Microbial Community Analysis of Field-Grown Soybeans with Different Nodulation Phenotypes

Abstract

Microorganisms associated with the stems and roots of nonnodulated (Nod؊ soybeans, whereas the abundance of basidiomycetes was just the opposite. The phylogenetic analyses suggested that these basidiomycetous fungi might represent a root-associated group in the Auriculariales. Principal-component analysis of the ARISA results showed that there was no clear relationship between nodulation phenotype and bacterial community structure in the stem. In contrast, both the bacterial and fungal community structures in the roots were related to nodulation phenotype. The principal-component analysis further suggested that bacterial community structure in roots could be classified into three groups according to the nodulation phenotype (Nod ؊ , Nod ؉

Community shifts of soybean stem-associated bacteria responding to different nodulation phenotypes and N levels

“…Thus, there is a possibility that nodulation phenotype and host nitrogen status may affect the structure of the microbial community in shoots, as observed earlier in roots (Ikeda et al, 2008a). However, the cultureindependent analysis of soybean stem-associated microbial communities failed because of serious interference by plant DNA in the PCR amplification (Ikeda et al, 2008a). To overcome this problem, a method was recently developed for enriching the bacterial cells collected from soybean stems .…”

“…To overcome this problem, a method was recently developed for enriching the bacterial cells collected from soybean stems . The enrichment method allows the construction of a clone library of the bacterial 16S ribosomal RNA (rRNA) genes, which provides better resolution for examining the microbial community structures compared with the limited analyses in previous studies based mainly on fingerprinting methods (Offre et al, 2007;Ikeda et al, 2008a).…”

“…Although plants are known to control the degrees of nodulation and mycorrhization of roots by rhizobia and mycorrhizae, respectively, through autoregulation systems (Carroll et al, 1985;Meixner et al, 2007), the effects of the autoregulation systems on the other plant-associated microorganisms in the phytosphere remain unclear (Parniske, 2000). Recent studies have shown that the wild-type and symbiosisdefective mutants of legumes such as Medicago truncatula and Glycine max have different microbial community structures, and certain microbes associate preferentially with nodulated or mycorrhizal root systems (Offre et al, 2007;Ikeda et al, 2008a). Furthermore, transcriptional analyses revealed that both nodulation and mycorrhization systemically induced a series of defense genes in a host plant and consequently increased its disease resistance (Liu et al, 2007;Kinkema and Gresshoff, 2008).…”

The Genotype of the Calcium/Calmodulin-Dependent Protein Kinase Gene ( CCaMK ) Determines Bacterial Community Diversity in Rice Roots under Paddy and Upland Field Conditions

“…Recently, it was shown that symbiosis-defective mutants of Medicago truncatula (30) and soybean (16,32) possess bacterial and fungal communities in their roots different from those in wild-type host plants and that certain bacteria preferentially associate with mycorrhizal roots (41). These findings indicate that genetic alteration in RN/AM signaling pathways can also alter the microflora of the rhizosphere.…”

“…These findings indicate that genetic alteration in RN/AM signaling pathways can also alter the microflora of the rhizosphere. Interestingly, analyses of the rhizosphere of soybeans indicated that the bacterial community structures of nonnodulated soybeans were more similar to those of hypernodulated soybeans than to those of wild-type soybeans (16). Since nodulation is autoregulated by signal transduction between root and shoot tissues (31), it is of interest to compare bacterial communities in shoots between wild-type and symbiosis-defective mutants.…”