Root isoflavonoids and hairy root transformation influence key bacterial taxa in the soybean rhizosphere

Abstract

Rhizodeposits play a key role in shaping rhizosphere microbial communities. In soybean, isoflavonoids are a key rhizodeposit component that aid in plant defense and enable symbiotic associations with rhizobia. However, it is uncertain if and how they influence rhizosphere microbial communities. Isoflavonoid biosynthesis was silenced via RNA interference of isoflavone synthase in soybean hairy root composite plants. Rhizosphere soil fractions tightly associated with roots were isolated, and PCR amplicons from 16S rRNA gene variable regions V1-V3 and V3-V5 from these fractions were sequenced using 454. The resulting data was resolved using MOTHUR and vegan to identify bacterial taxa and evaluate changes in rhizosphere bacterial communities. The soybean rhizosphere was enriched in Proteobacteria and Bacteroidetes, and had relatively lower levels of Actinobacteria and Acidobacteria compared with bulk soil. Isoflavonoids had a small effect on bacterial community structure, and in particular on the abundance of Xanthomonads and Comamonads. The effect of hairy root transformation on rhizosphere bacterial communities was largely similar to untransformed plant roots with approximately 74% of the bacterial families displaying similar colonization underscoring the suitability of this technique to evaluate the influence of plant roots on rhizosphere bacterial communities. However, hairy root transformation had notable influence on Sphingomonads and Acidobacteria.

Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community

“…Bacteria in the Comamonadaceae and/or Microbacteriaceae may possess genes that allow them to use daidzein as a carbon source. Comamonadaceae are common in the soybean rhizosphere (Hamid et al, ; White et al, ), with >10% relative abundance (Figure S9). This family contains plant growth promoting bacteria such as Delftia sp., which enhance nodulation and pulse yield when co‐inoculated with Bradyrhizobium elkanii (Cagide, Riviezzi, Minteguiaga, Morel, & Castro‐Sowinski, ), and Variovorax paradoxus , a soybean endophyte with characteristics related to plant growth promotion (Lopes, Carpentieri‐Pipolo, Oro, Pagliosa, & Degrassi, ).…”

“…Soil type primary influences the assemblage of rhizosphere microbial communities (Liu et al, ; Xiao et al, ), and Comamonadaceae was abundant in the rhizosphere of successive soybean‐monoculture cropping (Hamid et al, ), which is concordant with our findings using soils from soybean field under continuous cropping. It should also be noted that daidzein is not the only metabolite to promote the abundance of Comamonadaceae in the soybean rhizosphere, because the silencing of IFS gene in soybean hairy roots resulted in the slight increase of Comamonadaceae in the rhizosphere of IFS‐silenced roots (White et al, ). A synthetic community‐based approach to the daidzein‐mediated interaction among soybean, Comamonadaceae, and other bacteria could identify the molecular basis of these interactions.…”

“…Isoflavones are a subgroup of flavonoids predominantly found in Fabaceae (Mazur, Duke, Wahala, Rasku, & Adlercreutz, 1998), and are produced via isoflavone synthase (IFS). The influences of isoflavones to bacterial communities were shown with IFS-silenced transgenic hairy roots (White, Ge, Brozel, & Subramanian, 2017) and with the addition of daidzein and genistein to soybean field soils (Guo, Kong, Wang, & Wang, 2011). Soybeans secrete daidzein into the rhizosphere to initiate symbiosis with rhizobia (Kosslak, Bookland, Barkei, Paaren, & Appelbaum, 1987).…”

The Interactions of Rhizodeposits with Plant Growth-Promoting Rhizobacteria in the Rhizosphere: A Review

“…Kuzyakov et al [64] reported that rhizodeposits supply energy to soil microbes for solubilization of organic nitrogen and other nutrients in soil organic matter. White et al [78] reported that isoflavonoids are vital rhizodeposits that help in plant defense and also facilitate symbiotic events with Rhizobia in soybean.…”

Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum

“…The rhizosphere, which is defined as a thin soil layer close to the root system and is actively influenced by metabolic activity [7], has often been used as the preferential site for the isolation of PGPB with potential applications as biofertilizers [8,9]. The habitat of rhizospheric soils differs physically, chemically and biologically from the nonrhizospheric soils (or bulk soil) because of the continuous release of a complex array of organic-based molecules such as rhizodeposits [10,11]. Qualitative and quantitative variations in rhizodeposits are thought to play an active role in shaping the rhizosphere microbiome by enriching population sizes of microbial representatives with competence to consume released compounds according to the plant genotype, age and local environmental conditions [12,13].…”