Nodulation-Dependent Communities of Culturable Bacterial Endophytes from Stems of Field-Grown Soybeans

Okubo, Takashi; Ikeda, Seishi; Kaneko, Takakazu; Eda, Shima; Mitsui, Hisayuki; Sato, Shusei; Tabata, Satoshi; Minamisawa, Kiwamu

doi:10.1264/jsme2.me09125

Cited by 35 publications

(27 citation statements)

References 47 publications

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“…Okubo et al (2009) also reported similar results of the strong dominance Figure 3 Principal-coordinate analysis for the 16S ribosomal RNA (rRNA) gene clone libraries of soybean stem-associated bacteria in different nodulation phenotypes. The ordination was constructed using Unifrac distances weighted by the relative abundances.…”

Section: Discussionsupporting

confidence: 53%

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: Discussionsupporting

confidence: 53%

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

et al. 2009

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“…glycinea. These differences may reflect a bias in the culturability of leaf-associated bacterial communities (35,39). Alternatively, the bacterial cell enrichment method employed in the present study may have a bias regarding the efficiencies of cell extraction from plant tissues for different taxonomic groups.…”

Section: Discussionmentioning

confidence: 95%

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

Ikeda

Anda

Inaba

et al. 2011

Appl Environ Microbiol

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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...

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“…1) clones (11,22,27,29,34,50,79,82,105,116,117,118) Clostridium magnum (GU129927.1) Clostridium sp. (AF281142.1) Uncultured Veillonellaceae (FJ393139.1) Uncultured Veillonellaceae (FJ393127.1) clones (6,13,17,19,32,36,37,39,47,49,56,59,67,71,74,80,85,93,94,99,100,106,107,108,111,112,120) clones (7,8,18,21,30,31,38,43,46,86,95,103,119) Sporolactobacillus laevolacticus (AB362643.1) clones (54,63,66,…”

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confidence: 99%

Performance and composition of bacterial communities in anaerobic fluidized bed reactors for hydrogen production: Effects of organic loading rate and alkalinity

Shida

Sader

Amorim

et al. 2012

International Journal of Hydrogen Energy

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Nodulation-Dependent Communities of Culturable Bacterial Endophytes from Stems of Field-Grown Soybeans

Cited by 35 publications

References 47 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

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

Performance and composition of bacterial communities in anaerobic fluidized bed reactors for hydrogen production: Effects of organic loading rate and alkalinity

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