Yong-Guan Zhu

Diverse and abundant antibiotic resistance genes in Chinese swine farms

Antibiotic resistance genes (ARGs) are emerging contaminants posing a potential worldwide human health risk. Intensive animal husbandry is believed to be a major contributor to the increased environmental burden of ARGs. Despite the volume of antibiotics used in China, little information is available regarding the corresponding ARGs associated with animal farms. We assessed type and concentrations of ARGs at three stages of manure processing to land disposal at three large-scale (10,000 animals per year) commercial swine farms in China. In-feed or therapeutic antibiotics used on these farms include all major classes of antibiotics except vancomycins. High-capacity quantitative PCR arrays detected 149 unique resistance genes among all of the farm samples, the top 63 ARGs being enriched 192-fold (median) up to 28,000-fold (maximum) compared with their respective antibiotic-free manure or soil controls. Antibiotics and heavy metals used as feed supplements were elevated in the manures, suggesting the potential for coselection of resistance traits. The potential for horizontal transfer of ARGs because of transposon-specific ARGs is implicated by the enrichment of transposases—the top six alleles being enriched 189-fold (median) up to 90,000-fold in manure—as well as the high correlation (r2 = 0.96) between ARG and transposase abundance. In addition, abundance of ARGs correlated directly with antibiotic and metal concentrations, indicating their importance in selection of resistance genes. Diverse, abundant, and potentially mobile ARGs in farm samples suggest that unmonitored use of antibiotics and metals is causing the emergence and release of ARGs to the environment.

Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam.

The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities under different long-term (17 years) fertilization practices were investigated using real-time polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE). A sandy loam with pH (H(2)O) ranging from 8.3 to 8.7 was sampled in years 2006 and 2007, including seven fertilization treatments of control without fertilizers (CK), those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): NP, NK, PK and NPK, half chemical fertilizers NPK plus half organic manure (1/2OMN) and organic manure (OM). The highest bacterial amoA gene copy numbers were found in those treatments receiving N fertilizer. The archaeal amoA gene copy numbers ranging from 1.54 x 10(7) to 4.25 x 10(7) per gram of dry soil were significantly higher than those of bacterial amoA genes, ranging from 1.24 x 10(5) to 2.79 x 10(6) per gram of dry soil, which indicated a potential role of AOA in nitrification. Ammonia-oxidizing bacteria abundance had significant correlations with soil pH and potential nitrification rates. Denaturing gradient gel electrophoresis patterns revealed that the fertilization resulted in an obvious change of the AOB community, while no significant change of the AOA community was observed among different treatments. Phylogenetic analysis showed a dominance of Nitrosospira-like sequences, while three bands were affiliated with the Nitrosomonas genus. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). These results suggest that long-term fertilization had a significant impact on AOB abundance and composition, while minimal on AOA in the alkaline soil.

Ammonia‐oxidizing archaea: important players in paddy rhizosphere soil?

The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in paddy soil with different nitrogen (N) fertilizer amendments for 5 weeks were investigated using quantitative real-time polymerase chain reaction, denaturing gradient gel electrophoresis (DGGE) jand clone library analysis based on the ammonia monooxygenase alpha-subunit (amoA) gene. Ammonia-oxidizing archaea predominated among ammonia-oxidizing prokaryotes in the paddy soil, and the AOA:AOB DNA-targeted amoA gene ratios ranged from 1.2 to 69.3. Ammonia-oxidizing archaea were more abundant in the rhizosphere than in bulk soil. Rice cultivation led to greater abundance of AOA than AOB amoA gene copies and to differences in AOA and AOB community composition. These results show that AOA is dominant in the rhizosphere paddy soil in this study, and we assume that AOA were influenced more by exudation from rice root (e.g. oxygen, carbon dioxide) than AOB.

Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment

Background: There is growing concern worldwide about the role of polluted soil and water environments in the development and dissemination of antibiotic resistance. Objective: Our aim in this study was to identify management options for reducing the spread of antibiotics and antibiotic-resistance determinants via environmental pathways, with the ultimate goal of extending the useful life span of antibiotics. We also examined incentives and disincentives for action. Methods: We focused on management options with respect to limiting agricultural sources; treatment of domestic, hospital, and industrial wastewater; and aquaculture. Discussion: We identified several options, such as nutrient management, runoff control, and infrastructure upgrades. Where appropriate, a cross-section of examples from various regions of the world is provided. The importance of monitoring and validating effectiveness of management strategies is also highlighted. Finally, we describe a case study in Sweden that illustrates the critical role of communication to engage stakeholders and promote action. Conclusions: Environmental releases of antibiotics and antibiotic-resistant bacteria can in many cases be reduced at little or no cost. Some management options are synergistic with existing policies and goals. The anticipated benefit is an extended useful life span for current and future antibiotics. Although risk reductions are often difficult to quantify, the severity of accelerating worldwide morbidity and mortality rates associated with antibiotic resistance strongly indicate the need for action.

Trace metal contamination in urban soils of China.

The contamination of urban soils can affect the health of people living in urban areas, and the surrounding ecosystems. Urbanization in China has taken place at an unprecedented pace in the last three decades. This paper provides an overview of studies on the quality of urban soils in China with special reference to trace metal contamination. It summarizes the characteristics of accumulation, spatial and temporal distribution, and major sources of various toxic or potentially toxic trace metals in urban soils as reported in recent literature. Levels of pollution in urban soil and road dust were discussed using the concentrations, enrichment factors, pollution indexes, and chemical fractionation of trace metals in major cities of China, and compared with other countries. In future studies, more pollutants in urban environments need to be included in multi-compartmental environmental surveillance for potential risk assessments. In addition to routine urban soil surveys by a harmonized methodology, a comprehensive assessment of soil quality is needed for the control and management of many urban brownfield sites. Taking into consideration pathways of exposure and site characteristics, risk assessment frameworks for major pollutants in urban soils, which integrate land use type and environmental availability, may be developed in the future.

Selenium in higher plants: understanding mechanisms for biofortification and phytoremediation

Selenium (Se) is an essential micronutrient for many organisms, including plants, animals and humans. As plants are the main source of dietary Se, plant Se metabolism is therefore important for Se nutrition of humans and other animals. However, the concentration of Se in plant foods varies between areas, and too much Se can lead to toxicity. As we discuss here, plant Se uptake and metabolism can be exploited for the purposes of developing high-Se crop cultivars and for plant-mediated removal of excess Se from soil or water. Here, we review key developments in the current understanding of Se in higher plants. We also discuss recent advances in the genetic engineering of Se metabolism, particularly for biofortification and phytoremediation of Se-contaminated environments.

An inventory of trace element inputs to agricultural soils in China

It is important to understand the status and extent of soil contamination with trace elements to make sustainable management strategies for agricultural soils. The inputs of trace elements to agricultural soils via atmospheric deposition, livestock manures, fertilizers and agrochemicals, sewage irrigation and sewage sludge in China were analyzed and an annual inventory of trace element inputs was developed. The results showed that atmospheric deposition was responsible for 43-85% of the total As, Cr, Hg, Ni and Pb inputs, while livestock manures accounted for approximately 55%, 69% and 51% of the total Cd, Cu and Zn inputs, respectively. Among the elements concerned, Cd was a top priority in agricultural soils in China, with an average input rate of 0.004 mg/kg/yr in the plough layer (0-20 cm). Due to the spatial and temporal heterogeneity of the sources, the inventory as well as the environmental risks of trace elements in soils varies on a regional scale. For example, sewage sludge and fertilizers (mainly organic and phosphate-based inorganic fertilizers) can also be the predominant sources of trace elements where these materials were excessively applied. This work provides baseline information to develop policies to control and reduce toxic element inputs to and accumulation in agricultural soils.

Exposure to inorganic arsenic from rice: A global health issue?

Many Bangladeshi suffer from arsenic-related health concerns. Most mitigation activities focus on identifying contaminated wells and reducing the amount of arsenic ingested from well water. Food as a source of arsenic exposure has been recently documented. The objectives of this study were to measure the main types of arsenic in commonly consumed foods in Bangladesh and estimate the average daily intake (ADI) of arsenic from food and water. Total, organic and inorganic, arsenic were measured in drinking water and in cooked rice and vegetables from Bangladeshi households. The mean total arsenic level in 46 rice samples was 358 μg/kg (range: 46 to 1110 μg/kg dry weight) and 333 μg/kg (range: 19 to 2334 μg/kg dry weight) in 39 vegetable samples. Inorganic arsenic calculated as arsenite and arsenate made up 87% of the total arsenic measured in rice, and 96% of the total arsenic in vegetables. Total arsenic in water ranged from 200 to 500 μg/L. Using individual, self-reported data on daily consumption of rice and drinking water the total arsenic ADI was 1176 μg (range: 419 to 2053 μg), 14% attributable to inorganic arsenic in cooked rice. The ADI is a conservative estimate; vegetable arsenic was not included due to limitations in self-reported daily consumption amounts. Given the arsenic levels measured in food and water and consumption of these items, cooked rice and vegetables are a substantial exposure pathway for inorganic arsenic. Intervention strategies must consider all sources of dietary arsenic intake.

Carbon cycling by arbuscular mycorrhizal fungi in soil-plant systems.

Arbuscular mycorrhizal fungi (AMF) play an important role in regulating carbon fluxes between the biosphere and the atmosphere. A recent study showed that live hyphae can turn over rapidly, in five to six days on average, suggesting that carbon flow to AMF hyphae might be respired back to the atmosphere quickly. However, that study gives a limited view of the residence time of AMF hyphae in soils. AMF hyphae can also contribute to soil carbon storage through other mechanisms.

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.