Research Article: RNA-seq reveals differentially expressed genes in rice (Oryza sativa) roots during interactions with plant-growth promoting bacteria, Azospirillum brasilense

Date Published: May 23, 2019

Publisher: Public Library of Science

Author(s): Jacklyn Thomas, Ha Ram Kim, Yasir Rahmatallah, Grant Wiggins, Qinqing Yang, Raj Singh, Galina Glazko, Arijit Mukherjee, Jin-Song Zhang.


Major non-legume crops can form beneficial associations with nitrogen-fixing bacteria like Azospirillum brasilense. Our current understanding of the molecular aspects and signaling that occur between important crops like rice and these nitrogen-fixing bacteria is limited. In this study, we used an experimental system where the bacteria could colonize the plant roots and promote plant growth in wild type rice and symbiotic mutants (dmi3 and pollux) in rice. Our data suggest that plant growth promotion and root penetration is not dependent on these genes. We then used this colonization model to identify regulation of gene expression at two different time points during this interaction: at 1day post inoculation (dpi), we identified 1622 differentially expressed genes (DEGs) in rice roots, and at 14dpi, we identified 1995 DEGs. We performed a comprehensive data mining to classify the DEGs into the categories of transcription factors (TFs), protein kinases (PKs), and transporters (TRs). Several of these DEGs encode proteins that are involved in the flavonoid biosynthetic pathway, defense, and hormone signaling pathways. We identified genes that are involved in nitrate and sugar transport and are also implicated to play a role in other plant-microbe interactions. Overall, findings from this study will serve as an excellent resource to characterize the host genetic pathway controlling the interactions between non-legumes and beneficial bacteria which can have long-term implications towards sustainably improving agriculture.

Partial Text

Plants can form beneficial mutualistic associations with a diverse array of microbes including soil bacteria rhizobia, arbuscular mycorrhizal fungi (AMF), plant-growth promoting bacteria (PGPB), etc. [1–3]. Among these associations, the legume-rhizobia symbiosis is the most studied and efficient symbiosis. It occurs between plants from the legume family (pea, soybean, beans, etc.) and rhizobia culminating in the development of root nodules inside which the rhizobia fix atmospheric nitrogen for the host plant in exchange for carbohydrates [2, 3]. Decades of genetic and biochemical studies have identified the plant and microbial signals controlling the establishment of this symbiosis [2, 3]. Genetic studies in legumes also identified several plant genes involved at different stages (from initiation to regulation) of this symbiosis [2, 3]. Some of the genes required in the initial stages include a cation channel (DMI1/POLLUX and CASTOR), a nuclear calcium and calmodulin-dependent kinase (DMI3/CCaMK), a substrate of DMI3 (IPD3/CYCLOPS), and a receptor-like kinase (DMI2/SYMRK) among others [2, 3]. Later studies showed that some of these genes are also required for the establishment of symbiosis with arbuscular mycorrhizal fungi leading to the concept of the common symbiotic pathway (CSP) [2–4]. Some genes from the CSP have also been shown to be required in actinorhizal symbiosis and non-symbiotic interactions [4]. The large body of elegant genetic studies in legumes has significantly improved our understanding of the host genetic pathways controlling legume-rhizobia symbiosis. Unfortunately, the same depth of information does not exist for other beneficial plant-microbe interactions such as the ones occurring between non-legumes and plant-growth promoting bacteria.

Non-legume crops such as rice, maize, and wheat can benefit from associations with plant-growth promoting bacteria. These bacteria promote plant growth by several mechanisms including nitrogen fixation and phytohormone secretion [5]. Although several studies have looked into the colonization mechanisms by which different nitrogen-fixing bacteria penetrate plant roots, not much is known about the molecular mechanisms controlling these associations. In this study, we established an experimental system in which Azospirillum brasilense could colonize rice roots under sterile, controlled conditions and promote plant growth. Interestingly, A. brasilense promoted growth in two rice symbiotic mutants (pollux and dmi3). The POLLUX and DMI3 genes belong to a very well-characterized pathway in plant-microbe symbioses known as the common symbiotic pathway (CSP) [4]. Genes belonging to the CSP are required for the establishment of the two major plant-microbe endosymbioses: legume-rhizobia symbiosis and arbuscular mycorrhizal symbiosis. Besides these symbioses, the actinorhizal symbiosis also requires genes from the CSP [4]. To the best of our knowledge, not much is known about this pathway’s role in interactions between plants and plant growth promoting bacteria like A. brasilense. Here we show that A. brasilense can promote plant growth independent of the CSP and can penetrate the roots of these symbiotic mutants. However, further studies need to be conducted to understand the role of this pathway during interactions between nitrogen-fixing bacteria and their host plants. Our results also suggest that the host plant probably uses other genetic pathway(s) to accommodate the microbe.