Common gene expression patterns are observed in rice roots during associations with plant growth-promoting bacteria, Herbaspirillum seropedicae and Azospirillum brasilense

Abstract

Non-legume plants such as rice and maize can form beneficial associations with plant growth-promoting bacteria (PGPB) such as Herbaspirillum seropedicae and Azospirillum brasilense. Several studies have shown that these PGPB promote plant growth via multiple mechanisms. Our current understanding of the molecular aspects and signaling between plants like rice and PGPB like Herbaspirillum seropedicae is limited. In this study, we used an experimental system where H. seropedicae could colonize the plant roots and promote growth in wild-type rice. Using this experimental setup, we identified 1688 differentially expressed genes (DEGs) in rice roots, 1 day post-inoculation (dpi) with H. seropedicae. Several of these DEGs encode proteins involved in the flavonoid biosynthetic pathway, defense, hormone signaling pathways, and nitrate and sugar transport. We validated the expression pattern of some genes via RT-PCR. Next, we compared the DEGs identified in this study to those we previously identified in rice roots during associations with another PGPB, Azospirillum brasilense. We identified 628 genes that were differentially expressed during both associations. The expression pattern of these genes suggests that some of these are likely to play a significant role(s) during associations with both H. seropedicae and A. brasilense and are excellent targets for future studies.

What do we know from the transcriptomic studies investigating the interactions between plants and plant growth-promoting bacteria?

“…The advances in next-generation sequencing have led to a burst of transcriptomic studies investigating host gene expression changes during plant-PGPB interactions. Most of these studies have been performed on the Nipponbare cultivar of rice ( Wu et al, 2018 ; Brusamarello-Santos et al, 2019 ; King et al, 2019 ; Thomas et al, 2019 ; Cook et al, 2022 ; Wiggins et al, 2022 ). But, other rice cultivars, such as 9311, TKM9 and IR36, have also been used ( Chen et al, 2015 ; Xie et al, 2017 ; Rekha et al, 2018 ).…”

“…For instance, in rice, the pathogenesis-related (PR) genes are strongly induced upon inoculation with rice blast fungus, Magnaporthe oryzae , which causes one of the most severe diseases in rice ( Kawahara et al, 2012 ). However, the expression of several PR genes was reduced in host plants during interactions with different PGPB (e.g., A. brasilense , H. seropedicae, P. kururiensis, B. vietnamiensis ) ( Brusamarello-Santos et al, 2019 ; King et al, 2019 ; Thomas et al, 2019 ; Wiggins et al, 2022 ). Similarly, other defense genes such as chitinases, thionins, cinnamoyl-CoA-reductases, and genes encoding for disease resistance were downregulated during plant-PGPB interactions ( Brusamarello-Santos et al, 2019 ; Thomas et al, 2019 ; Wiggins et al, 2022 ).…”

“…However, the expression of several PR genes was reduced in host plants during interactions with different PGPB (e.g., A. brasilense , H. seropedicae, P. kururiensis, B. vietnamiensis ) ( Brusamarello-Santos et al, 2019 ; King et al, 2019 ; Thomas et al, 2019 ; Wiggins et al, 2022 ). Similarly, other defense genes such as chitinases, thionins, cinnamoyl-CoA-reductases, and genes encoding for disease resistance were downregulated during plant-PGPB interactions ( Brusamarello-Santos et al, 2019 ; Thomas et al, 2019 ; Wiggins et al, 2022 ). The expression pattern of these genes supports the concept that the host plant is adjusting its transcriptional responses to accommodate the beneficial microbe.…”

“…For instance, the plant cell wall-associated kinases (WAKs) have been implicated as important regulators of plant immunity against bacterial and fungal pathogens ( Kanneganti and Gupta, 2008 ; Amsbury, 2020 ). Several WAKs were differentially expressed in rice during interactions with A. brasilense and H. seropedicae ( Brusamarello-Santos et al, 2019 ; Thomas et al, 2019 ; Wiggins et al, 2022 ). Another well-characterized group of RLKs is the Lysin motif (LysM) RLKs that play important roles in the perception of microbial signals during legume-rhizobia symbiosis and AM symbiosis ( Buendia et al, 2018 ; Gough et al, 2018 ).…”

“…( Olanrewaju et al, 2017 ). Several auxin-responsive genes (e.g., SAUR genes, Aux/IAA genes, GH3 genes) were differentially expressed in rice and wheat during interactions with different PGPB ( Camilios-Neto et al, 2014 ; Chen et al, 2015 ; Xie et al, 2017 ; Rekha et al, 2018 ; Brusamarello-Santos et al, 2019 ; Thomas et al, 2019 ; Shinjo et al, 2020 ; Wiggins et al, 2022 ). Interestingly, some of these genes were suppressed in expression during these interactions.…”