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Characterization and identification of compost bacteria based on 16S rRNA gene sequencing

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Abstract

The aim of this study was to isolate and characterize bacteria from the compost of fruit and vegetable waste (FVW) for plant growth-promoting (PGP) activities and investigate the pro-active influence of bacterial isolates on wheat growth. Fourteen bacterial strains (RHC-1 to RHC-14) were isolated and purified in tryptic soya agar (TSA). In addition to being biochemically characterized, these bacterial strains were also tested for their PGP traits, such as phosphate (P)-solubilization, nifH gene amplification, indole-3-acetic acid (IAA) quantification and the production of ammonia, oxidase and catalase. Based on 16S rRNA gene sequencing, these bacterial strains were identified as belonging to species of Bacillus, Lysinibacillus, Lysobacter, Staphylococcus, Enterobacter, Pseudomonas and Serratia. All bacterial strains solubilized tri-calcium phosphate and produced IAA. Two bacterial strains RHC-8 (Enterobacter sp.) and RHC-13 (Pseudomonas sp.) solubilized the maximum amount of tri-calcium phosphate, i.e. 486 and 464 μg/ml, respectively. P-solubilization was associated with a significant drop in the pH of the broth culture from an initial pH of 7 to pH 4.43. In addition to P-solubilization and IAA production, six bacterial strains also carried the nifH gene and were further evaluated for their effect on wheat (Triticum aestivum) growth under controlled conditions. All six bacterial strains enhanced wheat growth as compared to uninoculated control plants. Two of the bacterial strains, RHC-8 and RHC-13, identified as Enterobacter aerogenes and Pseudomonas brenneri, respectively, were assessed as potential PGP rhizobacteria due to exhibiting characteristics of four or more PGP traits and enhancing wheat growth though their specific mechanism of action.

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Acknowledgments

Financial assistance from PMAS-Arid Agriculture University, Rawalpindi under the project entitled Preparation of Biofertilizer for Improving Legume N2-Fixation and Soil Health is highly acknowledged. DNA studies were carried out at the Plant Biotechnology Program, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Islamabad, Pakistan. Bacterial strains were commercially sequenced with funding from the Pakistan Science Foundation project no. PSF-UAAR/Agr-374.

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Authors and Affiliations

  1. Department of Soil Science & SWC, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan

    Rifat Hayat, Rizwan Ali Sheirdil & Muhammad Iftikhar-ul-Hassan

  2. Plant Biotechnology Program, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad, 45500, Pakistan

    Iftikhar Ahmed

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  1. Rifat Hayat
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  2. Rizwan Ali Sheirdil
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  3. Muhammad Iftikhar-ul-Hassan
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Correspondence to Rifat Hayat.

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Hayat, R., Sheirdil, R.A., Iftikhar-ul-Hassan, M. et al. Characterization and identification of compost bacteria based on 16S rRNA gene sequencing. Ann Microbiol 63, 905–912 (2013). https://doi.org/10.1007/s13213-012-0542-4

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  • DOI: https://doi.org/10.1007/s13213-012-0542-4

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