stress. Silicon plays an important role in cell wall stability by bridging between polyuronides and stimulating lignin synthesis. It can improve plant and leaf erectness, water use, and protect plants from pests and diseases. Silicon is also effective in alleviating toxicity of other metals such as Fe, Al, Cd, and Zn, which can be attributed to the interaction between Si and metals in the apoplasm or symplasm. Cobalt is essential for N2 fixing plants because it is part of the coenzyme cobalamin (vitamin B12), which is important in nodule metabolism. The chemistry of Se is similar to that of S and can replace S, to some extent, in proteins, particularly in Se hyperaccumulating plants. Selenium is essential for animals; therefore Se fertilization may be beneficial for human and animal health in areas with Se-deficient soils. Aluminum is beneficial to some plants, such as tea, and may alleviate proton toxicity and increase the activity of antioxidant enzymes.

Soil contamination in some areas of southern China has resulted in elevated dietary intake of cadmium (Cd), posing a potential risk to human health. A survey of paired soil-rice (n = 200) and soil-vegetable (n = 142) samples was conducted in Xiangtan county of Hunan province, southern China. The concentrations of Cd in all the samples were determined by inductively coupled plasma mass spectrometry. Dietary intakes of Cd from the consumption of locally produced rice and vegetables were estimated for different age groups. Among the 342 crop samples collected in the survey, 88% and 29% of rice grain and vegetable samples, respectively, exceeded the Chinese maximum permissible limit for Cd (0.2 mg dry weight kg−1, 0.2 mg fresh weight kg−1 and 0.1 mg fresh weight kg−1 for rice, leafy vegetables and for rootstalk and legume vegetables, respectively). The median dietary Cd intake varied from 66.5 to 116 μg Cd kg−1 body weight (BW) month−1, with children (4–11 years) exhibiting the highest intake. These values are 2.7–4.6 times the tolerable dietary intake of 25 μg kg−1 BW month−1 recommended by the Joint FAO/WHO Expert Committee on Food Additives. For the general population in Xiangtan county, rice contributed the majority (81%) of the Cd intake with vegetables contributing only 19%. The median hazard quotient calculated from dietary Cd intake was 2.4 times the permissible level, indicating a high risk to the local residents. This study highlights an urgent need to reduce the transfer of Cd from soil to the food chain in the investigated region.

<title>Abstract</title> Chemical innovation is essential for fungi to adapt to specific geographical environments and ecological niches. However, it remains unclear how genomic changes drive fungal specialized metabolic differentiation across the biosphere. Here, we studied the global genomic and metabolic diversity of the aflatoxin-producing <italic>Aspergillus flavus</italic> as a case. We generated paired genome and metabolome data for &gt; 550 strains from across China, and supplemented this with 187 publicly available genomes from other countries. We found that the global genetic diversity of <italic>A. flavus</italic> shows strong phylogeographic patterns, with specific clades associating with different environments. These clades exhibit distinct specialized metabolic profiles, with low-aflatoxin-producing clades often producing other mycotoxins instead. Furthermore, clade-specific gene clusters do exist that could be linked to clade-specific metabolites, implying that different niches select for the production of different toxins. Our results reveal that these different mycotoxin profiles are generally not explained by loss or gain of biosynthetic gene clusters, but are likely driven by regulatory and primary metabolic variation. Altogether, our findings provide a framework to understand fungal environmental adaptation and pave the path towards enhanced mycotoxin early risk prediction and ‘personalized’ geographical control strategies.

How arsenic (As) is transported in phloem remains unknown. To help answer this question, we quantified the chemical species of As in phloem and xylem exudates of castor bean (Ricinus communis) exposed to arsenate [As(V)], arsenite [As(III)], monomethylarsonic acid [MMA(V)], or dimethylarsinic acid. In the As(V)- and As(III)-exposed plants, As(V) was the main species in xylem exudate (55%–83%) whereas As(III) predominated in phloem exudate (70%–94%). The ratio of As concentrations in phloem to xylem exudate varied from 0.7 to 3.9. Analyses of phloem exudate using high-resolution inductively coupled plasma-mass spectrometry and accurate mass electrospray mass spectrometry coupled to high-performance liquid chromatography identified high concentrations of reduced and oxidized glutathione and some oxidized phytochelatin, but no As(III)-thiol complexes. It is thought that As(III)-thiol complexes would not be stable in the alkaline conditions of phloem sap. Small concentrations of oxidized glutathione and oxidized phytochelatin were found in xylem exudate, where there was also no evidence of As(III)-thiol complexes. MMA(V) was partially reduced to MMA(III) in roots, but only MMA(V) was found in xylem and phloem exudate. Despite the smallest uptake among the four As species supplied to plants, dimethylarsinic acid was most efficiently transported in both xylem and phloem, and its phloem concentration was 3.2 times that in xylem. Our results show that free inorganic As, mainly As(III), was transported in the phloem of castor bean exposed to either As(V) or As(III), and that methylated As species were more mobile than inorganic As in the phloem.

In a large scale survey of rice grains from markets (13 countries) and fields (6 countries), a total of 1578 rice grain samples were analysed for lead. From the market collected samples, only 0.6% of the samples exceeded the Chinese and EU limit of 0.2μgg−1 lead in rice (when excluding samples collected from known contaminated/mine impacted regions). When evaluating the rice grain samples against the Food and Drug Administration's (FDA) provisional total tolerable intake (PTTI) values for children and pregnant women, it was found that only people consuming large quantities of rice were at risk of exceeding the PTTI from rice alone. Furthermore, 6 field experiments were conducted to evaluate the proportion of the variation in lead concentration in rice grains due to genetics. A total of 4 of the 6 field experiments had significant differences between genotypes, but when the genotypes common across all six field sites were assessed, only 4% of the variation was explained by genotype, with 9.5% and 11% of the variation explained by the environment and genotype by environment interaction respectively. Further work is needed to identify the sources of lead contamination in rice, with detailed information obtained on the locations and environments where the rice is sampled, so that specific risk assessments can be performed.