Culturable Endophytic Bacterial Flora of the Maturing Leaves and Roots of Rice Plants (Oryza sativa) Cultivated in a Paddy Field

Mano, Hironobu; Tanaka, Fumiko; Nakamura, Chizuru; Kaga, Hiroko; Morisaki, Hisao

doi:10.1264/jsme2.22.175

Cited by 124 publications

(115 citation statements)

References 21 publications

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“…The type strain of A. ureilytica was originally reported as an isolate from air dust (Weon et al, 2007), but the closely related isolates (AB291857 and AB291900) have been identified on the surface and inside of rice leaves (Mano et al, 2007). The genus Aurantimonas has been recently established (Denner et al, 2003), and the biology of this genus in relation to the plant symbiosis is largely unknown, and needs to conduct further study.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2009

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The diversity of stem-associated bacteria of non-nodulated (Nod À ), wild-type nodulated (Nod þ ) and hypernodulated (Nod þ þ ) soybeans were evaluated by clone library analyses of the 16S ribosomal RNA gene. Soybeans were dressed with standard nitrogen (SN) fertilization (15 kg N ha -1 ) and heavy nitrogen (HN) fertilization (615 kg N ha -1 ). The relative abundance of Alphaproteobacteria in Nod þ soybeans (66%) was smaller than that in Nod À and Nod þ þ soybeans (75-76%) under SN fertilization, whereas that of Gammaproteobacteria showed the opposite pattern (23% in Nod þ and 12-16% in Nod À and Nod þ þ soybeans). Principal coordinate analysis showed that the bacterial communities of Nod À and Nod þ þ soybeans were more similar to each other than to that of Nod þ soybeans under SN fertilization. HN fertilization increased the relative abundance of Gammaproteobacteria in all nodulation phenotypes (33-57%) and caused drastic shifts of the bacterial community. The clustering analyses identified a subset of operational taxonomic units (OTUs) at the species level in Alpha-and Gammaproteobacteria responding to both the nodulation phenotypes and nitrogen fertilization levels. Meanwhile, the abundance of Betaproteobacteria was relatively constant in all libraries constructed under these environmental conditions. The relative abundances of two OTUs in Alphaproteobacteria (Aurantimonas sp. and Methylobacterium sp.) were especially sensitive to nodulation phenotype and were drastically decreased under HN fertilization. These results suggested that a subpopulation of proteobacteria in soybeans is controlled in a similar manner through both the regulation systems of plant-rhizobia symbiosis and the nitrogen signaling pathway in plants.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2009

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“…So far, a number of bacterial isolates from the rice phyllosphere have been characterized (Elbeltagy et al, 2000;Madhaiyan et al, 2007Madhaiyan et al, , 2009Mano et al, 2007) and potential beneficial interactions of phyllosphere bacteria with rice plants, such as plant growth promotion, for example, by bacterial nitrogen fixation or plant hormone production, and protection against pathogens have been studied (Madhaiyan et al, 2004;Maliti et al, 2005;De Costa et al, 2008;Yang et al, 2008;Chinnadurai et al, 2009;Pedraza et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

et al. 2011

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The above-and below-ground parts of rice plants create specific habitats for various microorganisms. In this study, we characterized the phyllosphere and rhizosphere microbiota of rice cultivars using a metaproteogenomic approach to get insight into the physiology of the bacteria and archaea that live in association with rice. The metaproteomic datasets gave rise to a total of about 4600 identified proteins and indicated the presence of one-carbon conversion processes in the rhizosphere as well as in the phyllosphere. Proteins involved in methanogenesis and methanotrophy were found in the rhizosphere, whereas methanol-based methylotrophy linked to the genus Methylobacterium dominated within the protein repertoire of the phyllosphere microbiota. Further, physiological traits of differential importance in phyllosphere versus rhizosphere bacteria included transport processes and stress responses, which were more conspicuous in the phyllosphere samples. In contrast, dinitrogenase reductase was exclusively identified in the rhizosphere, despite the presence of nifH genes also in diverse phyllosphere bacteria.

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“…First, Microvirgula aerodenitrificans, the most abundant one, is an aerobic denitrifier [60] and has been reported previously as a rice endorhizosphere inhabitant [15]. Secondly Caulobacter sp., which has also been reported to be associated rice in two other parts of the world [61][62] [15] and to have PGP properties [48]. In the endorhizosphere of the DANAC SD20A rice cultivar, strains belonging to the Azospirillum, Acinetobacter and Citrobacter genera were dominant.…”

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 93%

Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

Moronta-Barrios¹,

Gionechetti²,

Pallavicini³

et al. 2017

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Abstract:Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed the isolation of hundreds bacterial isolates obtained from endorhizosphere of two rice cultivars from Venezuela. The validation of plant-growth promoting bacterial activities in vitro has led us to select and characterize 15 isolates for in planta studies such as germination test, endophytism ability and plant growth promotion. Consequently, a set of 10 isolates was selected for the set-up of an endophytic consortium as a simplified model of the natural rice bacterial endomicrobiota. Upon inoculation, the colonization and abundance of each strain within the rice roots was tracked by a culture-independent technique in gnotobiotic conditions in a 30 days period. Four strains belonging to Pseudomonas, Agrobacterium and Delftia genera have shown a promising capacity for colonizing and coexistence in root tissues. On the other hand, a bacterial community taxonomic profiling of the rhizosphere and the endorhizosphere of both cultivars were obtained and are discussed. This study is part of a growing body of research on core crops microbiome and simplified microbiomes, which strengthens the formation process of the endophytic community leading to a better understanding of the rice microbiome.

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Culturable Endophytic Bacterial Flora of the Maturing Leaves and Roots of Rice Plants (Oryza sativa) Cultivated in a Paddy Field

Cited by 124 publications

References 21 publications

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

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

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

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