Autoregulation of Nodulation Interferes with Impacts of Nitrogen Fertilization Levels on the Leaf-Associated Bacterial Community in Soybeans

Abstract

The diversities leaf-associated bacteria on nonnodulated (Nod ؊ ؉؉ soybeans (46% to 76%) and, conversely, increased those of Gammaproteobacteria and Firmicutes in these mutant soybeans. In the Alphaproteobacteria, cluster analyses identified two operational taxonomic units (OTUs) (Aurantimonas sp. and Methylobacterium sp.) that were especially sensitive to nodulation phenotypes under SN fertilization and to nitrogen fertilization levels. Arbuscular mycorrhizal infection was not observed on the root tissues examined, presumably due to the rotation of paddy and upland fields. These results suggest that a subpopulation of leaf-associated bacteria in wild-type Nod ؉ soybeans is controlled in similar ways through the systemic regulation of autoregulation of nodulation, which interferes with the impacts of N levels on the bacterial community of soybean leaves.)Although diverse microorganisms reside in the phytosphere as endophytes, epiphytes, and rhizosphere bacteria, many questions about the driving forces and ecological rules underlying the relationships between these microbes and plants remain unanswered (18,39). During their evolution, legumes have developed two systems for attaining mutual symbioses with rhizobia and mycorrhizae. One of the systems genetically required for rhizobial and arbuscular mycorrhizal interactions in plants overlaps in a common signaling pathway (CSP) leading to successful symbioses (24). Plants also have a control system for regulating the degree of nodulation and mycorrhization on roots by rhizobia and mycorrhizae, respectively. This autoregulatory system occurs through long-distance signaling between shoots and roots (33). Leguminous plants deficient in the CSP and autoregulation systems develop nonnodulated (Nod Ϫ ) and hypernodulated (Nod ϩϩ ) roots, respectively. However, the degree to which plants use similar or identical systems, such as CSP and autoregulation, for interactions with other microorganisms in the phytosphere remains unclear.Recently, it was shown that the bacterial and fungal community structures in the roots of symbiosis-defective mutants of Medicago truncatula (32) and soybean (22) differ from those in the roots of wild-type host plants; it was also shown that certain microbes preferentially associate with arbuscular mycorrhizal roots (41) and nodulated (Nod ϩ ) roots (22). However, unexpectedly, analyses of the rhizosphere community in soybeans have revealed that the bacterial community in nonnodulated soybeans is more similar to that in hypernodulated soybeans than to that in wild-type soybeans (22).The autoregulation of nodulation occurs through long-distance signaling between shoots and roots (33), and a heavy supply of nitrate to the roots of leguminous plants inhibits nodulation through autoregulation (6, 34). Thus, it is possible that the nodulation phenotype and host nitrogen status affect the structure of the microbial community in aboveground tissues, such as stems and leaves, as has been observed in roots (22). Indeed, the results of our previous study o...

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

“…The results and previous data (18)(19)(20) strongly suggest that the manipulation of genetic factors underlying RN and AM symbioses would have significant effects on the diversity of plant-associated microbes. To investigate the roles of such plant genes in interacting with plant-associated Alphaproteobacteria such as the Sphingomonadales, the significance of the diversity and functionality of plant-associated Alphaproteobacteria in relation to rice plant growth should be examined.…”

“…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. Indeed, the results of our previous study of stem-and leaf-associated bacteria suggested that a subpopulation of Proteobacteria in soybean was controlled through the system that regulates RN symbiosis (18)(19)(20).…”

Aureimonas jatrophae sp. nov. and Aureimonas phyllosphaerae sp. nov., leaf-associated bacteria isolated from Jatropha curcas L.

“…At the time of writing, the genus Aureimonas contained three species, Aureimonas altamirensis (the type species), Aureimonas frigidaquae and Aureimonas ureilytica (Rathsack et al, 2011). Members of Aureimonas have been also isolated from the surfaces and internal tissues of rice leaves (Mano et al, 2007) and stems of hypernodulated soybeans (Anda et al, 2011). Culture-independent studies of the leaf-associated bacterial community in soybeans have shown that the majority of the population consists of members of Aureimonas closely related to A. ureilytica (Ikeda et al, 2010a(Ikeda et al, , b, 2011.…”

Distribution of Methanotrophs in the Phyllosphere

“…Several studies using metagenomic or metaproteomic approaches to the bacteria of plant leaves did not detect methanotrophs, 10,23) whereas other detected methanotrophs related to Methylosinus, Methylobacter, and Methylococcus, with findings that methanotrophs have a small population on leaves. [24][25][26] Methanotrophs were successfully cultivated from 12% of the phyllosphere samples (consisting of leaves, flowers, and bark), as against 59% of the rhizoplane samples. Thus, the leaves may be able only to sustain small populations of methanotrophs due to limited nutrients on the leaves or competition with other microorganisms.…”