Isolation and Identification of Natural Endophytic Rhizobia from Rice (Oryza sativa L.) Through rDNA PCR-RFLP and Sequence Analysis

Singh, R. K.; Mishra, R. B.; Jaiswal, H. K.; Kumar, Vinod; Pandey, Sarvesh; Rao, Sasi B.; Annapurna, K.

doi:10.1007/s00284-005-0136-5

Cited by 32 publications

(21 citation statements)

References 19 publications

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“…Despite the inability of nearly all non-legumes to form root nodules that accommodate the rhizobia to fix atmospheric nitrogen, it seems likely that rhizobial Nod factors could be sensed by non-legume plants and trigger downstream signaling pathways that allow, for example, endophytic colonization of bacteria that benefits the plant (Chi et al, 2005;Singh et al, 2006). Support of this possibility is that the legume genes encoding the putative Nod factor receptors (e.g.…”

Section: Discussionmentioning

confidence: 99%

Fungal Symbiosis in Rice Requires an Ortholog of a Legume Common Symbiosis Gene Encoding a Ca²⁺/Calmodulin-Dependent Protein Kinase

et al. 2007

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In natural ecosystems, many plants are able to establish mutually beneficial symbioses with microorganisms. Of critical importance to sustainable agriculture are the symbioses formed between more than 80% of terrestrial plants and arbuscular mycorrhizal (AM) fungi and between legumes and nitrogen-fixing rhizobial bacteria. Interestingly, the two symbioses share overlapping signaling pathways in legumes, suggesting that the evolutionarily recent root nodule symbiosis may have acquired functions from the ancient AM symbiosis. The Medicago truncatula DMI3 (DOESN'T MAKE INFECTIONS3) gene (MtDMI3) and its orthologs in legumes are required for both bacterial and fungal symbioses. MtDMI3 encodes a Ca 21 / calmodulin-dependent protein kinase (CCaMK) essential for the transduction of the Ca 21 signal induced by the perception of Nod factors. Putative orthologs of MtDMI3 are also present in non-legumes, but their function in AM symbiosis has not been demonstrated in any non-legume species. Here, we combine reverse genetic approaches and a cross-species complementation test to characterize the function of the rice (Oryza sativa) ortholog of MtDMI3, namely, OsDMI3, in AM symbiosis. We demonstrate that OsDMI3 is not only required for AM symbiosis in rice but also is able to complement a M. truncatula dmi3 mutant, indicating an equivalent role of MtDMI3 orthologs in non-legumes.

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Section: Discussionmentioning

confidence: 99%

Fungal Symbiosis in Rice Requires an Ortholog of a Legume Common Symbiosis Gene Encoding a Ca²⁺/Calmodulin-Dependent Protein Kinase

et al. 2007

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“…The selection of suitable endonucleases is the key step of the technique. Endonucleases have been selected through extensive experimentation with restriction enzyme cleavage to distinguish different species of bacteria (31,34), yeasts (9,30), filamentous fungi (21)(22)(23), and other organisms (4,5) in the recent years. As more DNA sequences are becoming readily available, the selection of endonucleases can be based on sequence analyses through the examination of recognition sites of restriction enzymes from the alignment of sequences, e.g., from bacteria (10), fungi (7,41), and other living organisms (1,48).…”

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confidence: 99%

Autoscreening of Restriction Endonucleases for PCR-Restriction Fragment Length Polymorphism Identification of Fungal Species, with Pleurotus spp. as an Example

Yang

Huang

Yao

2007

Appl Environ Microbiol

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A molecular method based on PCR-restriction fragment length polymorphism (RFLP) analysis of internal transcribed spacer (ITS) ribosomal DNA sequences was designed to rapidly identify fungal species, with members of the genus Pleurotus as an example. Based on the results of phylogenetic analysis of ITS sequences from Pleurotus, a PCR-RFLP endonuclease autoscreening (PRE Auto) program was developed to screen restriction endonucleases for discriminating multiple sequences from different species. The PRE Auto program analyzes the endonuclease recognition sites and calculates the sizes of the fragments in the sequences that are imported into the program in groups according to species recognition. Every restriction endonuclease is scored through the calculation of the average coefficient for the sequence groups and the average coefficient for the sequences within a group, and then virtual electrophoresis maps for the selected restriction enzymes, based on the results of the scoring system, are displayed for the rapid determination of the candidate endonucleases. A total of 85 haplotypes representing 151 ITS sequences were used for the analysis, and 2,992 restriction endonucleases were screened to find the candidates for the identification of species. This method was verified by an experiment with 28 samples representing 12 species of Pleurotus. The results of the digestion by the restriction enzymes showed the same patterns of DNA fragments anticipated by the PRE Auto program, apart from those for four misidentified samples. ITS sequences from 14 samples (of which nine sequences were obtained in this study), including four originally misidentified samples, confirmed the species identities revealed by the PCR-RFLP analysis. The method developed here can be used for the identification of species of other living microorganisms.

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“…A significant increase in biomass and grain yiel has also been recorded in greenhouse grown rice plants inoculated with Rhizobium leguminosarumbv. Phaseoli (Singh et al 2006).…”

Section: Resultsmentioning

confidence: 99%

Stimulate The Growth of Rice Using Endophytic Bacteria from Lowland Rice Plant Tissue

Gofar

Widjajanti

Marlina

2015

Sains Tanah - Journal of Soil Science and Agroclimatology

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Exploration and selection of endophytic bacteria from healthy food crops grown in lowland ecosystem is important to be conducted in order to get growth-stimulating endophytic bacteria at soil with low fertility level so that capable to optimize initial growth of food crops and subsequently can increase productivity level of lowland soil.The research objective was to isolate and to test the IAA-producing endophytic bacteria isolate in stimulating the rice crop growth at lowland area. Endophytic bacteria are isolated from tissues of rice, corn and peanut crops which grown at shallow swamp land in OganIlir and OganKomeringIlir Districts, South Sumatra, Indonesia. There was nine isolates of nitrogen-fixer endophytic bacteria that capable to contribute IAA phytohormone into their growth media. The P31 isolate from rice crop tisssue of 2 months old produce the best rice sprouts than other isolates. This isolate can contribute of about 10 mg kg -1 IAA to its growth medium and increase the crownsdry weight and the roots dry weight respectively with magnitudes of 133% and 225% compared to control treatment. Concentration and absorbtion of N for rice crops innoculated with P31 isolates had increased by 169% and 400%, recpectively. The P31 isolates had been identified as Burkholderiapseudomallei (also known as Pseudomonas pseudomallei).

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Isolation and Identification of Natural Endophytic Rhizobia from Rice (Oryza sativa L.) Through rDNA PCR-RFLP and Sequence Analysis

Cited by 32 publications

References 19 publications

Fungal Symbiosis in Rice Requires an Ortholog of a Legume Common Symbiosis Gene Encoding a Ca²⁺/Calmodulin-Dependent Protein Kinase

Fungal Symbiosis in Rice Requires an Ortholog of a Legume Common Symbiosis Gene Encoding a Ca²⁺/Calmodulin-Dependent Protein Kinase

Autoscreening of Restriction Endonucleases for PCR-Restriction Fragment Length Polymorphism Identification of Fungal Species, with Pleurotus spp. as an Example

Stimulate The Growth of Rice Using Endophytic Bacteria from Lowland Rice Plant Tissue

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Isolation and Identification of Natural Endophytic Rhizobia from Rice (Oryza sativa L.) Through rDNA PCR-RFLP and Sequence Analysis

Cited by 32 publications

References 19 publications

Fungal Symbiosis in Rice Requires an Ortholog of a Legume Common Symbiosis Gene Encoding a Ca2+/Calmodulin-Dependent Protein Kinase

Fungal Symbiosis in Rice Requires an Ortholog of a Legume Common Symbiosis Gene Encoding a Ca2+/Calmodulin-Dependent Protein Kinase

Autoscreening of Restriction Endonucleases for PCR-Restriction Fragment Length Polymorphism Identification of Fungal Species, with Pleurotus spp. as an Example

Stimulate The Growth of Rice Using Endophytic Bacteria from Lowland Rice Plant Tissue

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Product

Resources

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Fungal Symbiosis in Rice Requires an Ortholog of a Legume Common Symbiosis Gene Encoding a Ca²⁺/Calmodulin-Dependent Protein Kinase

Fungal Symbiosis in Rice Requires an Ortholog of a Legume Common Symbiosis Gene Encoding a Ca²⁺/Calmodulin-Dependent Protein Kinase