Comparison of Transcriptome Differences between Two Rice Cultivars Differing in Cadmium Translocation from Spike-Neck to Grain.

At present, the mechanism of varietal differences in cadmium (Cd) accumulation in rice is not well understood. Two rice cultivars, ZZY (high translocation-high grain Cd) and SJ18 (low translocation-low grain Cd), were used to analyze transcriptome differences in the spike-neck tissue in field trials. The results showed that, compared with ZZY, 22,367 differentially expressed genes (DEGs) were identified in SJ18, including 2941 upregulated and 19,426 downregulated genes. GO analysis enriched 59 downregulated terms, concerning 24 terms enriched for more than 1000 DEGs, including cellular and metabolic processes, biological regulation, localization, catalytic activity, transporter activity, signaling, etc. KEGG enrichment identified 21 significant downregulated pathways, regarding the ribosome, metabolic pathways, biosynthesis of secondary metabolism, signaling transduction, cell membrane and cytoskeleton synthesis, genetic information transfer, amino acid synthesis, etc. Weighted gene co-expression network analysis (WGCNA) revealed that these DEGs could be clustered into five modules. Among them, the yellow module was significantly related to SJ18 with hub genes related to OsHMA and OsActin, whereas the brown module was significantly related to ZZY with hub genes related to mitogen-activated protein kinase (MAPK), CBS, and glutaredoxin. This suggests that different mechanisms are involved in the process of spike-neck-grain Cd translocation among varieties. This study provides new insights into the mechanisms underlying differences in Cd transport among rice varieties.

Biochar loaded with root exudates of hyperaccumulator Leersia hexandra Swartz facilitated Cr(VI) reduction by shaping soil functional microbial communities.

Cr(VI) contamination is widely recognized as one of the major environmental hazards. To address the problem of remediation of soil Cr(VI) contamination and utilization of waste peanut shells, this study comprehensively investigated the effects of peanut shell-derived biochar loaded with root exudates of hyperaccumulator Leersia hexandra Swartz on Cr(VI) reduction and microbial community succession in soil. This study confirmed that root exudate-loaded peanut shell biochar reduced soil pH while simultaneously increasing DOC, sulfide, and Fe(II) concentrations, thereby facilitating the reduction of Cr(VI), achieving a reduction efficiency of 81.8%. Based on XPS and SEM elemental mapping analyses, Cr(VI) reduction occurred concurrently with the Fe and S redox cycles. Furthermore, the microbial diversity, abundance of the functional genera (Geobacter, Arthrobacter, and Desulfococcus) and the metabolic functions associated with Cr(VI) reduction were enhanced by root exudate-loaded biochar. Root exudate-loaded biochar can promote both direct Cr(VI) reduction mediated by the Cr(VI)-reducing bacteria Arthrobacter, and indirect Cr(VI) reduction through Cr/S/Fe co-transformation mediated by the sulfate-reducing bacteria Desulfococcus and Fe(III)-reducing bacteria Geobacter. This study demonstrates the effectiveness of peanut shell biochar loaded with root exudates of hyperaccumulator Leersia hexandra Swartz to promote soil Cr(VI) reduction, reveals the mechanism how root exudate-loaded biochar shapes functional microbial communities to facilitate Cr(VI) reduction, and proposes a viable strategy for Cr(VI) remediation and utilization of peanut shell.

Comparative transcriptome analysis reveals key genes and coordinated mechanisms in two rice cultivars differing in cadmium accumulation.

Although Cd accumulation varies among rice varieties is recognized, the underlying mechanisms are not well clarified. In this study, comparative transcriptome analysis were performed by hydroponic culture system with two rice varieties, Y1540 (high Cd accumulator) and Y15 (low Cd accumulator) under 20 µM Cd stress. Results revealed 17,320 differentially expressed genes (DEGs) in roots of Y15 (7,655 upregulated and 9,665 downregulated) and 17,386 DEGs in roots of Y1540 (8,823 upregulated and 8,563 downregulated) expose to 20 µM Cd stress. Gene ontology (GO) analysis enriched 24 and 26 terms in Y15 and Y1540 respectively, including 23 common terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment showed 27 and 28 significant pathways in Y15 and Y1540 respectively, with 19 common pathways. Different responses to Cd stress between cultivars were not only reflected in differently enriched GO terms and KEGG pathways but also in different DEGs of 23 common GO terms and significant sequences represented by p-values of 19 common KEGG pathways. Both cultivars resist Cd through common processes with different weights; hence glutathione metabolism, mineral absorption, biosynthesis of secondary metabolites, and degradation of aromatic compounds could be playing a more important role in Y1540, whereas ribosome biogenesis in eukaryotes, mismatch repair, aminoacyl-tRNA biosynthesis, and the cell cycle maybe playing a more important role in Y15. Weighted gene co-expression network analysis (WGCNA) showed that five and three modules were clustered in Y15 and Y1540, respectively, with yellow and brown modules in Y15 and brown modules in Y1540 being significantly related to Cd stress. Further analysis showed that most of hub genes in Y15 were related to signal transduction or transcription factors, while most of hub genes in Y1540 were related to binding, metabolic, and secondary metabolic processes, which demonstrated their different response patterns at transcriptomic level to Cd stress.

Comparative transcriptomic analysis reveals the important process in two rice cultivars with differences in cadmium accumulation.

To date, Cd remains a major contaminant in rice production. An in-depth exploration of the mechanism that causes genotypic differences in Cd enrichment in rice is necessary to develop strategies to regulate Cd enrichment in rice. Here, two rice cultivars (low grain Cd, ZZ143; and high grain Cd, YX409) displayed different transcriptomic profile patterns when subjected to 100µmol/L Cd stress. In fact, 18,721(9833 upregulated and 8888 downregulated) and 16,403 (8366 upregulated and 8037 downregulated) differentially expressed genes (DEGs) were found in ZZ143 and YX409, respectively. Gene ontology (GO) classification revealed 28 and 26 terms enriched in ZZ143 and YX409, respectively. ZZ143 had more enriched DEGs than YX409, primarily in cellular processes, metabolic processes, binding terms, catalytic activity, etc. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 21 and 24 pathways were significantly enriched in ZZ143 and YX409, respectively. Based on the DEGs, ZZ143 had a stronger ability for sulfur assimilation and Cys synthesis, whereas YX409 had a stronger ability to maintain cell wall stability. A series of DEGs involved in metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction pathways, and mitogen-activated protein kinase signaling pathways were identified, which maybe closely related to Cd resistance and the different Cd concentrations between cultivars. The above pathways and the greater number of identified DEGs in more than half of the GO terms and KEGG pathways suggest a higher absorption and stronger tolerance of the roots of ZZ143 than YX409 to Cd.

Citric acid secretion from rice roots contributes to reduction and immobilization of Cr(VI) by driving microbial sulfur and iron cycle in paddy soil.

Root exudates released by plants can promote microbial growth and activity, thereby affecting the transformation and availability of soil pollutants. However, the effects of the root exudates of rice plants on chromium (Cr) transformation in paddy soils and the underlying mechanisms are yet to be elucidated properly. The present study investigated how rice root exudates interact with rhizosphere microorganisms to influence the transformation of Cr and explored the key components in root exudates that affect Cr(VI) reduction. The results showed that the addition of root exudate and citric acid markedly decreased soil pH and increased dissolved organic carbon content that created favorable conditions and provided sufficient electron donors for Cr(VI) reduction, thereby greatly facilitating the reduction of Cr(VI) and the transformation of HOAc-extractable Cr into more stable oxidizable and residual Cr. Additionally, Desulfovibrio-related sulfate-reducing bacteria, Thiobacillus-related sulfide-oxidizing bacteria, and Geobacter-related Fe(III)-reducing bacteria were enriched with the addition of root exudate and citric acid. Among them, sulfate would be reduced by Desulfovibrio to sulfide, which would be further utilized by Thiobacillus to reduce Cr(VI), thereby enabling the continuous reduction of Cr(VI); simultaneously, Geobacter would sustain the reduction of Cr(VI) by reducing Fe(III) to Fe(II). Furthermore, based on the high-level secretion of citric acid in response to Cr(VI) exposure and the similar effects of root exudates and citric acid on Cr(VI) reduction, it is proposed that citric acid is the key component in rice root exudates that affects Cr(VI) reduction. These results suggest that root exudates (citric acid as the key component) contribute to the reduction and immobilization of Cr(VI) by driving microbial S and Fe cycles, with Desulfovibrio, Thiobacillus, and Geobacter being the keystone genera. The study provides a novel insight into the Fe/S/Cr co-transformation processes with microbial involvement, and the artificial root exudate mixtures designed to reduce Cr(VI).

Continuously applying compost for three years alleviated soil acidity and heavy metal bioavailability in a soil-asparagus lettuce system.

Soil acidification and heavy metal pollution are two common barrier factors threatening plant growth and agro-product quality. Applying manure compost is promising to alleviate soil acidity, while it may increase heavy metal accumulation in soil. In a 3-year field experiment, compost was applied for 12 consecutive harvest seasons at 15, 30, and 45 t ha-1 in a slightly acidic soil. Samples were taken at the twelfth season to examine the changes of soil properties, vegetable productivity, heavy metal accumulation and bioavailability in the soil-asparagus lettuce system. The results showed that the pH values of the topsoil were increased by 0.49-0.75 units in compost added soils compared with no compost control, soil organic matter (SOM) contents and cation exchange capacity (CEC) were increased by 34-101% and 43-44%, respectively. The soil nutrient contents were also increased in compost treatments. Continuously applying compost increased Cd, Cu, and Zn concentrations in topsoil by up to 32, 20, and 22% and decreased Pb by 10%, while soil available Cd and Zn concentrations were reduced by up to 54 and 86%, and available Cu was increased by 19-63%. The biomass of asparagus lettuce was increased by 30-59% in compost treatments, with Cd and Zn concentrations in the plant tissues reduced by 28-50% and 14-67%. Cu concentrations in the lettuce shoots were increased by 20-39%. The concentration factor and total uptake of Cd and Zn in lettuce were effectively reduced in compost treatments. Cd was more prone to be taken up, translocated and accumulated from soil to the lettuce plant than the other heavy metals. Continuously applying compost over 3 years increased soil pH, SOM, CEC, nutrient contents, and lettuce productivity, decreased Cd and Zn bioavailability in the soil-lettuce system, while posing a risk of increasing heavy metal accumulation in topsoil.

Multi-Component Passivators Regulate Heavy Metal Accumulation in Paddy Soil and Rice: A Three-Site Field Experiment in South China.

To fulfill sustainability principles, a three-site field experiment was conducted to screen suitably mixed passivators from lime + biochar (L + C, 9000 kgha-1 with a rate of 1:1) and lime + biochar + sepiolite (L + C + S, 9000 kg ha-1 with a rate of 1:1:1), in Yuecheng (YC), Zhuji (ZJ), and Fuyang (FY), where there are typical contaminated soils, in South China. Treated with passivators in soil, DTPA-extractable Cd, Crand Pb in soil were decreased by 9.87-26.3%, 37.2-67.5%, and 19.0-54.2%, respectively; Cd, Cr, and Pb in rice were decreased by 85.9-91.5%, 40.0-76.5%, and 16.4-45.4%, respectively; and these were followed by slightly higher efficacy of L + C + S than L + C. The differences between L + C and L + C + S mainly lie in soil microbial communities, enzymes, and fertility. In YC, treatment with L + C + S increased microbial carbon and activities of urease (EC3.5.1.5) and phosphatase (EC3.1.3.1) by 21.0%, 85.5%, and 22.3%; while treatment with L + C decreased microbial carbon and activities of phosphatase and sucrose (EC3.2.1.26) by 1.31%, 34.9%, and 43.4%, respectively. Moreover, the treatment of FY soils with L + C + S increased microbial carbon and activities of urease, phosphatase, and sucrase by 35.4%, 41.6%, 27.9%, and 7.37%; and L + C treatment only increased the microbial carbon and the activity of phosphatase by 3.14% and 30.3%, respectively. Furthermore, the organic matter and available nitrogen were also increased by 8.8-19.0% and 7.4-14.6% with L + C + S treatments, respectively. These suggested that the combination of L + C + S stimulated the growth of soil microbial communities and increased the activity of soil enzymes. Therefore, the L + C + S strategy can be a practical and effective measure for safe rice production as it was more suitable for the remediation of heavy metals in our experimental sites.

Responses of microbial community composition and function to biochar and irrigation management and the linkage to Cr transformation in paddy soil.

Combining biochar with irrigation management to alter the microbial community is a sustainable method for remediating soils contaminated by heavy metals. However, studies on how these treatments promote Cr(VI) reduction are limited, and the corresponding microbial mechanisms are unclear. Therefore, we conducted a pot experiment to explore the responses of soil microbial communities to combined biochar amendment and irrigation management strategies and their involvement in Cr transformation in paddy soils. Six treatments were established using varying concentrations of biochar (0, 1, and 2% [w/w]) combined with two irrigation management strategies (continuous flooding [CF] and dry-wet alternation [DWA]). The results showed that the combined biochar addition and irrigation management strategy significantly altered soil pH, redox potential, organic matter content, and Fe(II) and sulfide concentrations. In addition, the Cr(VI) concentration under CF irrigation management was conspicuously lower (48.2-54.4%) than that under DWA irrigation management. Biochar amendment also resulted in a substantial reduction (8.8-27.4%) in Cr(VI) concentration. Moreover, the changes in soil physicochemical properties remarkably affected the soil microbial community. The microbial diversity and abundance significantly increased with biochar amendment. Furthermore, the combined biochar amendment and CF strategy stimulated the growth of Geobacter- and Anaeromyxobacter-related Fe(III)-reducing bacteria, Gallionella-related Fe(II)-oxidizing bacteria, and Desulfovibro- and Clostridium-related sulfate-reducing bacteria, which simultaneously facilitated the generation of Fe(II) and sulfide, thereby enhancing Cr(VI) reduction. Consequently, our results suggest that the effectively increased abundance of Fe-reducing/oxidizing bacteria and sulfate-reducing bacteria via combined CF irrigation management and biochar addition may be a key factor in reducing Cr(VI) in paddy soil. The keystone genera responsible for Cr(VI) reduction were Geobacter, Anaeromyxobacter, Gallionella, Desulfovibro, and Clostridium. This study provides novel insights into the coupling mechanism of the Fe/S/Cr transformation mediated by Fe-reducing/oxidizing bacteria and sulfate-reducing bacteria.

The effect of sepiolite application on rice Cd uptake - A two-year field study in Southern China.

Sepiolite (SEP) is a clay mineral with great potential to stabilize soil heavy metals. A two-year field experiment was conducted to explore the optimum use of SEP to immobilize soil Cd and to promote the consumption safety of rice grown in a typical paddy field in Southern China. SEP was applied once or twice over the two-year study at three levels (0.1, 0.5, and 1%, w/w) before rice planting. The results showed that SEP effectively reduced rice grain Cd concentrations by 47-49% in the first year and by 44-50% in the second year due to the residue effect. Application of SEP for two consecutive years reduced the rice grain Cd concentration by up to 75%, achieving a safe level (<0.2 mg kg-1). SEP also reduced Zn concentrations in rice grains (by 6-10%), while the Cd/Zn ratios of rice grains were decreased by 24-72% over the two years, implying it was much safer for consumption. SEP significantly increased the soil pH (0.9-1.8 units) and available phosphorus, and it reduced the soil available Cd (by 20-95%) and Zn concentrations (by 30-99%). In brief, SEP effectively stabilized soil Cd and reduced uptake by rice; the effect was dose-dependent and 0.5% (w/w) was optimum in the present study. The main mechanism of SEP to stabilize soil Cd is the increase in soil pH analogous to liming. This study shows that SEP application can be an efficient way to remediate Cd contaminated rice paddies and fulfill the goal of safe production of rice and thereby reduce the health risks associated with consuming rice.