Identification of key genes and modules in response to Cadmium stress in different rice varieties and stem nodes by weighted gene co-expression network analysis

Abstract Soil cadmium (Cd) pollution threatens food safety. This study aimed to identify genes related to Cd accumulation in rice. Low- (Shennong 315, short for S315) and high- (Shendao 47, short for S47) Cd-accumulative rice cultivars were incubated with CdCl2·2.5H2O. RNA-seq and weighted gene co-expression network analysis (WGCNA) were performed to identify the modules and genes associated with Cd-accumulative traits of rice. After Cd stress treatment, the Cd content in various tissues of S315 was significantly higher than that of S47. In the stem nodes, the Cd distribution results of the two varieties indicated that the unelongated nodes near the root (short for node A) had a stronger ability to block Cd transfer upwards than the panicle node (short for node B). Cd stress induced huge changes in gene expression profiles. After analyzing the differentially expressed genes (DEGs) in significantly correlated WGCNA modules, we found that genes related to heavy metal transportation had higher expression levels in node A than that in node B, such as Copper transporter 6 (OS04G0415600), Zinc transporter 10 (OS06G0566300), and some heavy-metal associated proteins (OS11G0147500, OS03G0861400, and OS10G0506100). In the comparison results between S315 and S47, the expression of chitinase (OS03G0679700 and OS06G0726200) was increased by Cd treatment in S315. In addition, OsHSPs (OS05G0460000, OS08G0500700), OsHSFC2A (OS02G0232000), and OsDJA5 (OS03G0787300) were found differentially expressed after Cd treatment in S315, but changed less in S47. In summary, different rice varieties have different processes and intensities in response to Cd stress. The node A might function as the key tissue for blocking Cd upward transport into the panicle via vigorous processes, including of heavy metal transportation, response to stress, and cell wall

Influence of Different Vegetation Types on Soil Physicochemical Parameters and Fungal Communities

This study assessed the effects of Betula dahurica (BD), Betula platyphylla (BP), Larix gmelinii (LG), Quercus mongolica (QM), and a mixed conifer–broadleaf forest composed of LG and QM (LGQM) on the soil physicochemical parameters and community structure of fungi in the Zhongyangzhan Black-billed Capercaillie Nature Reserve. Fungal community structures were characterized via ITS rRNA sequencing. The effects of soil parameters on the community structure of soil fungi were assessed by Pearson correlation analysis and redundancy analysis (RDA). LGQM exhibited lower C/N, available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP) compared with the QM broadleaf forest. The fungal Shannon and Simpson diversity indices were highest in BP, whereas LG exhibited the highest ACE index. The Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota fungal phyla were dominant across all vegetation types. Each of the different vegetation types studied herein exhibited a unique fungal community structure. The RDA results indicated that fungal community structures were primarily shaped by the total N, available N, and available P of soil. Our findings thus indicated that forests restored with different species of trees may exhibit variations in soil quality and characteristics despite sharing the same climate. Furthermore, broadleaved and coniferous forests exhibited a unique fungal community diversity and composition

Influence of Different Vegetation Types on Soil Physicochemical Parameters and Fungal Communities

This study assessed the effects of Betula dahurica (BD), Betula platyphylla (BP), Larix gmelinii (LG), Quercus mongolica (QM), and a mixed conifer–broadleaf forest composed of LG and QM (LGQM) on the soil physicochemical parameters and community structure of fungi in the Zhongyangzhan Black-billed Capercaillie Nature Reserve. Fungal community structures were characterized via ITS rRNA sequencing. The effects of soil parameters on the community structure of soil fungi were assessed by Pearson correlation analysis and redundancy analysis (RDA). LGQM exhibited lower C/N, available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP) compared with the QM broadleaf forest. The fungal Shannon and Simpson diversity indices were highest in BP, whereas LG exhibited the highest ACE index. The Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota fungal phyla were dominant across all vegetation types. Each of the different vegetation types studied herein exhibited a unique fungal community structure. The RDA results indicated that fungal community structures were primarily shaped by the total N, available N, and available P of soil. Our findings thus indicated that forests restored with different species of trees may exhibit variations in soil quality and characteristics despite sharing the same climate. Furthermore, broadleaved and coniferous forests exhibited a unique fungal community diversity and composition

Combination of Water-Saving Irrigation and Nitrogen Fertilization Regulates Greenhouse Gas Emissions and Increases Rice Yields in High-Cold Regions, Northeast China

Increased rice production, which benefitted from cropping areas expansion and continuous N applications, resulted in severe increases in greenhouse gases (GHG) emissions from 1983 to 2019 in Heilongjiang Province, China. Therefore, field trials were performed in the high-cold Harbin region, Northeast China, to determine the efficiency of incorporating water regimes with N fertilization in minimizing the impact of rice production on GHG emissions. Two water-saving irrigation strategies, intermittent irrigation (W1) and control irrigation (W2), were used relative to continuous flooding (W0), and we combined them with six fertilized treatments. Our results demonstrated that W1 and W2 significantly decreased seasonal CH4 emissions by 19.7–30.0% and 11.4–29.9%, enhanced seasonal N2O emissions by 77.0–127.0% and 16.2–42.4%, and increased significantly yields by 5.9–12.7% and 0–4.7%, respectively, compared with W0. Although trade-offs occurred between CH4 and N2O emissions, W1 and W2 resulted in significant reductions in global warming potential (GWP). Moreover, low N rates (<120 kg N ha−1) performed better in GWP than high N rates. N fertilization and irrigation regimes had remarkable effects on rice yields and GWP. In conclusion, the incorporation of W1 and a N application under 120 kg N ha−1 could simultaneously mitigate GWP while enhancing production in black soils in high-cold Northeast China

Crop Residue Return Rather Than Organic Manure Increases Soil Aggregate Stability under Corn–Soybean Rotation in Surface Mollisols

Fertilization practices change soil organic carbon content and distribution, which is relevant to crop rotation and soil aggregates. However, how fertilization management under corn–soybean rotation affects soil organic carbon and aggregate stability at different soil depths in Mollisols is unclear. The effects of 6–yr fertilization under corn–soybean rotation on aggregate stability, soil organic carbon content and storage, and size distribution in soil aggregates were investigated. Five different fertilization practices were carried out in 2013: corn and soybean without fertilizer; corn with chemical fertilizer, soybean without fertilizer; corn with chemical fertilizer, soybean without fertilizer, returning the corn and soybean residues; corn and soybean with chemical fertilizer; and corn with chemical fertilizer, soybean with farmyard manure. Compared with corn and soybean without fertilizer, returning the corn and soybean residues increased bulk SOC content, and enhanced mean weight diameter and geometric mean diameter values at 0–10 cm because of increased water–stable aggregates (WSA) larger than 2 mm proportion and decreased WSA proportion. Simultaneously, corn with chemical fertilizer and soybean with farmyard manure increased bulk soil organic carbon content but reduced mean weight diameter and geometric mean diameter values at 0–20 cm due to increased WSA proportion and decreased WSA>2mm proportion. Altogether, the application of consecutive returning crop residues and chemical fertilizer in alternate years is the most favorable approach for soil organic carbon accumulation and aggregate stability at 0–10 cm under corn–soybean rotation in Mollisols

Crop Residue Return Rather Than Organic Manure Increases Soil Aggregate Stability under Corn–Soybean Rotation in Surface Mollisols

Fertilization practices change soil organic carbon content and distribution, which is relevant to crop rotation and soil aggregates. However, how fertilization management under corn–soybean rotation affects soil organic carbon and aggregate stability at different soil depths in Mollisols is unclear. The effects of 6–yr fertilization under corn–soybean rotation on aggregate stability, soil organic carbon content and storage, and size distribution in soil aggregates were investigated. Five different fertilization practices were carried out in 2013: corn and soybean without fertilizer; corn with chemical fertilizer, soybean without fertilizer; corn with chemical fertilizer, soybean without fertilizer, returning the corn and soybean residues; corn and soybean with chemical fertilizer; and corn with chemical fertilizer, soybean with farmyard manure. Compared with corn and soybean without fertilizer, returning the corn and soybean residues increased bulk SOC content, and enhanced mean weight diameter and geometric mean diameter values at 0–10 cm because of increased water–stable aggregates (WSA) larger than 2 mm proportion and decreased WSA<0.053mm proportion. Simultaneously, corn with chemical fertilizer and soybean with farmyard manure increased bulk soil organic carbon content but reduced mean weight diameter and geometric mean diameter values at 0–20 cm due to increased WSA<0.053mm proportion and decreased WSA>2mm proportion. Altogether, the application of consecutive returning crop residues and chemical fertilizer in alternate years is the most favorable approach for soil organic carbon accumulation and aggregate stability at 0–10 cm under corn–soybean rotation in Mollisols