Roles of straw return in shaping denitrifying bacteria in rice rhizosphere soils through effects on root exudates and soil metabolites

doi:10.1007/s42832-024-0261-3

2025, Vol. 7

Issue (1) : 240261 https://doi.org/10.1007/s42832-024-0261-3

Roles of straw return in shaping denitrifying bacteria in rice rhizosphere soils through effects on root exudates and soil metabolites

Pei Chen^1,³, Yu Cheng^1,², Ning Wang^1,²(

), Jian-Guang Yu^1,², Ying Zhao⁴, Li-Hong Xue^1,²

¹. Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
². School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212001, China
³. School of the Environment and Safety Engineering, Jinan University, Jinan 212001, China
⁴. School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China

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Abstract

● Straw return lowered the abundances of nirS and nosZ genes in low nitrogen soil.

● Straw return elevated the abundances of nirK , nirS , and nosZ genes in high nitrogen soil.

● Straw return decreased the relative abundances of root exudates in low nitrogen soil.

● Straw return increased the relative abundances of root exudates in high nitrogen soil.

● Alerted composition of root exudates and soil metabolites shaped rhizosphere denitrifying bacteria.

Rhizosphere denitrification is affected by straw return. However, the roles of root exudates and soil metabolites in shaping denitrifying bacteria under wheat straw return are relatively unexplored. Here, wheat straw was amended at 2% (w/w) to two paddy soils with different levels of nitrogen for rice cultivation, which altered the denitrifying bacterial community compositions of both soils. However, straw amendment decreased the abundances of the nirS and nosZ genes by 63.7% and 30.3% in the low nitrogen soil from Taizhou (TZ) but increased the nirK, nirS, and nosZ gene abundances by 116%, 81.0%, and 155.5% for the high nitrogen soil from Yixing (YX). Correspondingly, straw amendment decreased the relative abundance of root exudates in the categories of amino acids and benzenes for rice cultivated in TZ soil but increased the relative abundance of root exudates in the categories of amino acids for rice grown in YX soil. With elevated root exudates, straw amendment enhanced the relative abundances of many soil metabolites in YX soil such as sorbitol, myristic acid, and pentadecanoic acid, with fold changes > 2. These results suggest that straw return may alter the composition of root exudates and soil metabolites thereby affecting rhizosphere denitrifying bacterial communities and function genes.

Keywords straw return denitrifying bacteria soil organic carbon root exudates metabolites

Corresponding Author(s): Ning Wang

Issue Date: 15 October 2024

Cite this article:

Pei Chen,Yu Cheng,Ning Wang, et al. Roles of straw return in shaping denitrifying bacteria in rice rhizosphere soils through effects on root exudates and soil metabolites[J]. Soil Ecology Letters, 2025, 7(1): 240261.

URL:

https://academic.hep.com.cn/sel/EN/10.1007/s42832-024-0261-3
https://academic.hep.com.cn/sel/EN/Y2025/V7/I1/240261

Tab.1 Effects of wheat straw amendment (2%, w/w) in two paddy soils from Taizhou (TZ) and Yixing (YX) cities, Jiangsu, China, on the properties of rhizosphere soils.

Fig.1 Effects of wheat straw amendment at 2% (w/w) on the copy number of three denitrification genes (nirK, nirS, and nosZ) in rhizosphere soils TZ (A) and YX (B). The two soils were amended with wheat straw and then planted with rice for 62 days for the determination of gene copy number using quantitative real-time PCR. Control: control treatment without straw return; Straw: straw treatment with straw return at 2%. *: significant difference at p < 0.05.

Fig.2 Effects of wheat straw amendment at 2% (w/w) on the community compositions of nirK-, nirS-, and nosZ-type denitrifying bacteria at the class level in TZ and YX rhizosphere soils. (A–C) Bar plots showing bacterial composition at the class level. (D–F) Canonical correspondence analysis (CCA) of bacterial composition. The two soils were amended with wheat straw and then planted with rice for 62 days for the determination of gene copy number using quantitative real-time PCR. Control: control treatment without straw return; Straw: straw treatment with straw return at 2%.

Fig.3 Effects of wheat straw amendment at 2% (w/w) on root exudates for rice growing in TZ and YX soils. (A) Classification of root exudates for rice growing in TZ soil without (Control TZ) and with straw amendment (Straw TZ); (B) Classification of root exudates for rice growing in YX soil without (Control YX) and with straw amendment (Straw YX); (C) Differential root exudates for rice growing in TZ soil between control and straw treatments; (D) Differential root exudates for rice growing in YX soil between control and straw amendment treatments. Root exudates were classified as carbohydrates, alcohols, amines, benzenes, amino acids, fatty acids, organic acids, and unclassified acids. The percentage of each category of root exudates was calculated by dividing the sum of the peak areas of each category by the sum of all peak areas. Substances with relative contribution < 0.5% were classified as Other. Standard scaler value was measured by preprocessing the percentage of root exudates with the normalization method.

Fig.4 Different soil metabolites that identified between control and straw amendment treatments for rhizosphere soils of TZ (A) and YX (B). The two soils were amended with wheat straw at 2% (w/w) and then planted with rice for 62 days for the determination of rhizosphere soil metabolites using untargeted metabolomics. Control: control treatment without straw return; Straw: straw treatment with straw return at 2%.

Fig.5 Pearson correlation of gene abundance (A), alpha diversity based on the Sobs index (B), and beta diversity based on NMDS (c) of nirK-, nirS-, and nosZ-type denitrifying bacteria with soil total organic carbon (TOC) and the major category of soil metabolites.

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