Understanding plant–microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis

Abstract

Understanding the beneficial plant–microbe interactions is becoming extremely critical for deploying microbes imparting plant fitness and achieving sustainability in agriculture. Diazotrophic bacteria have the unique ability to survive without external sources of nitrogen and simultaneously promote host plant growth, but the mechanisms of endophytic interaction in cereals and legumes have not been studied extensively. We have studied the early interaction of two diazotrophic bacteria, Gluconacetobacter diazotrophicus (GAB) and Bradyrhizobium japonicum (BRH), in 15-day-old seedlings of rice and soybean up to 120 h after inoculation (hai) under low-nitrogen medium. Root colonization of GAB in rice was higher than that of BRH, and BRH colonization was higher in soybean roots as observed from the scanning electron microscopy at 120 hai. Peroxidase enzyme was significantly higher at 24 hai but thereafter was reduced sharply in soybean and gradually in rice. The roots of rice and soybean inoculated with GAB and BRH harvested from five time points were pooled, and transcriptome analysis was executed along with control. Two pathways, “Plant pathogen interaction” and “MAPK signaling,” were specific to Rice-Gluconacetobacter (RG), whereas the pathways related to nitrogen metabolism and plant hormone signaling were specific to Rice-Bradyrhizobium (RB) in rice. Comparative transcriptome analysis of the root tissues revealed that several plant–diazotroph-specific differentially expressed genes (DEGs) and metabolic pathways of plant–diazotroph-specific transcripts, viz., chitinase, brassinosteroid, auxin, Myeloblastosis (MYB), nodulin, and nitrate transporter (NRT), were common in all plant–diazotroph combinations; three transcripts, viz., nitrate transport accessory protein (NAR), thaumatin, and thionin, were exclusive in rice and another three transcripts, viz., no apical meristem, Petunia (NAC), abscisic acid (ABA), and ammonium transporter, were exclusive in soybean. Differential expression of these transcripts and reduction in pathogenesis-related (PR) protein expression show the early interaction. Based on the interaction, it can be inferred that the compatibility of rice and soybean is more with GAB and BRH, respectively. We propose that rice is unable to identify the diazotroph as a beneficial microorganism or a pathogen from an early response. So, it expressed the hypersensitivity-related transcripts along with PR proteins. The molecular mechanism of diazotrophic associations of GAB and BRH with rice vis-à-vis soybean will shed light on the basic understanding of host responses to beneficial microorganisms.

Lemnaceae as Novel Crop Candidates for CO2 Sequestration and Additional Applications

“…In other scenarios, elevated CO 2 decreased, and thus interfered with, high-affinity uptake of nitrogen compounds under limiting nitrogen supply [78]. The plant microbiome can stimulate root growth and nutrient uptake in various species [80], including rice [81,82], maize [83], and soybean [82]. Duckweeds [84] and soybean [85] can thrive under low nitrogen supply due to partnerships with N 2 -fixing endophytic microbial symbionts, such as Rhizobium lemnae for Lemna species [86] and various rhizobia species for soybean [87].…”

A multifaceted crosstalk between brassinosteroid and gibberellin regulates the resistance of cucumber to Phytophthora melonis

“…Beyond their primary functions in the plant growth and development, BRs are also involved in growth‐defense trade‐offs. The BR signaling pathway exhibits cross‐talk with various immune‐related pathways triggered by diverse microbe‐ and pathogen‐associated molecular patterns at the receptor, cytoplasmic, or transcriptional level (Antolín‐Llovera et al., 2012; Bar et al., 2010; Bjornson et al., 2016; Chen & Shimamoto, 2011; Feng et al., 2021; Kalachova et al., 2022; Lin et al., 2014; Ranf et al., 2012; Saini et al., 2022; Turnbull et al., 2019; Yang et al., 2007; Yu et al., 2018; Zhang & Zhou, 2010). In Nicotiana benthamiana – Phytophthora sojae interactions, the virulence effector aldose 1‐epimerase (AEP1) activates plant immunity through mediating P. sojae extracellular sugar uptake, which depends on the BR receptor brassinosteroid insensitive 1‐associated receptor kinase 1 (BAK1) (Xu et al., 2021).…”