Transcriptomic and Metabolomic Analysis of Soybean Nodule Number Improvements with the Use of Water-Soluble Humic Materials

Abstract

Water-soluble humic materials (WSHMs) can enhance the nodule numbers of soybean plants. In this study, targeted metabolomics and transcriptomics were used to understand this mechanism. Results showed that 500 mg/L WSHM increased the adsorption and colonization of rhizobia in soybean roots. High-performance liquid chromatography and targeted metabolomics showed that WSHMs could regulate the content and distribution of endogenous hormones of soybean plants at the initial stage of soybean nodulation. Transcriptomic analysis showed a total of 2406 differentially expressed genes (DEGs) by the 25th day, accounting for 4.89% of total annotation genes (49159). These DEGs were found to contribute primarily to the MAPK signaling pathway, glycolysis/gluconeogenesis, and plant hormone signal transduction according to the −log 10 (Padjust) value in the KEGG pathway. Subsequently, DEGs related to these hormones were selected for verification using quantity-PCR. The WSHM increased the number of nodules by regulating the expression of endogenous hormones in soybean plants.

Fulvic Acid Promotes Legume–Rhizobium Symbiosis by Stimulating Endogenous Flavonoids Synthesis and Secretion

“…Previous studies have shown that HA promotes plant growth by increasing the concentration of IAA in plants, 21,47 and WSHM did enhance soybean nodulation by regulating the plant hormones, including IAA, gibberellin acid, abscisic acid, jasmonic acid, and salicylic acid. 21 In this study, RT-qPCR was performed for the key genes in the isoflavonoid synthesis pathway (Figure 5). The significantly up-regulated expression of all of the examined genes at the sixth hour in WSHM treatment was consistent with the enhanced flavonoid synthesis observed in the analysis of root exudates.…”

“…18,19 Based upon the previous studies, the activity of HS as biostimulants has been explained by (1) inducing changes in root morphology and modulate plant nutrient acquisition, 20 (2) regulating the synthesis of hormones in plants, 21 (3) improving growth and survive of rhizobia by regulating protein synthesis and quorum sensing, 21−25 and (5) inducing the expression of nodulation genes by the isoflavonoid-like molecules in HS. 22,25 Except the effects on plants and rhizobia mentioned above, WSHM or FA treatment also significantly reshaped the transcript profiles of plants, 21,25 inevitably influencing plant metabolism and the composition of root exudates, which are the primary regulators of plant−rhizosphere dialogue, mediating the exchange of substances and information between plants and rhizosphere microorganisms. 26 Previous studies have evidenced that soybean root exudates changed the expression of genes relating to two-component system, chemotaxis, and metabolic adaptation processes of Bradyrhizobium diazoef f iciens.…”

Soluble humic acid suppresses plant immunity and ethylene to promote soybean nodulation

“…Thus, the data obtained in the present study suggest that, instead of ACC, WSHM directly regulates ethylene to promote soybean nodulation. In addition, recent studies have shown that decreasing ethylene content in nodules is also critical for the development of bacteroid and for their ability to fix nitrogen (Cao et al, 2022; Zhang et al, 2023). Therefore, WSHM might enhance the nitrogenase activity of nodules via the inhibition of ethylene.…”

“…Thus, it is not surprising that WSHM compensates for BR‐induced nodulation suppression by inhibiting ethylene synthesis as revealed in the present study. Although WSHM could increase the ethylene precursor ACC content in soybean roots (Zhang et al, 2023), it did not represent an increase in ethylene content, as ACC needs to be converted to ethylene under the action of ACC oxidase, and then regulates nodulation in legumes by ethylene signalling (Guinel, 2015). Although it has been found that ACC can act independently of ethylene signalling and may serve as a new hormone molecule (Mou et al, 2020), there is no report on ACC directly regulating nodulation in legumes.…”

“…As an active component of soil humus, humic acid (HA) has been used as bioregulator (Nardi et al, 2021) or biostimulator (Vujinović et al, 2020) to improve plant growth and crop yield, especially to promote nodulation, nitrogen fixation and growth of legumes (Capstaff et al, 2020; Guo Gao et al, 2015; Qiu et al, 2021; Zhang et al, 2023). Previously, it has been proved that water‐soluble HA (WSHM/FA) could promote SNF by regulating the early nodulation signalling genes of legumes (Capstaff et al, 2020), affecting the contents and distributions of endogenous hormones in plants (Zhang et al, 2023), increasing quorum density, upregulating nod gene expression, and increasing host root colonisation of rhizobia (Guo Gao et al, 2015; Qiu et al, 2021; Xu et al, 2018). These findings demonstrated that HA might promote growth and nodulation by regulating/stimulating some signalling systems or metabolism pathways in both members of the symbiosis.…”