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Assessment of bacterial diversity in agricultural by-product compost by sequencing of cultivated isolates and amplified rDNA restriction analysis

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An Erratum to this article was published on 11 February 2014

Abstract

An investigation of bacterial diversity in compost was performed using molecular chronometer in order to reveal its phylogeny. Thirty-three bacterial isolates isolated from compost were analyzed by 16S rRNA gene sequencing which revealed phylogenetic lineage of class Bacilli, γ, β-Proteobacteria, and Actinobacteria. Among these lineages, isolates belonging to class Bacilli consisted of species from genera Staphylococcus, Bacillus, Terribacillus, and Lysinibacillus. From phylum Actinobacteria: Microbacterium barkeri and Kocuria sp. were identified. Other bacterial groups had phylogenetic linkage with genera Comamonas and Acidovorax (class β-Proteobacteria); Serratia, Klebsiella, and Enterobacter (class γ-Proteobacteria). Similar isolates were analyzed through ARDRA. Amplified product of 16S rRNA gene from each isolates was subjected to cleavage by enzymes HpaII, HinfI, and MspI in separate reaction tubes. HpaII generated 2–6 bands ranging from 90–688 bp, HinfI generated 2–5 bands of 71–1,038 bp, and MspI 2–7 bands of 69–793 bp. The restriction patterns from HpaII, HinfI, and MspI were normalized separately and combined by means of pattern recognition software “Diversity Database.” HpaII had highest discrimination index (0.72) than HinfI (0.68) and MspI (0.65), and the combination of all three showed discrimination index (0.69). Numerical analysis of ARDRA patterns demonstrated sufficient phylogenetic information for characterizing bacterial diversity. Phylogenetic relationship obtained among isolates through ARDRA was compared with 16S rRNA gene sequence and ARDRA results showed sufficiently similar 16S rRNA gene sequence analysis, but not an overlapping. It has been observed that ARDRA technique facilitates the identification of bacteria in less than 36 h as compared to traditional 16S rRNA gene sequencing.

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Acknowledgments

We acknowledge the assistance of Dr. Kailash N. Bhardwaj, UGC-Dr. D.S. Kothari Post Doc fellow during the preparation of this manuscript.

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Correspondence to Ramesh Chander Kuhad.

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An erratum to this article is available at http://dx.doi.org/10.1186/1471-2180-14-33.

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Figure S1

Dendrogram based on UPGMA clustering with coefficient of combined HpaII ARDRA patterns obtained from the isolates isolated from compost. (PPT 37 kb)

Figure S2

Dendrogram based on UPGMA clustering with coefficient of combined HinfI ARDRA patterns obtained from the isolates isolated from compost (PPT 38 kb)

Figure S3

Dendrogram based on UPGMA clustering with coefficient of combined MspI ARDRA patterns obtained from the isolates isolated from compost. (PPT 37 kb)

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Chandna, P., Mallik, S. & Kuhad, R.C. Assessment of bacterial diversity in agricultural by-product compost by sequencing of cultivated isolates and amplified rDNA restriction analysis. Appl Microbiol Biotechnol 97, 6991–7003 (2013). https://doi.org/10.1007/s00253-012-4434-0

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