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Characterization of N2-fixing plant growth promoting endophytic and epiphytic bacterial community of Indian cultivated and wild rice (Oryza spp.) genotypes

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Main conclusion

The diversity of endophytic and epiphytic diazotrophs in different parts of rice plants has specificity to the niche (i.e. leaf, stem and root) of different genotypes and nutrient availability of the organ.

Inoculation of the indigenous, polyvalent diazotrophs can facilitate and sustain production of non-leguminous crops like rice. Therefore, N2-fixing plant growth promoting bacteria (PGPB) were isolated from different parts of three Indian cultivated [Oryza sativa L. var. Sabita (semi deep/deep water)/Swarna (rain fed shallow lowland)/Swarna-Sub1(submergence tolerant)] and a wild (O. eichingeri) rice genotypes which respond differentially to nitrogenous fertilizers. Thirty-five isolates from four rice genotypes were categorized based on acetylene reduction assay on nitrogenase activity, biochemical tests, BIOLOG and 16S rRNA gene sequencing. The bacteria produced 9.36–155.83 nmole C2H4 mg−1 dry bacteria h−1 and among them nitrogenase activity of 11 potent isolates was complemented by nifH–sequence analysis. Phylogenetic analysis based on 16S rDNA sequencing divided them into five groups (shared 95–100 % sequence homology with type strains) belonging to five classes—alpha (Ancylobacter, Azorhizobium, Azospirillum, Rhizobium, Bradyrhizobium, Sinorhizobium, Novosphingobium, spp.), beta (Burkholderia sp.), gamma (Acinetobacter, Aeromonas, Azotobacter, Enterobacter, Klebsiella, Pantoea, Pseudomonas, Stenotrophomonas spp.) Proteobacteria, Bacilli (Bacillus, Paenibacillus spp.) and Actinobacteria (Microbacterium sp.). Besides, all bacterial strains possessed the intrinsic PGP traits of like indole (0.44–7.4 µg ml−1), ammonia (0.18–6 mmol ml−1), nitrite (0.01–3.4 mol ml−1), and siderophore (from 0.16–0.57 μmol ml−1) production. Inoculation of rice (cv. Swarna) seedlings with selected isolates had a positive impact on plant growth parameters like shoot and root elongation which was correlated with in vitro PGP attributes. The results indicated that the diverse polyvalent phytonic PGP bacteria, which may be exploited as bio-inoculants to improve rice production.

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Acknowledgments

This work has been financially support by Indian Council of Agricultural Research (ICAR) project “AMAAS” (application of microorganisms in agriculture and allied sector).

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Authors and Affiliations

  1. Microbiology Laboratory, Crop Production Division, ICAR-Central Rice Research Institute, Cuttack, 753006, Odisha, India

    Avishek Banik & Tushar Kanti Dangar

  2. Department of Microbiology, The University of Burdwan, Burdwan, 713104, West Bengal, India

    Subhra Kanti Mukhopadhaya

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  1. Avishek Banik
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  2. Subhra Kanti Mukhopadhaya
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Correspondence to Tushar Kanti Dangar.

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Banik, A., Mukhopadhaya, S.K. & Dangar, T.K. Characterization of N2-fixing plant growth promoting endophytic and epiphytic bacterial community of Indian cultivated and wild rice (Oryza spp.) genotypes. Planta 243, 799–812 (2016). https://doi.org/10.1007/s00425-015-2444-8

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