Effects of deoxymugineic acid from rice root exudates on bacterial community composition in rhizosphere and root endosphere

doi:10.3785/j.issn.1008-9209.2022.05.181

Journal of Zhejiang University (Agriculture and Life Sciences)

2023, Vol. 49

Issue (3): 376-388 DOI: 10.3785/j.issn.1008-9209.2022.05.181

Resource utilization & environmental protection

Effects of deoxymugineic acid from rice root exudates on bacterial community composition in rhizosphere and root endosphere

Linze YANG^1,²(

),Huixia SHOU^1,²(

)

^1.Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya 572025, Hainan, China
^2.Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China

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Abstract

Under the iron-deficiency condition, roots of graminaceous plants secrete mugineic acids into the soil. To determine the effects of rice root exudate 2 $′$ -deoxymugineic acid (DMA) on rhizosphere and root endosphere bacterial community, wild type rice named as Nipponbare and osbhlh156 and iro2 mutant rices that loss the ability to secrete DMA were used as experimental materials in this study. The rhizosphere and root endosphere microorganisms were sampled for DNA extraction and 16S rRNA gene amplicon sequencing and data analysis. The results showed that soil types and cultivation conditions had significant impacts on rhizosphere and root endosphere bacterial community composition. In contrast, the root exudate DMA had relatively less impact, but not negligible. The bacterial species and diversity decreased from rhizosphere to root endosphere, which confirmed that the root endosphere bacteria were gradually selected and colonized inside root by interacting with plants. Nine microbial taxa, including Bradyrhizobium and Dictyobacter, etc., were selected as biomarkers, to distinguish whether there is DMA secretion in the rice rhizosphere. Through functional prediction, it was found that the bacterial taxa with adenosine triphosphate-binding cassette (ABC) transporter function may be involved in plant iron transport and related function. This study clarifies the effects of DMA on the composition of rhizosphere and root endosphere bacterial community of rice and provides data support for the comprehensive analysis of the role of microorganisms in response to iron deficiency in rice.

Key words： rice iron deficiency deoxymugineic acid rhizosphere root endosphere bacterial community

Received: 18 May 2022 Published: 25 June 2023

CLC:

Q945.15

Corresponding Authors: Huixia SHOU E-mail: lefthash_ylz@zju.edu.cn;huixia@zju.edu.cn

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Cite this article:

Linze YANG,Huixia SHOU. Effects of deoxymugineic acid from rice root exudates on bacterial community composition in rhizosphere and root endosphere. Journal of Zhejiang University (Agriculture and Life Sciences), 2023, 49(3): 376-388.

URL:

https://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2022.05.181 OR https://www.zjujournals.com/agr/Y2023/V49/I3/376

水稻根系分泌物脱氧麦根酸对根际和根内细菌群落组成的影响

缺铁条件下禾本科植物根系会向土壤内分泌麦根酸类物质。为明确水稻根系分泌物脱氧麦根酸对根际和根内细菌群落的影响，本研究以野生型水稻日本晴及其无2 $′$ -脱氧麦根酸（2 $′$ -deoxymugineic acid, DMA）分泌能力的2个突变体水稻osbhlh156、iro2为实验材料，对根际和根内微生物取样后进行DNA提取、16S rRNA基因扩增子测序和数据分析。结果表明：土壤类型和栽培方式显著影响了水稻根际、根内细菌群落的组成，而根系分泌物DMA对细菌群落的影响相对较小；细菌物种数量和多样性从根际到根内逐渐降低，因此根内细菌是在与植物的相互作用下被逐步定殖到根中的；水稻根际有无DMA分泌物可用慢生根瘤菌属（Bradyrhizobium）、火山盘杆菌属（Dictyobacter）等9个微生物类群（生物标志物）进行区分；具有三磷酸腺苷结合盒（adenosine triphosphate-binding cassette, ABC）转运蛋白相关功能的细菌可能参与了植物铁转运过程并行使相关功能。本研究结果明确了DMA对水稻根际和根内细菌群落组成的影响，为全面解析微生物在水稻缺铁响应过程中的作用提供了数据支撑。

关键词： 水稻, 缺铁, 脱氧麦根酸, 根际, 根内, 细菌群落

Table 1 Physical and chemical properties of soils used in the experiment

Fig. 1 Growth performance of wild type and iro2 and osbhlh156 mutant rices under flooded or upland conditionsWT: Wild type (the same as below). Triple asterisks (***) indicate extremely highly significant differences under different cultivation conditions of the same rice cultivar at the 0.001 probability level.

Fig. 2 DMA exudation in root and Fe content of leaf of wild type and iro2 and osbhlh156 mutant ricesIn Fig. A, triple asterisks (***) indicate extremely highly significant differences as compared with WT at the 0.001 probability level, and n=6; In Fig. B, single asterisk (*), double asterisks (**), and triple asterisks (***) indicate significant differences under different cultivation conditions of the same rice cultivar at the 0.05, 0.01, and 0.001 probability levels, respectively, and n=3. Calculated by dry mass.

Fig. 3 Alpha diversity analysis of the bacterial community composition in rhizosphere and root endosphereA. Boxplots of observed OTUs among different treatments; B. Venn diagrams of common and unique OTUs for three genotypes in different soil types. Different lowercase letters above boxes indicate significant differences at the 0.05 probability level.

Fig. 4 Constrained principal coordinate analysis of β diversity based on Bray-Curtis distance among different treatments

Fig. 5 Constrained principal coordinate analysis of β diversity based on Bray-Curtis distance among different genotypes

Fig. 6 Bacterial composition of different treatments at the phylum level (Proteobacteria to class level)A. Rhizosphere; B. Root endosphere.

Fig. 7 Volcano plots of differential OTUs abundance variation analysis between different treatmentsA₁. Changxing soil; A₂. Jinhua soil; B₁. WT in Jinhua soil; B₂. iro2 in Jinhua soil; B₃. osbhlh156 in Jinhua soil; C₁. Rhizosphere in Changxing soil; C₂. Root endosphere in Changxing soil; D₁. Rhizosphere in Changxing soil. FC: Fold change. Symbols marked as significant decrease and significant enrichment indicate significant differences at the 0.05 probability level and the 0.1 FDR level.

Fig. 8 Functional prediction of rhizosphere and root endosphere bacterial community in WT and iro2 and osbhlh156 mutant rices


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