Community- and Genome-Based Views of Plant-Associated Bacteria: Plant–Bacterial Interactions in Soybean and Rice

Abstract

Diverse microorganisms are living as endophytes in plant tissues and as epiphytes on plant surfaces in nature. Questions about driving forces shaping the microbial community associated with plants remain unanswered. Because legumes developed systems to attain endosymbioses with rhizobia as well as mycorrhizae during their evolution, the above questions can be addressed using legume mutants relevant to genes for symbiosis. Analytical methods for the microbial community have recently been advanced by enrichment procedures of plant-associated microbes and culture-independent analyses targeting the small subunit of rRNA in microbial ecology. In this review, we first deal with interdisciplinary works on the global diversity of bacteria associated with field-grown soybeans with different nodulation genotypes and nitrogen application. A subpopulation of Proteobacteria in aerial parts of soybean shoots was likely to be regulated through both the autoregulation system for plant-rhizobium symbiosis and the nitrogen signaling pathway, suggesting that legumes accommodate a taxonomically characteristic microbial community through unknown plant-microbe communications. In addition to the community views, we then show multiphasic analysis of a beneficial rice endophyte for comparative bacterial genomics and plant responses. The significance and perspectives of community- and genome-based approaches are discussed to achieve a better understanding of plant-microbe interactions.

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.…”

“…Surprisingly, phylogenetic analyses revealed almost no Alphaproteobacteria in PR or UR plants (Table 4), despite their being a ubiquitous bacterial group in common environments, including the rhizosphere and phytosphere (8,19,48), as observed in PD and UD plants (Table 4). This low abundance of Alphaproteobacteria in R plants was mainly caused by population shifts of the Sphingomonadales and Rhizobiales among the genotypes (Fig.…”

“…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).…”

“…The CSP plays an important role in accommodating RN and AM symbionts, by which plant cells actively decompose their cell wall structures to facilitate microbial colonization and endosymbiosis (34). It would be interesting to examine the intracellular and intercellular niches of the endophytic microbial communities that respond to CSP genes (19).…”

Mapping of quantitative trait loci related to primary rice root growth as a response to inoculation with Azospirillum sp. strain B510

“…The beneficial effects of endophytes on host plants, such as increased crop yield and protection from pathogens, have been well characterized [1,2]. The genus Azospirillum [3] promotes plant growth and is thus used as a plant-promoting agronomic application [4].…”