Unveiling potential roles of earthworms in mitigating the presence of virulence factor genes in terrestrial ecosystems.

Earthworms can redistribute soil microbiota, and thus might affect the profile of virulence factor genes (VFGs) which are carried by pathogens in soils. Nevertheless, the knowledge of VFG profile in the earthworm guts and its interaction with earthworm gut microbiome is still lacking. Herein, we characterized earthworm gut and soil microbiome and VFG profiles in natural and agricultural ecosystems at a national scale using metagenomics. VFG profiles in the earthworm guts significantly differed from those in the surrounding soils, which was mainly driven by variations of bacterial communities. Furthermore, the total abundance of different types of VFGs in the earthworm guts was about 20-fold lower than that in the soils due to the dramatic decline (also by approximately 20-fold) of VFG-carrying bacterial pathogens in the earthworm guts. Additionally, five VFGs related to nutritional/metabolic factors and stress survival were identified as keystones merely in the microbe-VFG network in the earthworm guts, implying their pivotal roles in facilitating pathogen colonization in earthworm gut microhabitats. These findings suggest the potential roles of earthworms in reducing risks related to the presence of VFGs in soils, providing novel insights into earthworm-based bioremediation of VFG contamination in terrestrial ecosystems.

VFG-Chip: A high-throughput qPCR microarray for profiling virulence factor genes from the environment.

As zoonotic pathogens are threatening public health globally, the virulence factor genes (VFGs) they carry underlie latent risk in the environment. However, profiling VFGs in the environment is still in its infancy due to lack of efficient and reliable quantification tools. Here, we developed a novel high-throughput qPCR (HT-qPCR) chip, termed as VFG-Chip, to comprehensively quantify the abundances of targeted VFGs in the environment. A total of 96 VFGs from four bacterial pathogens including Klebsiella pneumoniae, Acinetobacter baumannii, Escherichia coli, and Salmonella enterica were targeted by 120 primer pairs, which were involved in encoding five types of virulence factors (VFs) like toxin, adherence, secretion system, immune evasion/invasion, and iron uptake. The specificity of VFG-Chip was both verified computationally and experimentally, with high identity of amplicon sequencing and melting curves analysis proving its robust capability. The VFG-Chip also displayed high sensitivity (by plasmid serial dilution test) and amplification efficiency averaging 97.7%. We successfully applied the VFG-Chip to profile the distribution of VFGs along a wastewater treatment system with 69 VFGs detected in total. Overall, the VFG-Chip provides a robust tool for comprehensively quantifying VFGs in the environment, and thus provides novel information in assessing the health risks of zoonotic pathogens in the environment.

Optimal soil Eh, pH for simultaneous decrease of bioavailable Cd, As in co-contaminated paddy soil under water management strategies.

The co-contamination with cadmium (Cd) and arsenic (As) in the paddy soil is the most seriously combined pollution of toxic elements in China, and it is rather difficult to decrease bioavailable Cd and As levels in soil because of the opposite ionic forms of bioavailable Cd (cation) and As (anion). This study explored the optimal conditions of Eh and pH in different soils for simultaneous decrease of Cd and As bioavailabilities in the soil-rice system through soil culture and rice pot experiments under water management strategies. The results showed that near neutral soil pH (7.0) were eventually observed under long-term flooding conditions. Under unflooded conditions, soil pH is the dominant factor influencing bioavailabilities of Cd and As, while under flooded conditions, Eh becomes the most important factor. Pot experiments showed that flooding significantly reduced the Cd concentration in rice grains from 54.5% to 95.5%, but concomitantly increased rice As concentration substantially (214%-302%). By evaluating the trade-off value between the bioavailabilities of Cd and As in the soil, the minimal trade-off value was obtained when the soil Eh was -130 mV and the pH was 6.8.

Mechanisms of Fe biofortification and mitigation of Cd accumulation in rice (Oryza sativa L.) grown hydroponically with Fe chelate fertilization.

Cadmium contaminated rice from China has become a global food safety issue. Some research has suggested that chelate addition to substrates can affect metal speciation and plant metal content. We investigated the mitigation of Cd accumulation in hydroponically-grown rice supplied with EDTANa2Fe(II) or EDDHAFe(III). A japonica rice variety (Nipponbare) was grown in modified Kimura B solution containing three concentrations (0, 10, 100 µΜ) of the iron chelates EDTANa2Fe(II) or EDDHAFe(III) and 1 µΜ Cd. Metal speciation in solution was simulated by Geochem-EZ; growth and photosynthetic efficiency of rice were evaluated, and accumulation of Cd and Fe in plant parts was determined. Net Cd fluxes in the meristematic zone, growth zone, and maturation zone of roots were monitored by a non-invasive micro-test technology. Expression of Fe- and Cd-related genes in Fe-sufficient or Fe-deficient roots and leaves were studied by QRT-PCR. Compared to Fe deficiency, a sufficient or excess supply of Fe chelates significantly enhanced rice growth by elevating photosynthetic efficiency. Both Fe chelates increased the Fe content and decreased the Cd content of rice organs, except for the Cd content of roots treated with excess EDDHAFe(III). Compared to EDDHAFe(III), EDTANa2Fe(II) exhibited better mitigation of Cd accumulation in rice by generating the EDTANa2Cd complex in solution, decreasing net Cd influx and increasing net Cd efflux in root micro-zones. Application of EDTANa2Fe(II) and EDDHAFe(III) also reduced Cd accumulation in rice by inhibiting expression of genes involved in transport of Fe and Cd in the xylem and phloem. The 'win-win' situation of Fe biofortification and Cd mitigation in rice was achieved by application of Fe chelates. Root-to-stem xylem transport of Cd and redistribution of Cd in leaves by phloem transport can be regulated in rice through the use of Fe chelates that influence Fe availability and Fe-related gene expression. Fe fertilization decreased Cd influx and increased Cd efflux in rice roots.