Publications

Compost-based organic fertilizers made from animal manures often contain high levels of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). However, whether ARGs and MGEs are present intracellularly or extracellularly remains unclear. In the present study, we quantified extracellular ARGs and MGEs (eARGs and eMGEs) and intracellular ARGs and MGEs (iARGs and iMGEs) in 51 commercial organic fertilizers derived from different raw material types by quantitative polymerase chain reaction (qPCR) and metagenomic sequencing. Results from qPCR showed that eARGs and eMGEs accounted for 11 - 56% and 4 - 45% of the total ARGs and MGEs, respectively. Metagenomic analyses showed comparable diversity, mobility and host compositionsbetween eARGs and iARGs. Twenty-four percent of ARGs were present in plasmids, while 56.7% of potentially mobile ARGs were found to be associated with plasmids. Risk patterns were similar between eARGs and iARGs, with high-risk ARGs in the two forms accounting for 6.7% and 8.2% of the total abundances, respectively. Variation partitioning analysis indicated that raw material type and their interactions with environmental factors and bacterial community significantly affected the composition of eARGs (67.3%) and iARGs (67.2%), indicating that the composition of ARGs was largely driven by deterministic mechanisms, which was further substantiated by the null model and neutral community model. Taken together, eARGs are an important reservoir of ARGs in manure composts. More attention should be paid to the contribution of eARGs to the dissemination of antibiotic resistance into the general environment and the corresponding mitigation strategies.

Most of the cadmium (Cd) accumulated in rice grains is derived from its remobilization in soils during the grain filling period when paddy water is drained. The factors affecting Cd remobilization upon drainage remain poorly understood. Here, we show that the free radical effect produced from the oxidation of ferrous sulfides is an important mechanism affecting the oxidative remobilization of Cd during soil drainage. When soils were flooded, microbial sulfate reduction results in the formation of various metal sulfides including CdS and FeS. Upon soil drainage, the oxidation of FeS produced considerable amounts of hydroxyl free radicals (OH•), which could oxidize CdS directly and thereby promote the oxidative dissolution of CdS and increase Cd mobilization in soils. FeS and CdS could also form a within-sulfide voltaic cell, with FeS protecting the oxidative dissolution of CdS due to the lower electrochemical potential of the former. However, this voltaic effect was short-lived and was surpassed by the free radical effect. The amounts and composition of metal sulfides formed during soil flooding vary with soils, and the oxidative dissolution of CdS is affected by both the free radical and voltaic effects offered by different metal sulfides. These effects are also applicable to the biogeochemistry of other chalcophile trace elements coupled with sulfur and iron redox cycles during the anoxic-oxic transition in many environments.

The role of root hairs in Cd acquisition from soil was investigated in three pot experiments using a root hairless mutant (bald root barley, brb) and its wild-type (WT) cultivar of barley (Hordeum vulgare). brb had significantly lower concentrations and lower total amounts of Cd in shoots than WT. The Cd uptake efficiency based on total root length was 8–45% lower in brb than in WT. The difference between brb and WT increased with increasing extractable Cd in soil under the experimental conditions used. Additions of phosphate to soil decreased Cd extractability. Both soil and foliar additions of phosphate decreased root length, and root hair formation in WT. These effects resulted in decreased Cd uptake with increasing P supply. Cd uptake in WT correlated significantly with root length, root hair length and density, and soil extractable Cd. Root hairs contribute significantly to Cd uptake by barley.

Arsenic (As) contamination of paddy soils threatens rice cultivation and the health of populations relying on rice as a staple crop. In the present study, isotopic dilution techniques were used to determine the chemically labile (E value) and phytoavailable (L value) pools of As in a range of paddy soils from Bangladesh, India, and China and two arable soils from the UK varying in the degree and sources of As contamination. The E value accounted for 6.2–21.4% of the total As, suggesting that a large proportion of soil As is chemically nonlabile. L values measured with rice grown under anaerobic conditions were generally larger than those under aerobic conditions, indicating increased potentially phytoavailable pool of As in flooded soils. In an incubation study, As was mobilized into soil pore water mainly as arsenite under flooded conditions, with Bangladeshi soils contaminated by irrigation of groundwater showing a greater potential of As mobilization than other soils. Arsenic mobilization was best predicted by phosphate-extractable As in the soils.

Mineral binding is a major mechanism for soil carbon (C) stabilization, and mineral availability for C binding critically affects C storage. Yet, the mechanisms regulating mineral availability are poorly understood. Here, we showed that organic amendments in three long-term (23, 154, and 170 yrs, respectively) field experiments significantly increased mineral availability, particularly of short-range-ordered (SRO) phases. Two microcosm studies demonstrated that the presence of roots significantly increased mineral availability and promoted the formation of SRO phases. Mineral transformation experiments and isotopic labeling experiments provided direct evidence that citric acid, a major component of root exudates, promoted the formation of SRO minerals, and that SRO minerals acted as "nuclei" for C retention. Together, these findings indicate that soil organic amendments initialize a positive feedback loop by increasing mineral availability and promoting the formation of SRO minerals for further C binding, thereby possibly serving as a management tool for enhancing carbon storage in soils.

Reductive mobilization of arsenic (As) in paddy soils under flooded conditions is an important reason for the relatively high accumulation of As in rice, posing a risk to food safety and human health. The extent of As mobilization varies widely among paddy soils, but the reasons are not well understood. In this study, we investigated As mobilization in six As-contaminated paddy soils (total As ranging from 73 to 122 mg kg−1) in flooded incubation and pot experiments. Arsenic speciation in the solution and solid phases were determined. The magnitude of As mobilization into the porewater varied by > 100 times among the six soils. Porewater As concentration correlated closely with the concentration of oxalate-extractable As, suggesting that As associated with amorphous iron (oxyhydr)oxides represents the potentially mobilizable pool of As under flooded conditions. Soil containing a high level of manganese oxides showed the lowest As mobilization, likely because Mn oxides retard As mobilization by slowing down the drop of redox potential upon soil flooding and maintaining a higher arsenate to arsenite ratio in the solid and solution phases. Additions of a synthetic Mn oxide (hausmannite) to two paddy soils increased arsenite oxidation, decreased As mobilization into the porewater and decreased As concentrations in rice grain and straw. Consistent with previous studies using simplified model systems or pure mineral phases, the present study shows that Mn oxides and amorphous Fe (oxyhydr)oxides are important factors controlling reductive As mobilization in As-contaminated paddy soils. In addition, this study also suggests a potential mitigation strategy using exogenous Mn oxides to decrease As uptake by rice in paddy soils containing low levels of indigenous Mn oxides, although further work is needed to verify its efficacy and possible secondary effects under field conditions.

Metal(loid) resistance genes (MRGs) play important roles in conferring resistance to metal(loid)s in bacterial communities. How MRGs respond to bacterial succession during manure composting remains largely unknown. Metagenomics was used in the present study to investigate the compositional changes of MRGs, their candidate hosts and association with integrons during thermophilic composting of chicken manures. MRGs conferring resistance to 20 metal(loid)s were detected, and their diversity and abundance (normalized to the abundance of 16S rRNA genes) were significantly reduced during composting. MRGs associated with integron were exclusively observed in proteobacterial species. Class 1 integron likely played an important role in maintaining mercury-resistance mer operon genes in composts. Escherichia coli harbored the most abundant MRGs in the original composting material, whereas species of Actinobacteria and Bacilli became more important in carrying MRGs during the late phases. There were significant linear relationships between the relative abundance of some specific bacterial species (E. coli, Actinobacteria species and Enterococcus faecium) and the abundance of MRGs they potentially harbored. The succession of these bacteria contributed to an overall linear regression between the relative abundance of all predicted candidate hosts and the abundance of total MRGs. Our results suggest that the succession of bacterial community was the main driver of MRG dynamics during thermophilic composting.

Perfluorooctanoic acid (PFOA) is widely used in the manufacture of many industrial and household products. To assess the potential environmental risk of PFOA, its accumulation, translocation and phytotoxic effects were investigated using the model plant species Arabidopsis thaliana. Exposure to 18 μM PFOA-F in agar plates did not affect plant growth, but 181–1811 μM PFOA-F inhibited root and shoot growth. PFOA was more phytotoxic on shoot growth than NaF at the equivalent F concentration, with the latter having 3.9–7.6 times higher EC50 for shoot biomass than PFOA. PFOA was efficiently translocated from roots to shoots, where it existed as intact PFOA molecules without transformation evidenced by the 19F NMR spectra. PFOA caused a significant increase in the concentration of H2O2 and malondialdehyde (MDA) in shoots, indicating that oxidative stress is a likely cause of PFOA phytotoxicity.

Considerable proportions of rice grains produced in some areas in southern China contain high concentrations of cadmium (Cd), leading to unsafe levels of dietary Cd intake. Cultivars of Indica rice, widely grown in southern China, are particularly prone to high Cd accumulation in the grain. Effective methods are needed to decrease Cd accumulation in Indica rice.OsHMA3, encoding a tonoplast Cd transporter, was overexpressed in an elite Indica rice cultivar (Zhongjiazao 17) driven by CaMV 35S promoter. The effects on Cd translocation, accumulation and tolerance, as well as on the agronomic traits and micronutrient concentrations were evaluated.OsHMA3 overexpression markedly decreased Cd translocation from roots to shoots and increased Cd tolerance. OsHMA3 overexpression decreased Cd concentrations in brown rice by 94-98%, to levels just above the detection limit, when rice plants were grown in two Cd-contaminated paddy soils. OsHMA3 overexpression generally had no significant effect on grain yield and the concentrations of the essential micronutrients including zinc, iron, copper and manganese in field trials.Overexpression of OsHMA3 is a highly effective method to reduce Cd accumulation in Indica rice, producing rice grains that were almost Cd free with little effect on grain yield or essential micronutrient concentrations.

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